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Head ST, Dezem F, Todor A, Yang J, Plummer J, Gayther S, Kar S, Schildkraut J, Epstein MP. Cis- and trans-eQTL TWASs of breast and ovarian cancer identify more than 100 susceptibility genes in the BCAC and OCAC consortia. Am J Hum Genet 2024; 111:1084-1099. [PMID: 38723630 PMCID: PMC11179407 DOI: 10.1016/j.ajhg.2024.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 05/21/2024] Open
Abstract
Transcriptome-wide association studies (TWASs) have investigated the role of genetically regulated transcriptional activity in the etiologies of breast and ovarian cancer. However, methods performed to date have focused on the regulatory effects of risk-associated SNPs thought to act in cis on a nearby target gene. With growing evidence for distal (trans) regulatory effects of variants on gene expression, we performed TWASs of breast and ovarian cancer using a Bayesian genome-wide TWAS method (BGW-TWAS) that considers effects of both cis- and trans-expression quantitative trait loci (eQTLs). We applied BGW-TWAS to whole-genome and RNA sequencing data in breast and ovarian tissues from the Genotype-Tissue Expression project to train expression imputation models. We applied these models to large-scale GWAS summary statistic data from the Breast Cancer and Ovarian Cancer Association Consortia to identify genes associated with risk of overall breast cancer, non-mucinous epithelial ovarian cancer, and 10 cancer subtypes. We identified 101 genes significantly associated with risk with breast cancer phenotypes and 8 with ovarian phenotypes. These loci include established risk genes and several novel candidate risk loci, such as ACAP3, whose associations are predominantly driven by trans-eQTLs. We replicated several associations using summary statistics from an independent GWAS of these cancer phenotypes. We further used genotype and expression data in normal and tumor breast tissue from the Cancer Genome Atlas to examine the performance of our trained expression imputation models. This work represents an in-depth look into the role of trans eQTLs in the complex molecular mechanisms underlying these diseases.
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Affiliation(s)
- S Taylor Head
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Felipe Dezem
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Andrei Todor
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Jingjing Yang
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Jasmine Plummer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Simon Gayther
- Department of Biomedical Sciences, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Siddhartha Kar
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Joellen Schildkraut
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Michael P Epstein
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA.
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2
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Alshehri KM, Abdella EM. Galloyl-oligochitosan nano-vehicles for effective and controlled propolis delivery targeting upgrading its antioxidant and antiproliferative potential. Int J Biol Macromol 2024; 270:132283. [PMID: 38735605 DOI: 10.1016/j.ijbiomac.2024.132283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/04/2024] [Accepted: 05/09/2024] [Indexed: 05/14/2024]
Abstract
A new conjugate, galloyl-oligochitosan nanoparticles (GOCNPs), was fabricated and used as nano-vehicle for effective and controlled delivery of propolis extract (PE) in the form of PE#GOCNPs, targeting improving its pharmaceutical potential. H-bonding interactions between the carboxyl, amino, and hydroxyl groups of the GOCNPs and PE resulted in successful encapsulation, with an entrapment efficacy of 97.3 %. The PE#GOCNPs formulation also exhibited excellent physicochemical stability and time-triggered drug release characteristics under physiological conditions. Furthermore, PE#GOCNPs showed significant activity against MCF-7 and HEPG2 carcinoma cells by scavenging free oxygen radicals and upregulating antioxidant enzymes. Additionally, PE#GOCNPs displayed anti-inflammatory properties by increasing IL10 and reducing pro-inflammatory cytokines more effectively than celecoxib. Furthermore, PE#GOCNPs reduced the expression of epidermal growth factor receptor (EGFR) and survivin genes. Furthermore, the encapsulated PE demonstrated significant activity in suppressing sonic hedgehog protein (SHH). The use of GOCNPs in combination with propolis presents a promising new strategy for chemotherapy with reduced toxicity and enhanced biocompatibility. This novel approach has the potential to revolutionize the field of chemotherapy. Future studies should focus on the application of the encapsulated PE in various cancer cell lines, distinct gene expression factors, and cell cycles.
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Affiliation(s)
| | - Ehab M Abdella
- Department of Biology, Al-Baha University, Saudi Arabia; Zoology department faculty of science Beni-Suef University, Beni-Suef, Egypt.
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Zheng G, Chattopadhyay S, Sundquist J, Sundquist K, Ji J. Antihypertensive drug targets and breast cancer risk: a two-sample Mendelian randomization study. Eur J Epidemiol 2024; 39:535-548. [PMID: 38396187 PMCID: PMC11219410 DOI: 10.1007/s10654-024-01103-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 01/15/2024] [Indexed: 02/25/2024]
Abstract
Findings on the correlation between the use of antihypertensive medication and the risk of breast cancer (BC) have been inconsistent. We performed a two-sample Mendelian randomization (MR) using instrumental variables to proxy changes in gene expressions of antihypertensive medication targets to interrogate this. Genetic instruments for expression of antihypertensive drug target genes were identified with expression quantitative trait loci in blood, which should be associated with systolic blood pressure to proxy for the effect of antihypertensive drug. The association between genetic variants and BC risk were obtained from genome-wide association study summary statistics. The summary-based MR was employed to estimate the drug effects on BC risk. We further performed sensitivity analyses to confirm the discovered MR associations such as assessment of horizontal pleiotropy, colocalization, and multiple tissue enrichment analyses. The overall BC risk was only associated with SLC12A2 gene expression at a Bonferroni-corrected threshold. One standard deviation (SD) decrease of SLC12A2 gene expression in blood was associated with a decrease of 1.12 (95%CI, 0.80-1.58) mmHg of systolic blood pressure, but a 16% increased BC risk (odds ratio, 1.16, 95% confidential interval, 1.06-1.28). This signal was further observed for estrogen receptor positive (ER +) BC (1.17, 1.06-1.28). In addition, one SD decrease in expression of PDE1B in blood was associated with 7% decreased risk of ER + BC (0.93, 0.90-0.97). We detected no evidence of horizontal pleiotropy for these associations and the probability of the causal variants being shared between the gene expression and BC risk was 81.5, 40.5 and 66.8%, respectively. No significant association was observed between other target gene expressions and BC risk. Changes in expression of SLC12A2 and PDE1B mediated possibly via antihypertensive drugs may result in increased and decreased BC risk, respectively.
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Affiliation(s)
- Guoqiao Zheng
- Center for Primary Health Care Research, Lund University/Region Skåne, Jan Waldenströms Gata 35, 205 02, Malmö, Sweden.
| | - Subhayan Chattopadhyay
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Jan Sundquist
- Center for Primary Health Care Research, Lund University/Region Skåne, Jan Waldenströms Gata 35, 205 02, Malmö, Sweden
- Department of Family Medicine and Community Health, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Community-Based Healthcare Research and Education (CoHRE), Department of Functional Pathology, School of Medicine, Shimane University, Matsue, Japan
| | - Kristina Sundquist
- Center for Primary Health Care Research, Lund University/Region Skåne, Jan Waldenströms Gata 35, 205 02, Malmö, Sweden
- Department of Family Medicine and Community Health, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Community-Based Healthcare Research and Education (CoHRE), Department of Functional Pathology, School of Medicine, Shimane University, Matsue, Japan
| | - Jianguang Ji
- Center for Primary Health Care Research, Lund University/Region Skåne, Jan Waldenströms Gata 35, 205 02, Malmö, Sweden.
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4
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Jia G, Ping J, Guo X, Yang Y, Tao R, Li B, Ambs S, Barnard ME, Chen Y, Garcia-Closas M, Gu J, Hu JJ, Huo D, John EM, Li CI, Li JL, Nathanson KL, Nemesure B, Olopade OI, Pal T, Press MF, Sanderson M, Sandler DP, Shu XO, Troester MA, Yao S, Adejumo PO, Ahearn T, Brewster AM, Hennis AJM, Makumbi T, Ndom P, O'Brien KM, Olshan AF, Oluwasanu MM, Reid S, Butler EN, Huang M, Ntekim A, Qian H, Zhang H, Ambrosone CB, Cai Q, Long J, Palmer JR, Haiman CA, Zheng W. Genome-wide association analyses of breast cancer in women of African ancestry identify new susceptibility loci and improve risk prediction. Nat Genet 2024; 56:819-826. [PMID: 38741014 PMCID: PMC11284829 DOI: 10.1038/s41588-024-01736-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/25/2024] [Indexed: 05/16/2024]
Abstract
We performed genome-wide association studies of breast cancer including 18,034 cases and 22,104 controls of African ancestry. Genetic variants at 12 loci were associated with breast cancer risk (P < 5 × 10-8), including associations of a low-frequency missense variant rs61751053 in ARHGEF38 with overall breast cancer (odds ratio (OR) = 1.48) and a common variant rs76664032 at chromosome 2q14.2 with triple-negative breast cancer (TNBC) (OR = 1.30). Approximately 15.4% of cases with TNBC carried six risk alleles in three genome-wide association study-identified TNBC risk variants, with an OR of 4.21 (95% confidence interval = 2.66-7.03) compared with those carrying fewer than two risk alleles. A polygenic risk score (PRS) showed an area under the receiver operating characteristic curve of 0.60 for the prediction of breast cancer risk, which outperformed PRS derived using data from females of European ancestry. Our study markedly increases the population diversity in genetic studies for breast cancer and demonstrates the utility of PRS for risk prediction in females of African ancestry.
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Affiliation(s)
- Guochong Jia
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jie Ping
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yaohua Yang
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Public Health Genomics, Department of Public Health Sciences, UVA Comprehensive Cancer Center, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bingshan Li
- Department of Molecular Physiology & Biophysics, Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center of Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Yu Chen
- Division of Epidemiology, Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA
| | | | - Jian Gu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer J Hu
- Department of Public Health Sciences, University of Miami School of Medicine, Miami, FL, USA
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Esther M John
- Departments of Epidemiology & Population Health and of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Christopher I Li
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - James L Li
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Katherine L Nathanson
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Basser Center for BRCA, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Barbara Nemesure
- Department of Family, Population and Preventive Medicine, Renaissance School of Medicine, Stony Brook University, New York, NY, USA
| | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Tuya Pal
- Division of Genetic Medicine, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Michael F Press
- Department of Pathology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Maureen Sanderson
- Department of Family and Community Medicine, Meharry Medical College, Nashville, TN, USA
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Melissa A Troester
- Department of Epidemiology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, USA
| | - Prisca O Adejumo
- Department of Nursing, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Thomas Ahearn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Abenaa M Brewster
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anselm J M Hennis
- George Alleyne Chronic Disease Research Centre, University of the West Indies, Bridgetown, Barbados
- Department of Family, Population and Preventive Medicine, Stony Brook University, New York, NY, USA
| | | | - Paul Ndom
- Yaounde General Hospital, Yaounde, Cameroon
| | - Katie M O'Brien
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Andrew F Olshan
- Department of Epidemiology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mojisola M Oluwasanu
- Department of Health Promotion and Education, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Sonya Reid
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ebonee N Butler
- Department of Epidemiology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Maosheng Huang
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Atara Ntekim
- Department of Radiation Oncology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Huijun Qian
- Department of Statistics and Operation Research, University of North Carolina, Chapel Hill, NC, USA
| | - Haoyu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Julie R Palmer
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.
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5
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Beck JJ, Slunecka JL, Johnson BN, Van Asselt AJ, Finnicum CT, Ageton C, Krie A, Nickles H, Cowan K, Maxwell J, Boomsma DI, de Geus E, Ehli EA, Hottenga JJ. Breast Cancer Polygenic Risk Score Validation and Effects of Variable Imputation. Cancers (Basel) 2024; 16:1578. [PMID: 38672660 PMCID: PMC11048743 DOI: 10.3390/cancers16081578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/30/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Breast cancer (BC) is a complex disease affecting one in eight women in the USA. Advances in population genomics have led to the development of polygenic risk scores (PRSs) with the potential to augment current risk models, but replication is often limited. We evaluated 2 robust PRSs with 313 and 3820 SNPs and the effects of multiple genotype imputation replications in BC cases and control populations. Biological samples from BC cases and cancer-free controls were drawn from three European ancestry cohorts. Genotyping on the Illumina Global Screening Array was followed by stringent quality control measures and 20 genotype imputation replications. A total of 468 unrelated cases and 4337 controls were scored, revealing significant differences in mean PRS percentiles between cases and controls (p < 0.001) for both SNP sets (313-SNP PRS: 52.81 and 48.07; 3820-SNP PRS: 55.45 and 49.81), with receiver operating characteristic curve analysis showing area under the curve values of 0.596 and 0.603 for the 313-SNP and 3820-SNP PRS, respectively. PRS fluctuations (from ~2-3% up to 9%) emerged across imputation iterations. Our study robustly reaffirms the predictive capacity of PRSs for BC by replicating their performance in an independent BC population and showcases the need to average imputed scores for reliable outcomes.
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Affiliation(s)
- Jeffrey J. Beck
- Avera Genetics, Avera McKennan Hospital & University Health Center, Sioux Falls, SD 57105, USA (E.A.E.)
| | - John L. Slunecka
- Avera Genetics, Avera McKennan Hospital & University Health Center, Sioux Falls, SD 57105, USA (E.A.E.)
| | - Brandon N. Johnson
- Avera Genetics, Avera McKennan Hospital & University Health Center, Sioux Falls, SD 57105, USA (E.A.E.)
| | - Austin J. Van Asselt
- Avera Genetics, Avera McKennan Hospital & University Health Center, Sioux Falls, SD 57105, USA (E.A.E.)
| | - Casey T. Finnicum
- Avera Genetics, Avera McKennan Hospital & University Health Center, Sioux Falls, SD 57105, USA (E.A.E.)
| | | | - Amy Krie
- Avera Cancer Institute, Sioux Falls, SD 57105, USA
| | | | - Kenneth Cowan
- Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer at University of Nebraska Medical Center, Omaha, NE 68105, USA
| | - Jessica Maxwell
- Fred and Pamela Buffet Cancer Center and Eppley Institute for Research in Cancer at University of Nebraska Medical Center, Omaha, NE 68105, USA
| | - Dorret I. Boomsma
- Department of Biological Psychology, Netherlands Twin Register, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands (J.-J.H.)
| | - Eco de Geus
- Department of Biological Psychology, Netherlands Twin Register, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands (J.-J.H.)
| | - Erik A. Ehli
- Avera Genetics, Avera McKennan Hospital & University Health Center, Sioux Falls, SD 57105, USA (E.A.E.)
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, Netherlands Twin Register, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands (J.-J.H.)
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6
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Sun J, Luo J, Jiang F, Zhao J, Zhou S, Wang L, Zhang D, Ding Y, Li X. Exploring the cross-cancer effect of circulating proteins and discovering potential intervention targets for 13 site-specific cancers. J Natl Cancer Inst 2024; 116:565-573. [PMID: 38039160 DOI: 10.1093/jnci/djad247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/23/2023] [Accepted: 11/20/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND The proteome is an important reservoir of potential therapeutic targets for cancer. This study aimed to examine the causal associations between plasma proteins and cancer risk and to identify proteins with cross-cancer effects. METHODS Genetic instruments for 3991 plasma proteins were extracted from a large-scale proteomic study. Summary-level data of 13 site-specific cancers were derived from publicly available datasets. Proteome-wide Mendelian randomization and colocalization analyses were used to investigate the causal effect of circulating proteins on cancers. Protein-protein interactions and druggability assessment were conducted to prioritize potential therapeutic targets. Finally, systematical Mendelian randomization analysis between healthy lifestyle factors and cancer-related proteins was conducted to identify which proteins could act as interventional targets by lifestyle changes. RESULTS Genetically determined circulating levels of 58 proteins were statistically significantly associated with 7 site-specific cancers. A total of 39 proteins were prioritized by colocalization, of them, 11 proteins (ADPGK, CD86, CLSTN3, CSF2RA, CXCL10, GZMM, IL6R, NCR3, SIGLEC5, SIGLEC14, and TAPBP) were observed to have cross-cancer effects. Notably, 5 of these identified proteins (CD86, CSF2RA, CXCL10, IL6R, and TAPBP) have been targeted for drug development in cancer therapy; 8 proteins (ADPGK, CD86, CXCL10, GZMM, IL6R, SIGLEC5, SIGLEC14, TAPBP) could be modulated by healthy lifestyles. CONCLUSION Our study identified 39 circulating protein biomarkers with convincing causal evidence for 7 site-specific cancers, with 11 proteins demonstrating cross-cancer effects, and prioritized the proteins as potential intervention targets by either drugs or lifestyle changes, which provided new insights into the etiology, prevention, and treatment of cancers.
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Affiliation(s)
- Jing Sun
- Department of Big Data in Health Science School of Public Health, and Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jia Luo
- Department of Epidemiology and Health Statistics, the School of Public Health of Qingdao University, Qingdao, Shandong Province, China
| | - Fangyuan Jiang
- Department of Big Data in Health Science School of Public Health, and Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jianhui Zhao
- Department of Big Data in Health Science School of Public Health, and Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Siyun Zhou
- Department of Big Data in Health Science School of Public Health, and Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lijuan Wang
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Dongfeng Zhang
- Department of Epidemiology and Health Statistics, the School of Public Health of Qingdao University, Qingdao, Shandong Province, China
| | - Yuan Ding
- Department of Hepatobiliary and Pancreatic Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xue Li
- Department of Big Data in Health Science School of Public Health, and Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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7
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Tang M, Wu X, Zhang W, Cui H, Zhang L, Yan P, Yang C, Wang Y, Chen L, Xiao C, Liu Y, Zou Y, Yang C, Zhang L, Yao Y, Liu Z, Li J, Jiang X, Zhang B. Epidemiological and Genetic Analyses of Schizophrenia and Breast Cancer. Schizophr Bull 2024; 50:317-326. [PMID: 37467357 PMCID: PMC10919785 DOI: 10.1093/schbul/sbad106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/21/2023]
Abstract
BACKGROUND AND HYPOTHESIS While the phenotypic association between schizophrenia and breast cancer has been observed, the underlying intrinsic link is not adequately understood. We aim to conduct a comprehensive interrogation on both phenotypic and genetic relationships between schizophrenia and breast cancer. STUDY DESIGN We first used data from UK Biobank to evaluate a phenotypic association and performed an updated meta-analysis incorporating existing cohort studies. We then leveraged genomic data to explore the shared genetic architecture through a genome-wide cross-trait design. STUDY RESULTS Incorporating results of our observational analysis, meta-analysis of cohort studies suggested a significantly increased incidence of breast cancer among women with schizophrenia (RR = 1.30, 95% CIs = 1.14-1.48). A positive genomic correlation between schizophrenia and overall breast cancer was observed (rg = 0.12, P = 1.80 × 10-10), consistent across ER+ (rg = 0.10, P = 5.74 × 10-7) and ER- subtypes (rg = 0.09, P = .003). This was further corroborated by four local signals. Cross-trait meta-analysis identified 23 pleiotropic loci between schizophrenia and breast cancer, including five novel loci. Gene-based analysis revealed 27 shared genes. Mendelian randomization demonstrated a significantly increased risk of overall breast cancer (OR = 1.07, P = 4.81 × 10-10) for genetically predisposed schizophrenia, which remained robust in subgroup analysis (ER+: OR = 1.10, P = 7.26 × 10-12; ER-: OR = 1.08, P = 3.50 × 10-6). No mediation effect and reverse causality was found. CONCLUSIONS Our study demonstrates an intrinsic link underlying schizophrenia and breast cancer, which may inform tailored screening and management of breast cancer in schizophrenia.
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Affiliation(s)
- Mingshuang Tang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xueyao Wu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Wenqiang Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Huijie Cui
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Li Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Peijing Yan
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chao Yang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yutong Wang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Lin Chen
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chenghan Xiao
- Department of Maternal, Child and Adolescent Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Yunjie Liu
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yanqiu Zou
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chunxia Yang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ling Zhang
- Department of Iatrical Polymer Material and Artificial Apparatus, College of Polymer Science and Engineering, Sichuan University, Chengdu, China
| | - Yuqin Yao
- Department of Occupational and Environmental Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Zhenmi Liu
- Department of Maternal, Child and Adolescent Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Jiayuan Li
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xia Jiang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Nutrition and Food Hygiene, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Ben Zhang
- Department of Epidemiology and Biostatistics, Institute of Systems Epidemiology, and West China-PUMC C. C. Chen Institute of Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Occupational and Environmental Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
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8
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Chen H, Wang Z, Gong L, Wang Q, Chen W, Wang J, Ma X, Ding R, Li X, Zou X, Plass M, Lian C, Ni T, Wei GH, Li W, Deng L, Li L. A distinct class of pan-cancer susceptibility genes revealed by an alternative polyadenylation transcriptome-wide association study. Nat Commun 2024; 15:1729. [PMID: 38409266 PMCID: PMC10897204 DOI: 10.1038/s41467-024-46064-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 02/12/2024] [Indexed: 02/28/2024] Open
Abstract
Alternative polyadenylation plays an important role in cancer initiation and progression; however, current transcriptome-wide association studies mostly ignore alternative polyadenylation when identifying putative cancer susceptibility genes. Here, we perform a pan-cancer 3' untranslated region alternative polyadenylation transcriptome-wide association analysis by integrating 55 well-powered (n > 50,000) genome-wide association studies datasets across 22 major cancer types with alternative polyadenylation quantification from 23,955 RNA sequencing samples across 7,574 individuals. We find that genetic variants associated with alternative polyadenylation are co-localized with 28.57% of cancer loci and contribute a significant portion of cancer heritability. We further identify 642 significant cancer susceptibility genes predicted to modulate cancer risk via alternative polyadenylation, 62.46% of which have been overlooked by traditional expression- and splicing- studies. As proof of principle validation, we show that alternative alleles facilitate 3' untranslated region lengthening of CRLS1 gene leading to increased protein abundance and promoted proliferation of breast cancer cells. Together, our study highlights the significant role of alternative polyadenylation in discovering new cancer susceptibility genes and provides a strong foundational framework for enhancing our understanding of the etiology underlying human cancers.
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Affiliation(s)
- Hui Chen
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Zeyang Wang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Lihai Gong
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Qixuan Wang
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Wenyan Chen
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Jia Wang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Xuelian Ma
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Ruofan Ding
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Xing Li
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Xudong Zou
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Mireya Plass
- Gene Regulation of Cell Identity Group, Regenerative Medicine Program, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Program for Advancing Clinical Translation of Regenerative Medicine of Catalonia, P-CMR[C], L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Center for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, 28029, Spain
| | - Cheng Lian
- Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Ting Ni
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438, China
| | - Gong-Hong Wei
- Department of Biochemistry and Molecular Biology of School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, 90410, Finland
| | - Wei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, The University of California, Irvine, CA, 92697, USA.
| | - Lin Deng
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, 518055, China.
| | - Lei Li
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518055, China.
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9
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Head ST, Dezem F, Todor A, Yang J, Plummer J, Gayther S, Kar S, Schildkraut J, Epstein MP. Cis- and trans-eQTL TWAS of breast and ovarian cancer identify more than 100 risk associated genes in the BCAC and OCAC consortia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566218. [PMID: 38014246 PMCID: PMC10680675 DOI: 10.1101/2023.11.09.566218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Transcriptome-wide association studies (TWAS) have investigated the role of genetically regulated transcriptional activity in the etiologies of breast and ovarian cancer. However, methods performed to date have only considered regulatory effects of risk associated SNPs thought to act in cis on a nearby target gene. With growing evidence for distal (trans) regulatory effects of variants on gene expression, we performed TWAS of breast and ovarian cancer using a Bayesian genome-wide TWAS method (BGW-TWAS) that considers effects of both cis- and trans-expression quantitative trait loci (eQTLs). We applied BGW-TWAS to whole genome and RNA sequencing data in breast and ovarian tissues from the Genotype-Tissue Expression project to train expression imputation models. We applied these models to large-scale GWAS summary statistic data from the Breast Cancer and Ovarian Cancer Association Consortia to identify genes associated with risk of overall breast cancer, non-mucinous epithelial ovarian cancer, and 10 cancer subtypes. We identified 101 genes significantly associated with risk with breast cancer phenotypes and 8 with ovarian phenotypes. These loci include established risk genes and several novel candidate risk loci, such as ACAP3, whose associations are predominantly driven by trans-eQTLs. We replicated several associations using summary statistics from an independent GWAS of these cancer phenotypes. We further used genotype and expression data in normal and tumor breast tissue from the Cancer Genome Atlas to examine the performance of our trained expression imputation models. This work represents a first look into the role of trans-eQTLs in the complex molecular mechanisms underlying these diseases.
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Affiliation(s)
- S. Taylor Head
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Felipe Dezem
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Andrei Todor
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Jingjing Yang
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Jasmine Plummer
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Simon Gayther
- Department of Biomedical Sciences, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Siddhartha Kar
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Joellen Schildkraut
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Michael P. Epstein
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA
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10
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Quan L, Demant P. Clustering of colon, lung, and other cancer susceptibility genes with protein tyrosine phosphatases and protein kinases in multiple short genomic regions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.07.566108. [PMID: 37986945 PMCID: PMC10659278 DOI: 10.1101/2023.11.07.566108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Interactions of large gene families are poorly understood. We found that human, mouse, and rat colon and lung cancer susceptibility genes, presently considered as separate gene families, were frequently pairwise linked. The orthologous mouse map positions of 142 of 159 early discovered colon and lung cancer susceptibility genes formed 41 genomic clusters conserved >70 million years. These linked gene pairs concordantly affected both tumors and their majority was linked with two other gene families - protein tyrosine phosphatases and cancer driver protein kinases. 25% of both protein tyrosine phosphatases and protein kinases mapped <1 cM from a colon or lung cancer susceptibility gene, and 50% in <3 cM. Similar linkage was detected with most other human susceptibility genes that controlled 29 different cancer types. This concentration of tumor susceptibility genes with protein tyrosine phosphatases and driver protein kinases in multiple relatively short genomic regions suggests their possible functional diversity.
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11
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Long E, Yin J, Shin JH, Li Y, Kane A, Patel H, Luong T, Xia J, Han Y, Byun J, Zhang T, Zhao W, Landi MT, Rothman N, Lan Q, Chang YS, Yu F, Amos C, Shi J, Lee JG, Kim EY, Choi J. Context-aware single-cell multiome approach identified cell-type specific lung cancer susceptibility genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.559336. [PMID: 37808664 PMCID: PMC10557605 DOI: 10.1101/2023.09.25.559336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Genome-wide association studies (GWAS) identified over fifty loci associated with lung cancer risk. However, the genetic mechanisms and target genes underlying these loci are largely unknown, as most risk-associated-variants might regulate gene expression in a context-specific manner. Here, we generated a barcode-shared transcriptome and chromatin accessibility map of 117,911 human lung cells from age/sex-matched ever- and never-smokers to profile context-specific gene regulation. Accessible chromatin peak detection identified cell-type-specific candidate cis-regulatory elements (cCREs) from each lung cell type. Colocalization of lung cancer candidate causal variants (CCVs) with these cCREs prioritized the variants for 68% of the GWAS loci, a subset of which was also supported by transcription factor abundance and footprinting. cCRE colocalization and single-cell based trait relevance score nominated epithelial and immune cells as the main cell groups contributing to lung cancer susceptibility. Notably, cCREs of rare proliferating epithelial cell types, such as AT2-proliferating (0.13%) and basal cells (1.8%), overlapped with CCVs, including those in TERT. A multi-level cCRE-gene linking system identified candidate susceptibility genes from 57% of lung cancer loci, including those not detected in tissue- or cell-line-based approaches. cCRE-gene linkage uncovered that adjacent genes expressed in different cell types are correlated with distinct subsets of coinherited CCVs, including JAML and MPZL3 at the 11q23.3 locus. Our data revealed the cell types and contexts where the lung cancer susceptibility genes are functional.
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Affiliation(s)
- Erping Long
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Current affiliation: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jinhu Yin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ju Hye Shin
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Yuyan Li
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Alexander Kane
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Harsh Patel
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Thong Luong
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jun Xia
- Department of Biomedical Sciences, Creighton University, Omaha, NE, USA
| | - Younghun Han
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Jinyoung Byun
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Wei Zhao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yoon Soo Chang
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Fulong Yu
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, China
| | - Christopher Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jin Gu Lee
- Department of Thoracic and Cardiovascular Surgery, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Eun Young Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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12
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Subramanian A, Su S, Moding EJ, Binkley MS. Investigating the tissue specificity and prognostic impact of cis-regulatory cancer risk variants. Hum Genet 2023; 142:1395-1405. [PMID: 37474751 DOI: 10.1007/s00439-023-02586-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/07/2023] [Indexed: 07/22/2023]
Abstract
The tissue-specific incidence of cancers and their genetic basis are poorly understood. Although prior studies have shown global correlation across tissues for cancer risk single-nucleotide polymorphisms (SNPs) identified through genome-wide association studies (GWAS), any shared functional regulation of gene expression on a per SNP basis has not been well characterized. We set to quantify cis-mediated gene regulation and tissue sharing for SNPs associated with eight common cancers. We identify significant tissue sharing for individual SNPs and global enrichment for breast, colorectal, and Hodgkin lymphoma cancer risk SNPs in multiple tissues. In addition, we observe increasing tissue sharing for cancer risk SNPs overlapping with super-enhancers for breast cancer and Hodgkin lymphoma providing further evidence of tissue specificity. Finally, for genes under cis-regulation by breast cancer SNPs, we identify a phenotype characterized by low expression of tumor suppressors and negative regulators of the WNT pathway associated with worse freedom from progression and overall survival in patients who eventually develop breast cancer. Our results introduce a paradigm for functionally annotating individual cancer risk SNPs and will inform the design of future translational studies aimed to personalize assessment of inherited cancer risk across tissues.
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Affiliation(s)
- Ajay Subramanian
- Department of Radiation Oncology, Stanford Cancer Institute and Stanford University School of Medicine, Stanford, CA, USA
| | - Shengqin Su
- Department of Radiation Oncology, Stanford Cancer Institute and Stanford University School of Medicine, Stanford, CA, USA
| | - Everett J Moding
- Department of Radiation Oncology, Stanford Cancer Institute and Stanford University School of Medicine, Stanford, CA, USA
| | - Michael Sargent Binkley
- Department of Radiation Oncology, Stanford Cancer Institute and Stanford University School of Medicine, Stanford, CA, USA.
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13
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Sato G, Shirai Y, Namba S, Edahiro R, Sonehara K, Hata T, Uemura M, Matsuda K, Doki Y, Eguchi H, Okada Y. Pan-cancer and cross-population genome-wide association studies dissect shared genetic backgrounds underlying carcinogenesis. Nat Commun 2023; 14:3671. [PMID: 37340002 DOI: 10.1038/s41467-023-39136-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 05/31/2023] [Indexed: 06/22/2023] Open
Abstract
Integrating genomic data of multiple cancers allows de novo cancer grouping and elucidating the shared genetic basis across cancers. Here, we conduct the pan-cancer and cross-population genome-wide association study (GWAS) meta-analysis and replication studies on 13 cancers including 250,015 East Asians (Biobank Japan) and 377,441 Europeans (UK Biobank). We identify ten cancer risk variants including five pleiotropic associations (e.g., rs2076295 at DSP on 6p24 associated with lung cancer and rs2525548 at TRIM4 on 7q22 nominally associated with six cancers). Quantifying shared heritability among the cancers detects positive genetic correlations between breast and prostate cancer across populations. Common genetic components increase the statistical power, and the large-scale meta-analysis of 277,896 breast/prostate cancer cases and 901,858 controls identifies 91 newly genome-wide significant loci. Enrichment analysis of pathways and cell types reveals shared genetic backgrounds across said cancers. Focusing on genetically correlated cancers can contribute to enhancing our insights into carcinogenesis.
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Affiliation(s)
- Go Sato
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yuya Shirai
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Shinichi Namba
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Ryuya Edahiro
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kyuto Sonehara
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Tsuyoshi Hata
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Mamoru Uemura
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Tokyo, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Hidetoshi Eguchi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan.
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan.
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Department of Genome Informatics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan.
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14
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Lindström S, Wang L, Feng H, Majumdar A, Huo S, Macdonald J, Harrison T, Turman C, Chen H, Mancuso N, Bammler T, Gallinger S, Gruber SB, Gunter MJ, Le Marchand L, Moreno V, Offit K, De Vivo I, O’Mara TA, Spurdle AB, Tomlinson I, Fitzgerald R, Gharahkhani P, Gockel I, Jankowski J, Macgregor S, Schumacher J, Barnholtz-Sloan J, Bondy ML, Houlston RS, Jenkins RB, Melin B, Wrensch M, Brennan P, Christiani DC, Johansson M, Mckay J, Aldrich MC, Amos CI, Landi MT, Tardon A, Bishop DT, Demenais F, Goldstein AM, Iles MM, Kanetsky PA, Law MH, Amundadottir LT, Stolzenberg-Solomon R, Wolpin BM, Klein A, Petersen G, Risch H, Chanock SJ, Purdue MP, Scelo G, Pharoah P, Kar S, Hung RJ, Pasaniuc B, Kraft P. Genome-wide analyses characterize shared heritability among cancers and identify novel cancer susceptibility regions. J Natl Cancer Inst 2023; 115:712-732. [PMID: 36929942 PMCID: PMC10248849 DOI: 10.1093/jnci/djad043] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 11/07/2022] [Accepted: 02/14/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND The shared inherited genetic contribution to risk of different cancers is not fully known. In this study, we leverage results from 12 cancer genome-wide association studies (GWAS) to quantify pairwise genome-wide genetic correlations across cancers and identify novel cancer susceptibility loci. METHODS We collected GWAS summary statistics for 12 solid cancers based on 376 759 participants with cancer and 532 864 participants without cancer of European ancestry. The included cancer types were breast, colorectal, endometrial, esophageal, glioma, head and neck, lung, melanoma, ovarian, pancreatic, prostate, and renal cancers. We conducted cross-cancer GWAS and transcriptome-wide association studies to discover novel cancer susceptibility loci. Finally, we assessed the extent of variant-specific pleiotropy among cancers at known and newly identified cancer susceptibility loci. RESULTS We observed widespread but modest genome-wide genetic correlations across cancers. In cross-cancer GWAS and transcriptome-wide association studies, we identified 15 novel cancer susceptibility loci. Additionally, we identified multiple variants at 77 distinct loci with strong evidence of being associated with at least 2 cancer types by testing for pleiotropy at known cancer susceptibility loci. CONCLUSIONS Overall, these results suggest that some genetic risk variants are shared among cancers, though much of cancer heritability is cancer-specific and thus tissue-specific. The increase in statistical power associated with larger sample sizes in cross-disease analysis allows for the identification of novel susceptibility regions. Future studies incorporating data on multiple cancer types are likely to identify additional regions associated with the risk of multiple cancer types.
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Affiliation(s)
- Sara Lindström
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Lu Wang
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Helian Feng
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Arunabha Majumdar
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Mathematics, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - Sijia Huo
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - James Macdonald
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Tabitha Harrison
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Constance Turman
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Hongjie Chen
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Nicholas Mancuso
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Theo Bammler
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | | | - Steve Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Stephen B Gruber
- Department of Medical Oncology & Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Marc J Gunter
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | | | - Victor Moreno
- Oncology Data Analytics Program, Catalan Institute of Oncology-IDIBELL, L’Hospitalet de Llobregat, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- ONCOBEL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Spain
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | | | - Immaculata De Vivo
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Harvard Radcliffe Institute, Cambridge, MA, USA
| | - Tracy A O’Mara
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Ian Tomlinson
- Cancer Research Centre, The University of Edinburgh, Edinburgh, UK
| | | | - Rebecca Fitzgerald
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Puya Gharahkhani
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Ines Gockel
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
| | - Janusz Jankowski
- Institute for Clinical Trials, University College London, Holborn, UK
- University of the South Pacific, Suva, Fiji
| | - Stuart Macgregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | - Jill Barnholtz-Sloan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Trans-Divisional Research Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Melissa L Bondy
- Department of Epidemiology and Population Health, Stanford University, Palo Alto, CA, USA
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, MN, USA
| | - Beatrice Melin
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
| | - Margaret Wrensch
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Paul Brennan
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - David C Christiani
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Mattias Johansson
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - James Mckay
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Melinda C Aldrich
- Department of Thoracic Surgery, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Adonina Tardon
- University Institute of Oncology of the Principality of Asturias (IUOPA), University of Oviedo and Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Oviedo, Spain
| | | | - D Timothy Bishop
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
| | - Florence Demenais
- Université Paris Cité, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR-1124, Paris, France
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mark M Iles
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
| | - Peter A Kanetsky
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Matthew H Law
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, Queensland, Australia
| | | | - Laufey T Amundadottir
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rachael Stolzenberg-Solomon
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Brian M Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | | | - Alison Klein
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Gloria Petersen
- Department of Quantitative Health Science, Mayo Clinic, Rochester, MN, USA
| | - Harvey Risch
- Yale School of Public Health, Chronic Disease Epidemiology, New Haven, CT, USA
| | | | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mark P Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ghislaine Scelo
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Paul Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Siddhartha Kar
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Rayjean J Hung
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbuaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Bogdan Pasaniuc
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Peter Kraft
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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15
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Sun J, Wang L, Zhou X, Hu L, Yuan S, Bian Z, Chen J, Zhu Y, Farrington SM, Campbell H, Ding K, Zhang D, Dunlop MG, Theodoratou E, Li X. Cross-cancer pleiotropic analysis identifies three novel genetic risk loci for colorectal cancer. Hum Mol Genet 2023; 32:2093-2102. [PMID: 36928917 PMCID: PMC10244225 DOI: 10.1093/hmg/ddad044] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 03/11/2023] [Accepted: 03/16/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND To understand the shared genetic basis between colorectal cancer (CRC) and other cancers and identify potential pleiotropic loci for compensating the missing genetic heritability of CRC. METHODS We conducted a systematic genome-wide pleiotropy scan to appraise associations between cancer-related genetic variants and CRC risk among European populations. Single nucleotide polymorphism (SNP)-set analysis was performed using data from the UK Biobank and the Study of Colorectal Cancer in Scotland (10 039 CRC cases and 30 277 controls) to evaluate the overlapped genetic regions for susceptibility of CRC and other cancers. The variant-level pleiotropic associations between CRC and other cancers were examined by CRC genome-wide association study meta-analysis and the pleiotropic analysis under composite null hypothesis (PLACO) pleiotropy test. Gene-based, co-expression and pathway enrichment analyses were performed to explore potential shared biological pathways. The interaction between novel genetic variants and common environmental factors was further examined for their effects on CRC. RESULTS Genome-wide pleiotropic analysis identified three novel SNPs (rs2230469, rs9277378 and rs143190905) and three mapped genes (PIP4K2A, HLA-DPB1 and RTEL1) to be associated with CRC. These genetic variants were significant expressions quantitative trait loci in colon tissue, influencing the expression of their mapped genes. Significant interactions of PIP4K2A and HLA-DPB1 with environmental factors, including smoking and alcohol drinking, were observed. All mapped genes and their co-expressed genes were significantly enriched in pathways involved in carcinogenesis. CONCLUSION Our findings provide an important insight into the shared genetic basis between CRC and other cancers. We revealed several novel CRC susceptibility loci to help understand the genetic architecture of CRC.
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Affiliation(s)
- Jing Sun
- Department of Big Data in Health Science School of Public Health, and Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Lijuan Wang
- Department of Big Data in Health Science School of Public Health, and Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Xuan Zhou
- Department of Big Data in Health Science School of Public Health, and Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Lidan Hu
- The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310005, China
| | - Shuai Yuan
- Unit of Cardiovascular and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Zilong Bian
- Department of Big Data in Health Science School of Public Health, and Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Jie Chen
- Department of Big Data in Health Science School of Public Health, and Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Yingshuang Zhu
- Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Susan M Farrington
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Harry Campbell
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Kefeng Ding
- Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Dongfeng Zhang
- Department of Epidemiology and Health Statistics, The School of Public Health of Qingdao University, Qingdao 266071, China
| | - Malcolm G Dunlop
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Evropi Theodoratou
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, UK
- Cancer Research UK Edinburgh Centre, Medical Research Council Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Xue Li
- Department of Big Data in Health Science School of Public Health, and Center of Clinical Big Data and Analytics of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- The Key Laboratory of Intelligent Preventive Medicine of Zhejiang Province, Hangzhou, Zhejiang 310058, China
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16
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Guo Y, Li D, Hu Y. Appraising the associations between systemic iron status and epigenetic clocks: A genetic correlation and bidirectional Mendelian Randomization study. Am J Clin Nutr 2023:S0002-9165(23)48897-1. [PMID: 37146762 DOI: 10.1016/j.ajcnut.2023.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 04/25/2023] [Accepted: 05/01/2023] [Indexed: 05/07/2023] Open
Abstract
BACKGROUND Genetic correlations and bidirectional causal effects between systemic iron status and epigenetic clocks have not been fully investigated, although observational studies have suggested systemic iron status is associated with human aging. OBJECTIVES We explored the genetic correlations and bidirectional causal effects between systemic iron status and epigenetic clocks. METHODS Leveraging large-scale genome-wide association study summary-level statistics for four systemic iron status biomarkers (ferritin, serum iron, transferrin, transferrin saturation) (N = 48,972) and four measures for epigenetic age (GrimAge, PhenoAge, IEAA, HannumAge) (N = 34,710), genetic correlations and bidirectional causal effects were estimated between them mainly by applying linkage disequilibrium score (LDSC) regression, Mendelian randomization (MR), and MR based on Bayesian model averaging (MR-BMA). The main analyses were conducted employing multiplicative random effects inverse variance weighted MR. MR-Egger, weighted median, weighted mode, and MR-PRESSO were performed as sensitivity analyses to support the robustness of causal effects. RESULTS The LDSC results illustrated genetic correlations (Rg) between serum iron and PhenoAge (Rg = 0.1971, p = 0.048) and between transferrin saturation and PhenoAge (Rg = 0.196, p = 0.0469). We found that increased ferritin and transferrin saturation significantly increased all four measures of epigenetic age acceleration (all p < 0.0125, beta > 0). Each standard deviation genetically increases in serum iron only significantly associated with increased IEAA acceleration (beta = 0.36, 95% CI 0.16-0.57, p = 6.01E-04) and increased HannumAge acceleration (beta = 0.32, 95% CI 0.11-0.52, p = 2.69E-03). Evidence showed a suggestively significant causal effect of transferrin on epigenetic age acceleration (all 0.0125 < p <0.05). Additionally, reverse MR study indicated no significant causal effect of epigenetic clocks on systemic iron status. CONCLUSIONS All four iron status biomarkers had a significant or suggestively significant causal effect on epigenetic clocks, whereas reverse MR studies did not.
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Affiliation(s)
- Yu Guo
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150086, China
| | - Dahe Li
- Beidahuang Industry Group General Hospital, Harbin, China
| | - Yang Hu
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin 150086, China.
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17
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Hathaway F, Martins R, Sorscher S, Bzura A, Dudbridge F, Fennell DA. Family Matters: Germline Testing in Thoracic Cancers. Am Soc Clin Oncol Educ Book 2023; 43:e389956. [PMID: 37167572 DOI: 10.1200/edbk_389956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Most thoracic cancers arise via a series of stepwise somatic alterations driven by a well-defined carcinogen (ie, tobacco or asbestos for lung cancer and mesothelioma, respectively). A small proportion can emerge on a background of pathogenic germline variants (PGVs), which have the property of heritability. In general, PGVs may be initially suspected on the basis of the presence of specific clinical features. Such gene × environment interactions significantly increase the risk of developing lung cancer (1.5- to 3.2-fold). PGVs have been discovered involving the actionable driver oncogene, epidermal growth factor receptor (EGFR), with an EGFR T790M PGV rate of 0.3%-0.9% in the nonsquamous non-small-cell lung cancer subtype. Its appearance during routine somatic DNA sequencing in those patients who have not had a previous tyrosine kinase inhibitor should raise suspicion. In patients with sporadic mesothelioma, BAP1 is the most frequently mutated tumor driver, with a PGV rate between 2.8% and 8%, associated with a favorable prognosis. BAP1 PGVs accelerate mesothelioma tumorigenesis after asbestos exposure in preclinical models and may be partly predicted by clinical criteria. At present, routine germline genetic testing for thoracic cancers is not a standard practice. Expert genetic counseling is, therefore, required for patients who carry a PGV. Ongoing studies aim to better understand the natural history of patients harboring PGVs to underpin future cancer prevention, precise counseling, and cancer management with the goal of improving the quality and length of life.
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Affiliation(s)
- Feighanne Hathaway
- Department of Medicine, Section of Hematology/Oncology, The University of Chicago Comprehensive Cancer Center, Chicago, IL
| | - Renato Martins
- Department of Hematology, Oncology, Palliative Care, Virginia Commonwealth University, Richmond, VA
| | | | | | | | - Dean A Fennell
- The University of Leicester, Leicester, United Kingdom
- University Hospitals of Leicester NHS Trust, Leicester, United Kingdom
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18
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Zhang J, Tang K, Liu L, Guo C, Zhao K, Li S. Management of pulmonary nodules in women with pregnant intention: A review with perspective. Ann Thorac Med 2023; 18:61-69. [PMID: 37323371 PMCID: PMC10263075 DOI: 10.4103/atm.atm_270_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 09/04/2022] [Accepted: 09/13/2022] [Indexed: 06/17/2023] Open
Abstract
The process for the management of pulmonary nodules in women with pregnant intention remains a challenge. There was a certain proportion of targeted female patients with high-risk lung cancer, and anxiety for suspicious lung cancer in early stage also exists. A comprehensive review of hereditary of lung cancer, effects of sexual hormone on lung cancer, natural history of pulmonary nodules, and computed tomography imaging with radiation exposure based on PubMed search was completed. The heredity of lung cancer and effects of sexual hormone on lung cancer are not the decisive factors, and the natural history of pulmonary nodules and the radiation exposure of imaging should be the main concerns. The management of incidental pulmonary nodules in young women with pregnant intention is an intricate and indecisive problem we have to encounter. The balance between the natural history of pulmonary nodules and the radiation exposure of imaging should be weighed.
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Affiliation(s)
- Jiaqi Zhang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Kun Tang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
- Institute of Respiratory Disease of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Lei Liu
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chao Guo
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ke Zhao
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shanqing Li
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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19
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Guan Z, Begg CB, Shen R. Predicting Cancer Risk from Germline Whole-exome Sequencing Data Using a Novel Context-based Variant Aggregation Approach. CANCER RESEARCH COMMUNICATIONS 2023; 3:483-488. [PMID: 36969913 PMCID: PMC10032232 DOI: 10.1158/2767-9764.crc-22-0355] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 01/24/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Many studies have shown that the distributions of the genomic, nucleotide, and epigenetic contexts of somatic variants in tumors are informative of cancer etiology. Recently, a new direction of research has focused on extracting signals from the contexts of germline variants and evidence has emerged that patterns defined by these factors are associated with oncogenic pathways, histologic subtypes, and prognosis. It remains an open question whether aggregating germline variants using meta-features capturing their genomic, nucleotide, and epigenetic contexts can improve cancer risk prediction. This aggregation approach can potentially increase statistical power for detecting signals from rare variants, which have been hypothesized to be a major source of the missing heritability of cancer. Using germline whole-exome sequencing data from the UK Biobank, we developed risk models for 10 cancer types using known risk variants (cancer-associated SNPs and pathogenic variants in known cancer predisposition genes) as well as models that additionally include the meta-features. The meta-features did not improve the prediction accuracy of models based on known risk variants. It is possible that expanding the approach to whole-genome sequencing can lead to gains in prediction accuracy. Significance There is evidence that cancer is partly caused by rare genetic variants that have not yet been identified. We investigate this issue using novel statistical methods and data from the UK Biobank.
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Affiliation(s)
- Zoe Guan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Colin B. Begg
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ronglai Shen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
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20
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Mueller SH, Lai AG, Valkovskaya M, Michailidou K, Bolla MK, Wang Q, Dennis J, Lush M, Abu-Ful Z, Ahearn TU, Andrulis IL, Anton-Culver H, Antonenkova NN, Arndt V, Aronson KJ, Augustinsson A, Baert T, Freeman LEB, Beckmann MW, Behrens S, Benitez J, Bermisheva M, Blomqvist C, Bogdanova NV, Bojesen SE, Bonanni B, Brenner H, Brucker SY, Buys SS, Castelao JE, Chan TL, Chang-Claude J, Chanock SJ, Choi JY, Chung WK, Colonna SV, Cornelissen S, Couch FJ, Czene K, Daly MB, Devilee P, Dörk T, Dossus L, Dwek M, Eccles DM, Ekici AB, Eliassen AH, Engel C, Evans DG, Fasching PA, Fletcher O, Flyger H, Gago-Dominguez M, Gao YT, García-Closas M, García-Sáenz JA, Genkinger J, Gentry-Maharaj A, Grassmann F, Guénel P, Gündert M, Haeberle L, Hahnen E, Haiman CA, Håkansson N, Hall P, Harkness EF, Harrington PA, Hartikainen JM, Hartman M, Hein A, Ho WK, Hooning MJ, Hoppe R, Hopper JL, Houlston RS, Howell A, Hunter DJ, Huo D, Ito H, Iwasaki M, Jakubowska A, Janni W, John EM, Jones ME, Jung A, Kaaks R, Kang D, Khusnutdinova EK, Kim SW, Kitahara CM, Koutros S, Kraft P, Kristensen VN, Kubelka-Sabit K, Kurian AW, Kwong A, Lacey JV, Lambrechts D, Le Marchand L, Li J, Linet M, Lo WY, Long J, Lophatananon A, Mannermaa A, Manoochehri M, Margolin S, Matsuo K, Mavroudis D, Menon U, Muir K, Murphy RA, Nevanlinna H, Newman WG, Niederacher D, O'Brien KM, Obi N, Offit K, Olopade OI, Olshan AF, Olsson H, Park SK, Patel AV, Patel A, Perou CM, Peto J, Pharoah PDP, Plaseska-Karanfilska D, Presneau N, Rack B, Radice P, Ramachandran D, Rashid MU, Rennert G, Romero A, Ruddy KJ, Ruebner M, Saloustros E, Sandler DP, Sawyer EJ, Schmidt MK, Schmutzler RK, Schneider MO, Scott C, Shah M, Sharma P, Shen CY, Shu XO, Simard J, Surowy H, Tamimi RM, Tapper WJ, Taylor JA, Teo SH, Teras LR, Toland AE, Tollenaar RAEM, Torres D, Torres-Mejía G, Troester MA, Truong T, Vachon CM, Vijai J, Weinberg CR, Wendt C, Winqvist R, Wolk A, Wu AH, Yamaji T, Yang XR, Yu JC, Zheng W, Ziogas A, Ziv E, Dunning AM, Easton DF, Hemingway H, Hamann U, Kuchenbaecker KB. Aggregation tests identify new gene associations with breast cancer in populations with diverse ancestry. Genome Med 2023; 15:7. [PMID: 36703164 PMCID: PMC9878779 DOI: 10.1186/s13073-022-01152-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 12/16/2022] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Low-frequency variants play an important role in breast cancer (BC) susceptibility. Gene-based methods can increase power by combining multiple variants in the same gene and help identify target genes. METHODS We evaluated the potential of gene-based aggregation in the Breast Cancer Association Consortium cohorts including 83,471 cases and 59,199 controls. Low-frequency variants were aggregated for individual genes' coding and regulatory regions. Association results in European ancestry samples were compared to single-marker association results in the same cohort. Gene-based associations were also combined in meta-analysis across individuals with European, Asian, African, and Latin American and Hispanic ancestry. RESULTS In European ancestry samples, 14 genes were significantly associated (q < 0.05) with BC. Of those, two genes, FMNL3 (P = 6.11 × 10-6) and AC058822.1 (P = 1.47 × 10-4), represent new associations. High FMNL3 expression has previously been linked to poor prognosis in several other cancers. Meta-analysis of samples with diverse ancestry discovered further associations including established candidate genes ESR1 and CBLB. Furthermore, literature review and database query found further support for a biologically plausible link with cancer for genes CBLB, FMNL3, FGFR2, LSP1, MAP3K1, and SRGAP2C. CONCLUSIONS Using extended gene-based aggregation tests including coding and regulatory variation, we report identification of plausible target genes for previously identified single-marker associations with BC as well as the discovery of novel genes implicated in BC development. Including multi ancestral cohorts in this study enabled the identification of otherwise missed disease associations as ESR1 (P = 1.31 × 10-5), demonstrating the importance of diversifying study cohorts.
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Affiliation(s)
| | - Alvina G Lai
- Institute of Health Informatics, University College London, London, UK
| | | | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, 2371, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, 2371, Nicosia, Cyprus
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Michael Lush
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Zomoruda Abu-Ful
- Clalit National Cancer Control Center, Carmel Medical Center and Technion Faculty of Medicine, 35254, Haifa, Israel
| | - Thomas U Ahearn
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20850, USA
| | - Irene L Andrulis
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Hoda Anton-Culver
- Department of Medicine, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, 92617, USA
| | - Natalia N Antonenkova
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, 223040, Minsk, Belarus
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Kristan J Aronson
- Department of Public Health Sciences, and Cancer Research Institute, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Annelie Augustinsson
- Department of Cancer Epidemiology, Clinical Sciences, Lund University, 222 42, Lund, Sweden
| | - Thais Baert
- Leuven Multidisciplinary Breast Center, Department of Oncology, Leuven Cancer Institute, University Hospitals Leuven, 3000, Louvain, Belgium
| | - Laura E Beane Freeman
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20850, USA
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg (FAU), 91054, Erlangen, Germany
| | - Sabine Behrens
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Javier Benitez
- Biomedical Network On Rare Diseases (CIBERER), 28029, Madrid, Spain
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | - Marina Bermisheva
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, 450054, Russia
| | - Carl Blomqvist
- Department of Oncology, Helsinki University Hospital, University of Helsinki, 00290, Helsinki, Finland
- Department of Oncology, Örebro University Hospital, 70185, Örebro, Sweden
| | - Natalia V Bogdanova
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, 223040, Minsk, Belarus
- Department of Radiation Oncology, Hannover Medical School, 30625, Hannover, Germany
- Gynaecology Research Unit, Hannover Medical School, 30625, Hannover, Germany
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, 2730, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, 2730, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, IEO, European Institute of Oncology IRCCS, 20141, Milan, Italy
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Sara Y Brucker
- Department of Gynecology and Obstetrics, University of Tübingen, 72076, Tübingen, Germany
| | - Saundra S Buys
- Department of Medicine, Huntsman Cancer Institute, Salt Lake City, UT, 84112, USA
| | - Jose E Castelao
- Oncology and Genetics Unit, Instituto de Investigación Sanitaria Galicia Sur (IISGS), Xerencia de Xestion Integrada de Vigo-SERGAS, 36312, Vigo, Spain
| | - Tsun L Chan
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong, China
- Department of Molecular Pathology, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20850, USA
| | - Ji-Yeob Choi
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, 03080, Korea
- Cancer Research Institute, Seoul National University, Seoul, 03080, Korea
- Institute of Health Policy and Management, Seoul National University Medical Research Center, Seoul, 03080, Korea
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, 10032, USA
| | - Sarah V Colonna
- Department of Medicine, Huntsman Cancer Institute, Salt Lake City, UT, 84112, USA
| | - Sten Cornelissen
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni Van Leeuwenhoek Hospital, Amsterdam, 1066 CX, The Netherlands
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 65, Stockholm, Sweden
| | - Mary B Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Peter Devilee
- Department of Pathology, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, 30625, Hannover, Germany
| | - Laure Dossus
- Nutrition and Metabolism Section, International Agency for Research On Cancer (IARC-WHO), 69372, Lyon, France
| | - Miriam Dwek
- School of Life Sciences, University of Westminster, London, W1W 6UW, UK
| | - Diana M Eccles
- Faculty of Medicine, University of Southampton, Southampton, SO17 1BJ, UK
| | - Arif B Ekici
- Institute of Human Genetics, Comprehensive Cancer Center Erlangen-EMN, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg (FAU), 91054, Erlangen, Germany
| | - A Heather Eliassen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, 04107, Leipzig, Germany
- LIFE - Leipzig Research Centre for Civilization Diseases, University of Leipzig, 04103, Leipzig, Germany
| | - D Gareth Evans
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9WL, UK
- North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, M13 9WL, UK
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg (FAU), 91054, Erlangen, Germany
- David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Olivia Fletcher
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, 2730, Herlev, Denmark
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, International Cancer Genetics and Epidemiology Group, Fundación Pœblica Galega de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS, 15706, Santiago de Compostela, Spain
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92037, USA
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, 20032, China
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20850, USA
| | - José A García-Sáenz
- Medical Oncology Department, Centro Investigación Biomédica en Red de Cáncer (CIBERONC), Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), 28040, Madrid, Spain
| | - Jeanine Genkinger
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | | | - Felix Grassmann
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 65, Stockholm, Sweden
- Health and Medical University, 14471, Potsdam, Germany
| | - Pascal Guénel
- Center for Research in Epidemiology and Population Health (CESP), Team Exposome and Heredity, INSERM, University Paris-Saclay, 94805, Villejuif, France
| | - Melanie Gündert
- Molecular Epidemiology Group, German Cancer Research Center (DKFZ), C08069120, Heidelberg, Germany
- Molecular Biology of Breast Cancer, University Womens Clinic Heidelberg, University of Heidelberg, 69120, Heidelberg, Germany
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Lothar Haeberle
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg (FAU), 91054, Erlangen, Germany
| | - Eric Hahnen
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937, Cologne, Germany
- Center for Integrated Oncology (CIO), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937, Cologne, Germany
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Niclas Håkansson
- Institute of Environmental Medicine, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 65, Stockholm, Sweden
- Department of Oncology, 118 83, Sšdersjukhuset, Stockholm, Sweden
| | - Elaine F Harkness
- Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PT, UK
- Nightingale and Genesis Prevention Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, M23 9LT, UK
- NIHR Manchester Biomedical Research Unit, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, M13 9WL, UK
| | - Patricia A Harrington
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Jaana M Hartikainen
- Translational Cancer Research Area, University of Eastern Finland, 70210, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, 70210, Kuopio, Finland
| | - Mikael Hartman
- Saw Swee Hock School of Public Health, National University of Singapore, National University Health System, Singapore, 119077, Singapore
- Department of Surgery, National University Health System, Singapore, 119228, Singapore
| | - Alexander Hein
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg (FAU), 91054, Erlangen, Germany
| | - Weang-Kee Ho
- Department of Mathematical Sciences, Faculty of Science and Engineering, University of Nottingham Malaysia Campus, 43500, Semenyih, Selangor, Malaysia
- Breast Cancer Research Programme, Cancer Research Malaysia, Subang Jaya, 47500, Selangor, Malaysia
| | - Maartje J Hooning
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, 3015 GD, The Netherlands
| | - Reiner Hoppe
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376, Stuttgart, Germany
- University of Tübingen, 72074, Tübingen, Germany
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Anthony Howell
- Division of Cancer Sciences, University of Manchester, Manchester, M13 9PL, UK
| | - David J Hunter
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF, UK
| | - Dezheng Huo
- Center for Clinical Cancer Genetics, The University of Chicago, Chicago, IL, 60637, USA
| | - Hidemi Ito
- Division of Cancer Information and Control, Aichi Cancer Center Research Institute, Nagoya, 464-8681, Japan
- Division of Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Motoki Iwasaki
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center Institute for Cancer Control, Tokyo, 104-0045, Japan
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, 71-252, Szczecin, Poland
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, 71-252, Szczecin, Poland
| | - Wolfgang Janni
- Department of Gynaecology and Obstetrics, University Hospital Ulm, 89075, Ulm, Germany
| | - Esther M John
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, 94304, USA
| | - Michael E Jones
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Audrey Jung
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Daehee Kang
- Cancer Research Institute, Seoul National University, Seoul, 03080, Korea
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Elza K Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, 450054, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, 450000, Russia
| | - Sung-Won Kim
- Department of Surgery, Daerim Saint Mary's Hospital, Seoul, 07442, Korea
| | - Cari M Kitahara
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20850, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Vessela N Kristensen
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0450, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, 0379, Oslo, Norway
| | - Katerina Kubelka-Sabit
- Department of Histopathology and Cytology, Clinical Hospital Acibadem Sistina, Skopje, 1000, Republic of North Macedonia
| | - Allison W Kurian
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, 94304, USA
| | - Ava Kwong
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong, China
- Department of Surgery, The University of Hong Kong, Hong Kong, China
- Department of Surgery and Cancer Genetics Center, Hong Kong Sanatorium and Hospital, Hong Kong, China
| | - James V Lacey
- Department of Computational and Quantitative Medicine, City of Hope, Duarte, CA, 91010, USA
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, 91010, USA
| | - Diether Lambrechts
- VIB Center for Cancer Biology, 3001, Louvain, Belgium
- Laboratory for Translational Genetics, Department of Human Genetics, University of Leuven, 3000, Louvain, Belgium
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, 96813, USA
| | - Jingmei Li
- Human Genetics Division, Genome Institute of Singapore, Singapore, 138672, Singapore
| | - Martha Linet
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Wing-Yee Lo
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376, Stuttgart, Germany
- University of Tübingen, 72074, Tübingen, Germany
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Artitaya Lophatananon
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PL, UK
| | - Arto Mannermaa
- Translational Cancer Research Area, University of Eastern Finland, 70210, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, 70210, Kuopio, Finland
- Biobank of Eastern Finland, Kuopio University Hospital, Kuopio, Finland
| | - Mehdi Manoochehri
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Sara Margolin
- Department of Oncology, 118 83, Sšdersjukhuset, Stockholm, Sweden
- Department of Clinical Science and Education, Sšdersjukhuset, Karolinska Institutet, 118 83, Stockholm, Sweden
| | - Keitaro Matsuo
- Division of Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, 464-8681, Japan
| | - Dimitrios Mavroudis
- Department of Medical Oncology, University Hospital of Heraklion, 711 10, Heraklion, Greece
| | - Usha Menon
- Institute of Clinical Trials and Methodology, University College London, London, WC1V 6LJ, UK
| | - Kenneth Muir
- Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PL, UK
| | - Rachel A Murphy
- School of Population and Public Health, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Cancer Control Research, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, 00290, Helsinki, Finland
| | - William G Newman
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9WL, UK
- North West Genomics Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, M13 9WL, UK
| | - Dieter Niederacher
- Department of Gynecology and Obstetrics, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Katie M O'Brien
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, 27709, USA
| | - Nadia Obi
- Institute for Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Kenneth Offit
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | | | - Andrew F Olshan
- Department of Epidemiology, Gillings School of Global Public Health and UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Håkan Olsson
- Department of Cancer Epidemiology, Clinical Sciences, Lund University, 222 42, Lund, Sweden
| | - Sue K Park
- Cancer Research Institute, Seoul National University, Seoul, 03080, Korea
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, 03080, Korea
- Integrated Major in Innovative Medical Science, Seoul National University College of Medicine, Seoul, 03080, South Korea
| | - Alpa V Patel
- Department of Population Science, American Cancer Society, Atlanta, GA, 30303, USA
| | - Achal Patel
- Department of Epidemiology, Gillings School of Global Public Health and UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Charles M Perou
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Dijana Plaseska-Karanfilska
- Research Centre for Genetic Engineering and Biotechnology "Georgi D. Efremov", MASA, Skopje, 1000, Republic of North Macedonia
| | - Nadege Presneau
- School of Life Sciences, University of Westminster, London, W1W 6UW, UK
| | - Brigitte Rack
- Department of Gynaecology and Obstetrics, University Hospital Ulm, 89075, Ulm, Germany
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Research, Fondazione IRCCS Istituto Nazionale Dei Tumori (INT), 20133, Milan, Italy
| | - Dhanya Ramachandran
- Gynaecology Research Unit, Hannover Medical School, 30625, Hannover, Germany
| | - Muhammad U Rashid
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Department of Basic Sciences, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH & RC), Lahore, 54000, Pakistan
| | - Gad Rennert
- Clalit National Cancer Control Center, Carmel Medical Center and Technion Faculty of Medicine, 35254, Haifa, Israel
| | - Atocha Romero
- Medical Oncology Department, Hospital Universitario Puerta de Hierro, 28222, Madrid, Spain
| | - Kathryn J Ruddy
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Matthias Ruebner
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg (FAU), 91054, Erlangen, Germany
| | | | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, 27709, USA
| | - Elinor J Sawyer
- School of Cancer and Pharmaceutical Sciences, Comprehensive Cancer Centre, Guy's Campus, King's College London, London, SE1 9RT, UK
| | - Marjanka K Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni Van Leeuwenhoek Hospital, Amsterdam, 1066 CX, The Netherlands
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute - Antoni Van Leeuwenhoek Hospital, Amsterdam, 1066 CX, The Netherlands
| | - Rita K Schmutzler
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937, Cologne, Germany
- Center for Integrated Oncology (CIO), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50937, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Michael O Schneider
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg (FAU), 91054, Erlangen, Germany
| | - Christopher Scott
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Priyanka Sharma
- Department of Internal Medicine, Division of Medical Oncology, University of Kansas Medical Center, Westwood, KS, 66205, USA
| | - Chen-Yang Shen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan
- School of Public Health, China Medical University, Taichung, Taiwan
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec - Université Laval Research Center, Québec City, QC, G1V 4G2, Canada
| | - Harald Surowy
- Molecular Epidemiology Group, German Cancer Research Center (DKFZ), C08069120, Heidelberg, Germany
- Molecular Biology of Breast Cancer, University Womens Clinic Heidelberg, University of Heidelberg, 69120, Heidelberg, Germany
| | - Rulla M Tamimi
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, 10065, USA
| | - William J Tapper
- Faculty of Medicine, University of Southampton, Southampton, SO17 1BJ, UK
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, 27709, USA
- Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, 27709, USA
| | - Soo Hwang Teo
- Breast Cancer Research Programme, Cancer Research Malaysia, Subang Jaya, 47500, Selangor, Malaysia
- Department of Surgery, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Lauren R Teras
- Department of Population Science, American Cancer Society, Atlanta, GA, 30303, USA
| | - Amanda E Toland
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Rob A E M Tollenaar
- Department of Surgery, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Diana Torres
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Institute of Human Genetics, Pontificia Universidad Javeriana, 110231, Bogota, Colombia
| | - Gabriela Torres-Mejía
- Center for Population Health Research, National Institute of Public Health, 62100, Cuernavaca, Morelos, Mexico
| | - Melissa A Troester
- Department of Epidemiology, Gillings School of Global Public Health and UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Thérèse Truong
- Center for Research in Epidemiology and Population Health (CESP), Team Exposome and Heredity, INSERM, University Paris-Saclay, 94805, Villejuif, France
| | - Celine M Vachon
- Department of Quantitative Health Sciences, Division of Epidemiology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Joseph Vijai
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Clarice R Weinberg
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, 27709, USA
| | - Camilla Wendt
- Department of Clinical Science and Education, Sšdersjukhuset, Karolinska Institutet, 118 83, Stockholm, Sweden
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, 90570, Oulu, Finland
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre Oulu, 90570, Oulu, Finland
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, 171 77, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, 751 05, Uppsala, Sweden
| | - Anna H Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Taiki Yamaji
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center Institute for Cancer Control, Tokyo, 104-0045, Japan
| | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20850, USA
| | - Jyh-Cherng Yu
- Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, 114, Taiwan
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Argyrios Ziogas
- Department of Medicine, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, 92617, USA
| | - Elad Ziv
- Department of Medicine, Diller Family Comprehensive Cancer Center, Institute for Human Genetics, UCSF Helen, University of California San Francisco, San Francisco, CA, 94115, USA
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Harry Hemingway
- Institute of Health Informatics, University College London, London, UK
- Health Data Research UK, University College London, London, UK
- University College London Hospitals Biomedical Research Centre (UCLH BRC), London, UK
- The Alan Turing Institute, London, UK
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Karoline B Kuchenbaecker
- Division of Psychiatry, University College London, London, UK.
- UCL Genetics Institute, University College London, London, UK.
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21
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James LM, Georgopoulos AP. Immunogenetic Profiles and Associations of Breast, Cervical, Ovarian, and Uterine Cancers. Cancer Inform 2023; 22:11769351221148588. [PMID: 36684415 PMCID: PMC9846304 DOI: 10.1177/11769351221148588] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/13/2022] [Indexed: 01/18/2023] Open
Abstract
It is increasingly recognized that the human immune response influences cancer risk, progression, and survival; consequently, there is growing interest in the role of human leukocyte antigen (HLA), genes that play a critical role in initiating the immune response, on cancer. Recent evidence documented clustering of cancers based on immunogenetic profiles such that breast and ovarian cancers clustered together as did uterine and cervical cancers. Here we extend that line of research to evaluate the HLA profile of those 4 cancers and their associations. Specifically, we evaluated the associations between the frequencies of 127 HLA alleles and the population prevalences of breast, ovarian, cervical, and uterine cancer in 14 countries in Continental Western Europe. Factor analysis and hierarchical clustering were used to evaluate groupings of cancers based on their immunogenetic profiles. The results documented highly similar immunogenetic profiles for breast and ovarian cancers that were characterized predominantly by protective HLA effects. In addition, highly similar immunogenetic profiles for cervical and uterine cancers were observed that were, conversely, characterized by susceptibility effects. In light of the role of HLA in host immune system protection against non-self antigens, these findings suggest that certain cancers may be associated with similar contributory factors such as viral oncoproteins or neoantigens.
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Affiliation(s)
- Lisa M James
- Department of Veterans Affairs Health
Care System, The HLA Research Group, Brain Sciences Center, Minneapolis, MN,
USA,Department of Neuroscience, University
of Minnesota Medical School, Minneapolis, MN, USA,Department of Psychiatry, University of
Minnesota Medical School, Minneapolis, MN, USA
| | - Apostolos P Georgopoulos
- Department of Veterans Affairs Health
Care System, The HLA Research Group, Brain Sciences Center, Minneapolis, MN,
USA,Department of Neuroscience, University
of Minnesota Medical School, Minneapolis, MN, USA,Department of Psychiatry, University of
Minnesota Medical School, Minneapolis, MN, USA,Department of Neurology, University of
Minnesota Medical School, Minneapolis, MN, USA,Apostolos P Georgopoulos, Department of
Neuroscience, University of Minnesota Medical School, Brain Sciences Center
(11B), Minneapolis VAHCS, One Veterans Drive, Minneapolis, MN 55417, USA.
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22
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Golimbet VE, Klyushnik TP. [Genome-wide studies of comorbidity of somatic and mental diseases]. Zh Nevrol Psikhiatr Im S S Korsakova 2023; 123:60-64. [PMID: 37141130 DOI: 10.17116/jnevro202312304260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Studies of the genomic architecture of complex phenotypes, which include common somatic and mental diseases, have shown that they are characterized by a high degree of polygenicity, i.e. participation of a large number of genes associated with the risk of developing these diseases. In this regard, it is of interest to establish the genetic overlapping between these two groups of diseases. The aim of the review is to analyze genetic studies of the comorbidity of somatic and mental diseases in terms of the universality and specificity of mental disorders in somatic diseases, the reciprocal relationships of these types of pathologies, and the modulating influence of environmental factors on comorbidity. The results of the analysis indicate the existence of a common genetic predisposition to mental and somatic diseases. At the same time, the presence of common genes does not exclude the specificity of the development of mental disorders depending on a specific somatic pathology. It can be assumed that there are genes that are both unique to a particular somatic and comorbid mental illness, and genes that are common to these diseases. Common genes may have varying degrees of specificity, that is, they may be of a universal nature, which, for example, manifests itself in the development of MDD in various somatic diseases, or be specific only for a couple of individual diseases (schizophrenia - breast cancer). At the same time, common genes can have a multidirectional effect, which also contributes to the specificity of comorbidity. In addition, when searching for common genes for somatic and mental diseases, it is necessary to take into account the modulating influence of such confounders as treatment, unhealthy life style, behavioral characteristics, which can also differ in specificity depending on the diseases under consideration.
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23
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Duderstadt EL, Samuelson DJ. Rat Mammary carcinoma susceptibility 3 (Mcs3) pleiotropy, socioenvironmental interaction, and comparative genomics with orthologous human 15q25.1-25.2. G3 (BETHESDA, MD.) 2022; 13:6782958. [PMID: 36315068 PMCID: PMC9836357 DOI: 10.1093/g3journal/jkac288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/23/2022] [Indexed: 11/16/2022]
Abstract
Genome-wide association studies of breast cancer susceptibility have revealed risk-associated genetic variants and nominated candidate genes; however, the identification of causal variants and genes is often undetermined by genome-wide association studies. Comparative genomics, utilizing Rattus norvegicus strains differing in susceptibility to mammary tumor development, is a complimentary approach to identify breast cancer susceptibility genes. Mammary carcinoma susceptibility 3 (Mcs3) is a Copenhagen (COP/NHsd) allele that confers resistance to mammary carcinomas when introgressed into a mammary carcinoma susceptible Wistar Furth (WF/NHsd) genome. Here, Mcs3 was positionally mapped to a 7.2-Mb region of RNO1 spanning rs8149408 to rs107402736 (chr1:143700228-150929594, build 6.0/rn6) using WF.COP congenic strains and 7,12-dimethylbenz(a)anthracene-induced mammary carcinogenesis. Male and female WF.COP-Mcs3 rats had significantly lower body mass compared to the Wistar Furth strain. The effect on female body mass was observed only when females were raised in the absence of males indicating a socioenvironmental interaction. Furthermore, female WF.COP-Mcs3 rats, raised in the absence of males, did not develop enhanced lobuloalveolar morphologies compared to those observed in the Wistar Furth strain. Human 15q25.1-25.2 was determined to be orthologous to rat Mcs3 (chr15:80005820-82285404 and chr15:83134545-84130720, build GRCh38/hg38). A public database search of 15q25.1-25.2 revealed genome-wide significant and nominally significant associations for body mass traits and breast cancer risk. These results support the existence of a breast cancer risk-associated allele at human 15q25.1-25.2 and warrant ultrafine mapping of rat Mcs3 and human 15q25.1-25.2 to discover novel causal genes and variants.
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Affiliation(s)
- Emily L Duderstadt
- Present address for Emily L. Duderstadt: Procter and Gamble (P&G), 8700 Mason-Montgomery Road, Mason, OH 45040, USA
| | - David J Samuelson
- Corresponding author: Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, 319 Abraham Flexner Way, Louisville, KY 40202, USA.
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24
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Svishcheva GR, Tiys ES, Elgaeva EE, Feoktistova SG, Timmers PRHJ, Sharapov SZ, Axenovich TI, Tsepilov YA. A Novel Framework for Analysis of the Shared Genetic Background of Correlated Traits. Genes (Basel) 2022; 13:genes13101694. [PMID: 36292579 PMCID: PMC9602050 DOI: 10.3390/genes13101694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/12/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
We propose a novel effective framework for the analysis of the shared genetic background for a set of genetically correlated traits using SNP-level GWAS summary statistics. This framework called SHAHER is based on the construction of a linear combination of traits by maximizing the proportion of its genetic variance explained by the shared genetic factors. SHAHER requires only full GWAS summary statistics and matrices of genetic and phenotypic correlations between traits as inputs. Our framework allows both shared and unshared genetic factors to be effectively analyzed. We tested our framework using simulation studies, compared it with previous developments, and assessed its performance using three real datasets: anthropometric traits, psychiatric conditions and lipid concentrations. SHAHER is versatile and applicable to summary statistics from GWASs with arbitrary sample sizes and sample overlaps, allows for the incorporation of different GWAS models (Cox, linear and logistic), and is computationally fast.
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Affiliation(s)
- Gulnara R. Svishcheva
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 117971 Moscow, Russia
| | - Evgeny S. Tiys
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Elizaveta E. Elgaeva
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Sofia G. Feoktistova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Paul R. H. J. Timmers
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH8 9YL, UK
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh EH8 9YL, UK
| | - Sodbo Zh. Sharapov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Tatiana I. Axenovich
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Yakov A. Tsepilov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence:
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25
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Baca SC, Singler C, Zacharia S, Seo JH, Morova T, Hach F, Ding Y, Schwarz T, Huang CCF, Anderson J, Fay AP, Kalita C, Groha S, Pomerantz MM, Wang V, Linder S, Sweeney CJ, Zwart W, Lack NA, Pasaniuc B, Takeda DY, Gusev A, Freedman ML. Genetic determinants of chromatin reveal prostate cancer risk mediated by context-dependent gene regulation. Nat Genet 2022; 54:1364-1375. [PMID: 36071171 PMCID: PMC9784646 DOI: 10.1038/s41588-022-01168-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 07/19/2022] [Indexed: 12/25/2022]
Abstract
Many genetic variants affect disease risk by altering context-dependent gene regulation. Such variants are difficult to study mechanistically using current methods that link genetic variation to steady-state gene expression levels, such as expression quantitative trait loci (eQTLs). To address this challenge, we developed the cistrome-wide association study (CWAS), a framework for identifying genotypic and allele-specific effects on chromatin that are also associated with disease. In prostate cancer, CWAS identified regulatory elements and androgen receptor-binding sites that explained the association at 52 of 98 known prostate cancer risk loci and discovered 17 additional risk loci. CWAS implicated key developmental transcription factors in prostate cancer risk that are overlooked by eQTL-based approaches due to context-dependent gene regulation. We experimentally validated associations and demonstrated the extensibility of CWAS to additional epigenomic datasets and phenotypes, including response to prostate cancer treatment. CWAS is a powerful and biologically interpretable paradigm for studying variants that influence traits by affecting transcriptional regulation.
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Affiliation(s)
- Sylvan C. Baca
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA,The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Cassandra Singler
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Soumya Zacharia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Tunc Morova
- Vancouver Prostate Centre University of British Columbia, Vancouver, BC, Canada
| | - Faraz Hach
- Vancouver Prostate Centre University of British Columbia, Vancouver, BC, Canada
| | - Yi Ding
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA
| | - Tommer Schwarz
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA
| | | | - Jacob Anderson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - André P. Fay
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Cynthia Kalita
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Division of Genetics, Brigham & Women’s Hospital, Boston, MA, USA
| | - Stefan Groha
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,The Eli and Edythe L. Broad Institute, Cambridge, MA, USA
| | - Mark M. Pomerantz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Victoria Wang
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA,Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Simon Linder
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands,Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | | | - Wilbert Zwart
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands,Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Nathan A. Lack
- Vancouver Prostate Centre University of British Columbia, Vancouver, BC, Canada,School of Medicine, Koç University, Istanbul, Turkey
| | - Bogdan Pasaniuc
- Bioinformatics Interdepartmental Program, UCLA, Los Angeles, CA,Department of Computational Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA USA,Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - David Y. Takeda
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Alexander Gusev
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,The Eli and Edythe L. Broad Institute, Cambridge, MA, USA,Division of Genetics, Brigham & Women’s Hospital, Boston, MA, USA,These authors jointly supervised this work. Correspondence should be directed to M.L.F or A.G. ()
| | - Matthew L. Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA,The Eli and Edythe L. Broad Institute, Cambridge, MA, USA,These authors jointly supervised this work. Correspondence should be directed to M.L.F or A.G. ()
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26
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Byun J, Han Y, Li Y, Xia J, Long E, Choi J, Xiao X, Zhu M, Zhou W, Sun R, Bossé Y, Song Z, Schwartz A, Lusk C, Rafnar T, Stefansson K, Zhang T, Zhao W, Pettit RW, Liu Y, Li X, Zhou H, Walsh KM, Gorlov I, Gorlova O, Zhu D, Rosenberg SM, Pinney S, Bailey-Wilson JE, Mandal D, de Andrade M, Gaba C, Willey JC, You M, Anderson M, Wiencke JK, Albanes D, Lam S, Tardon A, Chen C, Goodman G, Bojeson S, Brenner H, Landi MT, Chanock SJ, Johansson M, Muley T, Risch A, Wichmann HE, Bickeböller H, Christiani DC, Rennert G, Arnold S, Field JK, Shete S, Le Marchand L, Melander O, Brunnstrom H, Liu G, Andrew AS, Kiemeney LA, Shen H, Zienolddiny S, Grankvist K, Johansson M, Caporaso N, Cox A, Hong YC, Yuan JM, Lazarus P, Schabath MB, Aldrich MC, Patel A, Lan Q, Rothman N, Taylor F, Kachuri L, Witte JS, Sakoda LC, Spitz M, Brennan P, Lin X, McKay J, Hung RJ, Amos CI. Cross-ancestry genome-wide meta-analysis of 61,047 cases and 947,237 controls identifies new susceptibility loci contributing to lung cancer. Nat Genet 2022; 54:1167-1177. [PMID: 35915169 PMCID: PMC9373844 DOI: 10.1038/s41588-022-01115-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 05/27/2022] [Indexed: 02/03/2023]
Abstract
To identify new susceptibility loci to lung cancer among diverse populations, we performed cross-ancestry genome-wide association studies in European, East Asian and African populations and discovered five loci that have not been previously reported. We replicated 26 signals and identified 10 new lead associations from previously reported loci. Rare-variant associations tended to be specific to populations, but even common-variant associations influencing smoking behavior, such as those with CHRNA5 and CYP2A6, showed population specificity. Fine-mapping and expression quantitative trait locus colocalization nominated several candidate variants and susceptibility genes such as IRF4 and FUBP1. DNA damage assays of prioritized genes in lung fibroblasts indicated that a subset of these genes, including the pleiotropic gene IRF4, potentially exert effects by promoting endogenous DNA damage.
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Affiliation(s)
- Jinyoung Byun
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Younghun Han
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Yafang Li
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Jun Xia
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Erping Long
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xiangjun Xiao
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Meng Zhu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, P. R. China
| | - Wen Zhou
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Ryan Sun
- Department of Biostatistics, University of Texas, M.D. Anderson Cancer Center, Houston, TX, USA
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec - Université Laval, Department of Molecular Medicine, Laval University, Quebec City, Quebec, Canada
| | - Zhuoyi Song
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ann Schwartz
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
- Karmanos Cancer Institute, Detroit, MI, USA
| | - Christine Lusk
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
- Karmanos Cancer Institute, Detroit, MI, USA
| | | | | | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Wei Zhao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rowland W Pettit
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Yanhong Liu
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Xihao Li
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Hufeng Zhou
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Kyle M Walsh
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA
| | - Ivan Gorlov
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Olga Gorlova
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Dakai Zhu
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Susan M Rosenberg
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Susan Pinney
- University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Diptasri Mandal
- Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | | | - Colette Gaba
- The University of Toledo College of Medicine and Life Sciences, University of Toledo, Toledo, OH, USA
| | - James C Willey
- The University of Toledo College of Medicine and Life Sciences, University of Toledo, Toledo, OH, USA
| | - Ming You
- Center for Cancer Prevention, Houston Methodist Research Institute, Houston, TX, USA
| | | | - John K Wiencke
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephan Lam
- Department of Integrative Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Adonina Tardon
- Public Health Department, University of Oviedo, ISPA and CIBERESP, Asturias, Spain
| | - Chu Chen
- Program in Epidemiology, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Stig Bojeson
- Department of Clinical Biochemistry, Herlev Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mattias Johansson
- Section of Genetics, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Thomas Muley
- Division of Cancer Epigenomics, DKFZ - German Cancer Research Center, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC-H), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Angela Risch
- Division of Cancer Epigenomics, DKFZ - German Cancer Research Center, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC-H), German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Biosciences and Medical Biology, Allergy-Cancer-BioNano Research Centre, University of Salzburg, Salzburg, Austria
- Cancer Cluster Salzburg, Salzburg, Austria
| | | | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Göttingen, Germany
| | - David C Christiani
- Department of Epidemiology, Harvard T.H.Chan School of Public Health, Boston, MA, USA
| | - Gad Rennert
- Clalit National Cancer Control Center at Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - Susanne Arnold
- University of Kentucky, Markey Cancer Center, Lexington, KY, USA
| | - John K Field
- Roy Castle Lung Cancer Research Programme, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Sanjay Shete
- Department of Biostatistics, University of Texas, M.D. Anderson Cancer Center, Houston, TX, USA
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | | | | | - Geoffrey Liu
- University Health Network- The Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Angeline S Andrew
- Departments of Epidemiology and Community and Family Medicine, Dartmouth College, Hanover, NH, USA
| | | | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, P. R. China
| | | | - Kjell Grankvist
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Mikael Johansson
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Neil Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Angela Cox
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Yun-Chul Hong
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jian-Min Yuan
- UPMC Hillman Cancer Center and Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Philip Lazarus
- Department of Pharmaceutical Sciences, College of Pharmacy, Washington State University, Spokane, WA, USA
| | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Melinda C Aldrich
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alpa Patel
- American Cancer Society, Atlanta, GA, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Fiona Taylor
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - John S Witte
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA
| | - Lori C Sakoda
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Margaret Spitz
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Paul Brennan
- Section of Genetics, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Xihong Lin
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - James McKay
- Section of Genetics, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA.
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
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27
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Long E, Patel H, Byun J, Amos CI, Choi J. Functional studies of lung cancer GWAS beyond association. Hum Mol Genet 2022; 31:R22-R36. [PMID: 35776125 DOI: 10.1093/hmg/ddac140] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/01/2022] [Accepted: 06/16/2022] [Indexed: 11/14/2022] Open
Abstract
Fourteen years after the first genome-wide association study (GWAS) of lung cancer was published, approximately forty-five genomic loci have now been significantly associated with lung cancer risk. While functional characterization was performed for several of these loci, a comprehensive summary of current molecular understanding of lung cancer risk has been lacking. Further, many novel computational and experimental tools now became available to accelerate the functional assessment of disease-associated variants, moving beyond locus-by-locus approaches. In this review, we first highlight the heterogeneity of lung cancer GWAS findings across histological subtypes, ancestries, and smoking status, which poses unique challenges to follow-up studies. We then summarize the published lung cancer post-GWAS studies for each risk-associated locus to assess the current understanding of biological mechanisms beyond the initial statistical association. We further summarize strategies for GWAS functional follow-up studies considering cutting-edge functional genomics tools and providing a catalog of available resources relevant to lung cancer. Overall, we aim to highlight the importance of integrating computational and experimental approaches to draw biological insights from the lung cancer GWAS results beyond association.
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Affiliation(s)
- Erping Long
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Harsh Patel
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jinyoung Byun
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, 77030, USA.,Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, 77030, USA.,Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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28
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Moody L, Xu GB, Pan YX, Chen H. Genome-wide cross-cancer analysis illustrates the critical role of bimodal miRNA in patient survival and drug responses to PI3K inhibitors. PLoS Comput Biol 2022; 18:e1010109. [PMID: 35639779 PMCID: PMC9187341 DOI: 10.1371/journal.pcbi.1010109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 06/10/2022] [Accepted: 04/15/2022] [Indexed: 11/24/2022] Open
Abstract
Heterogeneity of cancer means many tumorigenic genes are only aberrantly expressed in a subset of patients and thus follow a bimodal distribution, having two modes of expression within a single population. Traditional statistical techniques that compare sample means between cancer patients and healthy controls fail to detect bimodally expressed genes. We utilize a mixture modeling approach to identify bimodal microRNA (miRNA) across cancers, find consistent sources of heterogeneity, and identify potential oncogenic miRNA that may be used to guide personalized therapies. Pathway analysis was conducted using target genes of the bimodal miRNA to identify potential functional implications in cancer. In vivo overexpression experiments were conducted to elucidate the clinical importance of bimodal miRNA in chemotherapy treatments. In nine types of cancer, tumors consistently displayed greater bimodality than normal tissue. Specifically, in liver and lung cancers, high expression of miR-105 and miR-767 was indicative of poor prognosis. Functional pathway analysis identified target genes of miR-105 and miR-767 enriched in the phosphoinositide-3-kinase (PI3K) pathway, and analysis of over 200 cancer drugs in vitro showed that drugs targeting the same pathway had greater efficacy in cell lines with high miR-105 and miR-767 levels. Overexpression of the two miRNA facilitated response to PI3K inhibitor treatment. We demonstrate that while cancer is marked by considerable genetic heterogeneity, there is between-cancer concordance regarding the particular miRNA that are more variable. Bimodal miRNA are ideal biomarkers that can be used to stratify patients for prognosis and drug response in certain types of cancer. Bimodal genes can be defined as those having two modes of expression within the same population. A variety of statistical methodologies have been employed to assess bimodal gene expression, but current methods and their applications have been limited. Given the advances in next-generation sequencing as well as the extensive regulatory role of miRNA, assessing bimodality in miRNA-seq data can greatly broaden our understanding of factors underlying tumor progression. The goal of the current study was to utilize a novel mixture modeling approach to identify bimodal miRNA and then demonstrate their importance in cancer by evaluating their ability to predict overall survival and drug response. Our results showed that high levels of bimodal miRNA expression was characteristic of cancer. Additionally, several bimodal miRNA were common to multiple cancer types, suggesting that certain miRNA consistently account for tumor heterogeneity and may be involved in general oncogenic processes. Our study points to the potential of bimodal miRNA to facilitate precise prognostic evaluation and effective treatment strategies.
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Affiliation(s)
- Laura Moody
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Guanying Bianca Xu
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Yuan-Xiang Pan
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Hong Chen
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail:
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29
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James LM, Georgopoulos AP. Immunogenetic clustering of 30 cancers. Sci Rep 2022; 12:7235. [PMID: 35508592 PMCID: PMC9068692 DOI: 10.1038/s41598-022-11366-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/15/2022] [Indexed: 11/09/2022] Open
Abstract
Human leukocyte antigen (HLA) genes have been implicated in cancer risk and shared heritability of different types of cancer. In this immunogenetic epidemiological study we first computed a Cancer-HLA profile for 30 cancer types characterized by the correlation between the prevalence of each cancer and the population frequency of 127 HLA alleles, and then used multidimensional scaling to evaluate the possible clustering of those Cancer-HLA associations. The results indicated the presence of three clusters, broadly reflecting digestive-skin-cervical cancers, reproductive and endocrine systems cancers, and brain and androgen-associated cancers. The clustering of cancer types documented here is discussed in terms of mechanisms underlying shared Cancer-HLA associations.
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Affiliation(s)
- Lisa M James
- The HLA Research Group, Brain Sciences Center (11B), Department of Veterans Affairs Health Care System, Minneapolis VAHCS, One Veterans Drive, Minneapolis, MN, 55417, USA.,Department of Neuroscience, University of Minnesota Medical School, Minneapolis, MN, 55455, USA.,Department of Psychiatry, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Apostolos P Georgopoulos
- The HLA Research Group, Brain Sciences Center (11B), Department of Veterans Affairs Health Care System, Minneapolis VAHCS, One Veterans Drive, Minneapolis, MN, 55417, USA. .,Department of Neuroscience, University of Minnesota Medical School, Minneapolis, MN, 55455, USA. .,Department of Psychiatry, University of Minnesota Medical School, Minneapolis, MN, 55455, USA. .,Department of Neurology, University of Minnesota Medical School, Minneapolis, MN, 55455, USA.
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30
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Zeng Z, Bromberg Y. Inferring Potential Cancer Driving Synonymous Variants. Genes (Basel) 2022; 13:778. [PMID: 35627162 PMCID: PMC9140830 DOI: 10.3390/genes13050778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 02/01/2023] Open
Abstract
Synonymous single nucleotide variants (sSNVs) are often considered functionally silent, but a few cases of cancer-causing sSNVs have been reported. From available databases, we collected four categories of sSNVs: germline, somatic in normal tissues, somatic in cancerous tissues, and putative cancer drivers. We found that screening sSNVs for recurrence among patients, conservation of the affected genomic position, and synVep prediction (synVep is a machine learning-based sSNV effect predictor) recovers cancer driver variants (termed proposed drivers) and previously unknown putative cancer genes. Of the 2.9 million somatic sSNVs found in the COSMIC database, we identified 2111 proposed cancer driver sSNVs. Of these, 326 sSNVs could be further tagged for possible RNA splicing effects, RNA structural changes, and affected RBP motifs. This list of proposed cancer driver sSNVs provides computational guidance in prioritizing the experimental evaluation of synonymous mutations found in cancers. Furthermore, our list of novel potential cancer genes, galvanized by synonymous mutations, may highlight yet unexplored cancer mechanisms.
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Affiliation(s)
- Zishuo Zeng
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08873, USA
| | - Yana Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08873, USA
- Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA
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31
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Asare A, Yao H, Lara OD, Wang Y, Zhang L, Sood AK. Race-associated molecular changes in gynecologic malignancies. CANCER RESEARCH COMMUNICATIONS 2022; 2:99-109. [PMID: 35992327 PMCID: PMC9390975 DOI: 10.1158/2767-9764.crc-21-0018] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The difference in cancer morbidity and mortality between individuals of different racial groups is complex. Health disparities provide a framework to explore potential connections between poor outcomes and individuals of different racial backgrounds. This study identifies genomic changes in African-American patients with gynecologic malignancies, a population with well-established disparities in outcomes. Our data explore whether social health disparities might mediate interactions between the environment and tumor epigenomes and genomes that can be identified. Using The Cancer Genetic Ancestry Atlas, which encodes data from The Cancer Genome Atlas by ancestry and allows for systematic analyses of sequencing data by racial group, we performed large-scale, comparative analyses to identify novel targets with alterations in methylation, transcript, and microRNA expression between tumors from women of European American or African American racial groups across all gynecologic malignancies. We identify novel discrete genomic changes in these complex malignancies and suggest a framework for identifying novel therapeutic targets for future investigation.
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Affiliation(s)
- Amma Asare
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, Texas
| | - Hui Yao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Olivia D. Lara
- Department of Obstetrics and Gynecology, NYU Langone Health, New York
| | - Ying Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lin Zhang
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Anil K. Sood
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Corresponding Author: Anil K. Sood, Department of Gynecologic Oncology and Reproductive Medicine, Unit 1362, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030. Phone: 713-745-5266; E-mail:
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32
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Choi J, Jia G, Wen W, Tao R, Long J, Shu XO, Zheng W. Associations of genetic susceptibility to 16 cancers with risk of breast cancer overall and by intrinsic subtypes. HGG ADVANCES 2022; 3:100077. [PMID: 35047862 PMCID: PMC8756518 DOI: 10.1016/j.xhgg.2021.100077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 12/06/2021] [Indexed: 11/24/2022] Open
Abstract
Certain genetic variants are associated with risks of multiple cancers. We investigated breast cancer risk with overall genetic susceptibility to each of 16 other cancers. We constructed polygenic risk scores (PRS) for 16 cancers using risk variants identified by genome-wide association studies. We evaluated the associations of these PRSs with breast cancer risk (overall and by subtypes) using Breast Cancer Association Consortium data, including 106,278 cases and 91,477 controls of European ancestry. Odds ratios (OR) and 95% confidence intervals (CIs) were estimated to measure the association of each PRS with breast cancer risk. Data from the UK Biobank, including 4,337 cases and 209,983 non-cases, were used to replicate the findings. A 5%–8% significantly elevated risk of overall breast cancer was associated with per unit increase of the PRS for glioma and cancers of the corpus uteri, stomach, or colorectum. Analyses by subtype revealed that the PRS for corpus uteri cancer (OR = 1.09; 95% CI, 1.03–1.15) and stomach cancer (OR = 1.07; 95% CI, 1.03–1.12) were associated with estrogen receptor-positive breast cancer, while ovarian cancer PRS was associated with triple-negative breast cancer (OR = 1.25; 95% CI, 1.01–1.55). UK Biobank data supported the positive associations of overall breast cancer risk with PRS for melanoma and cancers of the stomach, colorectum, and ovary. Our study provides strong evidence for shared genetic susceptibility of breast cancer with several other cancers. Results from our study help uncover the genetic basis for breast and other cancers and identify individuals at high risk for multiple cancers.
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Affiliation(s)
- Jungyoon Choi
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Guochong Jia
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37203, USA
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33
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Arshad Z, McDonald JF. Changes in gene-gene interactions associated with cancer onset and progression are largely independent of changes in gene expression. iScience 2021; 24:103522. [PMID: 34917899 PMCID: PMC8666350 DOI: 10.1016/j.isci.2021.103522] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/07/2021] [Accepted: 11/23/2021] [Indexed: 12/12/2022] Open
Abstract
Recent findings indicate that changes underlying cancer onset and progression are not only attributable to changes in DNA structure and expression of individual genes but to changes in interactions among these genes as well. We examined co-expression changes in gene-network structure occurring during the onset and progression of nine different cancer types. Network complexity is generally reduced in the transition from normal precursor tissues to corresponding primary tumors. Cross-tissue cancer network similarity generally increases in early-stage cancers followed by a subsequent loss in cross-tissue cancer similarity as tumors reacquire cancer-specific network complexity. Gene-gene connections remaining stable through cancer development are enriched for “housekeeping” gene functions, whereas newly acquired interactions are associated with established cancer-promoting functions. Surprisingly, >90% of changes in gene-gene network interactions in cancers are not associated with changes in the expression of network genes relative to normal precursor tissues. Gene-gene network complexity is reduced in the transition from normal to cancer Network similarity across cancer types is higher in early-stage versus late-stage cancers Network interactions among housekeeping genes are stable through cancer development <10% of changes in network interactions in cancer involve changes in gene expression
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Affiliation(s)
- Zainab Arshad
- Integrated Cancer Research Center, School of Biological Sciences, Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, GA 30619, USA
| | - John F. McDonald
- Integrated Cancer Research Center, School of Biological Sciences, Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, GA 30619, USA
- Corresponding author
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34
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Ren N, Li B, Liu Q, Yang L, Liu X, Huang Q. Dinucleotide tag-based parallel reporter gene assay method enables efficient identification of regulatory mutations. Biotechnol J 2021; 17:e2100341. [PMID: 34894203 DOI: 10.1002/biot.202100341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 12/07/2021] [Accepted: 12/09/2021] [Indexed: 11/06/2022]
Abstract
BACKGROUND The causal single nucleotide polymorphisms (SNPs) leading to increased cancer predisposition mainly function as gene regulatory elements, the evaluation of which largely relies on the parallel reporter gene assay system. However, the common DNA barcodes used in parallel reporter gene assay systems typically because nucleotide composition bias, and many barcodes must be allocated for each sequence to reduce the bias effect. MAIN METHODS AND MAJOR RESULTS Here, a versatile dinucleotide-tag reporter system (DiR) that enables parallel analysis of regulatory elements with minimized bias based on next-generation sequencing is described. The DiR system is more robust than the classical luciferase assay method, particularly for the investigation of moderate-level regulatory elements. The authors applied the DiR-seq assay in the functional evaluation of SNPs with prostate cancer risk and nominated two and six regulatory SNPs in PC-3 and LNCaP cells, respectively. CONCLUSIONS AND IMPLICATIONS The DiR system has great potential to advance the functional study of SNPs associated with polygenic disease risks.
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Affiliation(s)
- Naixia Ren
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Bo Li
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Qingqing Liu
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Lele Yang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Xiaodan Liu
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Qilai Huang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
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35
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Reddy J, Fonseca MAS, Corona RI, Nameki R, Segato Dezem F, Klein IA, Chang H, Chaves-Moreira D, Afeyan LK, Malta TM, Lin X, Abbasi F, Font-Tello A, Sabedot T, Cejas P, Rodríguez-Malavé N, Seo JH, Lin DC, Matulonis U, Karlan BY, Gayther SA, Pasaniuc B, Gusev A, Noushmehr H, Long H, Freedman ML, Drapkin R, Young RA, Abraham BJ, Lawrenson K. Predicting master transcription factors from pan-cancer expression data. SCIENCE ADVANCES 2021; 7:eabf6123. [PMID: 34818047 PMCID: PMC8612691 DOI: 10.1126/sciadv.abf6123] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Critical developmental “master transcription factors” (MTFs) can be subverted during tumorigenesis to control oncogenic transcriptional programs. Current approaches to identifying MTFs rely on ChIP-seq data, which is unavailable for many cancers. We developed the CaCTS (Cancer Core Transcription factor Specificity) algorithm to prioritize candidate MTFs using pan-cancer RNA sequencing data. CaCTS identified candidate MTFs across 34 tumor types and 140 subtypes including predictions for cancer types/subtypes for which MTFs are unknown, including e.g. PAX8, SOX17, and MECOM as candidates in ovarian cancer (OvCa). In OvCa cells, consistent with known MTF properties, these factors are required for viability, lie proximal to superenhancers, co-occupy regulatory elements globally, co-bind loci encoding OvCa biomarkers, and are sensitive to pharmacologic inhibition of transcription. Our predictions of MTFs, especially for tumor types with limited understanding of transcriptional drivers, pave the way to therapeutic targeting of MTFs in a broad spectrum of cancers.
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Affiliation(s)
- Jessica Reddy
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
| | - Marcos A. S. Fonseca
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
| | - Rosario I. Corona
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
- Center for Bioinformatics and Functional Genomics,
Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Robbin Nameki
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
| | - Felipe Segato Dezem
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
- Center for Bioinformatics and Functional Genomics,
Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Isaac A. Klein
- Whitehead Institute for Biomedical Research,
Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Boston, MA, USA
| | - Heidi Chang
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
| | | | - Lena K. Afeyan
- Whitehead Institute for Biomedical Research,
Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of
Technology, Cambridge, MA, USA
| | | | - Xianzhi Lin
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
| | - Forough Abbasi
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
- Center for Bioinformatics and Functional Genomics,
Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alba Font-Tello
- Center for Functional Cancer Epigenetics, Dana-Farber
Cancer Institute, Boston, MA, USA
| | | | - Paloma Cejas
- Center for Functional Cancer Epigenetics, Dana-Farber
Cancer Institute, Boston, MA, USA
| | - Norma Rodríguez-Malavé
- Center for Bioinformatics and Functional Genomics,
Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ji-Heui Seo
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber
Cancer Institute, Boston, MA, USA
| | - De-Chen Lin
- Department of Medicine, Cedars-Sinai Medical
Center, Los Angeles, CA, USA
| | - Ursula Matulonis
- Division of Gynecologic Oncology, Dana Farber
Cancer Institute, Boston, MA, USA
| | - Beth Y. Karlan
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
- Cancer Population Genetics, Jonsson Comprehensive
Cancer Center, David Geffen School of Medicine, University of California, Los
Angeles, Los Angeles, CA, USA
| | - Simon A. Gayther
- Center for Bioinformatics and Functional Genomics,
Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Bogdan Pasaniuc
- Bioinformatics Interdepartmental Program,
University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School
of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine,
David Geffen School of Medicine, University of California, Los Angeles, Los
Angeles, CA, USA
- Department of Computational Medicine, David Geffen
School of Medicine, University of California, Los Angeles, Los Angeles, CA,
USA
| | - Alexander Gusev
- Center for Functional Cancer Epigenetics, Dana-Farber
Cancer Institute, Boston, MA, USA
- McGraw/Patterson Center for Population Sciences,
Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Henry Long
- Center for Functional Cancer Epigenetics, Dana-Farber
Cancer Institute, Boston, MA, USA
| | - Matthew L. Freedman
- Department of Medical Oncology, Dana-Farber Cancer
Institute, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber
Cancer Institute, Boston, MA, USA
- The Eli and Edythe L. Broad Institute, Cambridge,
MA, USA
| | - Ronny Drapkin
- Penn Ovarian Cancer Research Center, University of
Pennsylvania, Philadelphia, PA, USA
| | - Richard A. Young
- Whitehead Institute for Biomedical Research,
Cambridge, MA, USA
- Department of Biology, M.I.T., Cambridge, MA,
USA
| | - Brian J. Abraham
- Department of Computational Biology, St. Jude
Children’s Research Hospital, Memphis, TN, USA
- Corresponding author.
(B.J.A.);
(K.L.)
| | - Kate Lawrenson
- Women’s Cancer Research Program at the Samuel
Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles,
CA, USA
- Division of Gynecologic Oncology, Department of
Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA,
USA
- Center for Bioinformatics and Functional Genomics,
Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Corresponding author.
(B.J.A.);
(K.L.)
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36
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Zhou X, Lee SH. An integrative analysis of genomic and exposomic data for complex traits and phenotypic prediction. Sci Rep 2021; 11:21495. [PMID: 34728654 PMCID: PMC8564528 DOI: 10.1038/s41598-021-00427-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 10/12/2021] [Indexed: 12/18/2022] Open
Abstract
Complementary to the genome, the concept of exposome has been proposed to capture the totality of human environmental exposures. While there has been some recent progress on the construction of the exposome, few tools exist that can integrate the genome and exposome for complex trait analyses. Here we propose a linear mixed model approach to bridge this gap, which jointly models the random effects of the two omics layers on phenotypes of complex traits. We illustrate our approach using traits from the UK Biobank (e.g., BMI and height for N ~ 35,000) with a small fraction of the exposome that comprises 28 lifestyle factors. The joint model of the genome and exposome explains substantially more phenotypic variance and significantly improves phenotypic prediction accuracy, compared to the model based on the genome alone. The additional phenotypic variance captured by the exposome includes its additive effects as well as non-additive effects such as genome-exposome (gxe) and exposome-exposome (exe) interactions. For example, 19% of variation in BMI is explained by additive effects of the genome, while additional 7.2% by additive effects of the exposome, 1.9% by exe interactions and 4.5% by gxe interactions. Correspondingly, the prediction accuracy for BMI, computed using Pearson's correlation between the observed and predicted phenotypes, improves from 0.15 (based on the genome alone) to 0.35 (based on the genome and exposome). We also show, using established theories, that integrating genomic and exposomic data can be an effective way of attaining a clinically meaningful level of prediction accuracy for disease traits. In conclusion, the genomic and exposomic effects can contribute to phenotypic variation via their latent relationships, i.e. genome-exposome correlation, and gxe and exe interactions, and modelling these effects has a potential to improve phenotypic prediction accuracy and thus holds a great promise for future clinical practice.
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Affiliation(s)
- Xuan Zhou
- Australian Centre for Precision Health, University of South Australia, Adelaide, SA, 5000, Australia
- UniSA Allied Health and Human Performance, University of South Australia, Adelaide, SA, 5000, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - S Hong Lee
- Australian Centre for Precision Health, University of South Australia, Adelaide, SA, 5000, Australia.
- UniSA Allied Health and Human Performance, University of South Australia, Adelaide, SA, 5000, Australia.
- South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia.
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37
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Wang T, Lu H, Zeng P. Identifying pleiotropic genes for complex phenotypes with summary statistics from a perspective of composite null hypothesis testing. Brief Bioinform 2021; 23:6375058. [PMID: 34571531 DOI: 10.1093/bib/bbab389] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/06/2021] [Accepted: 08/28/2021] [Indexed: 12/13/2022] Open
Abstract
Pleiotropy has important implication on genetic connection among complex phenotypes and facilitates our understanding of disease etiology. Genome-wide association studies provide an unprecedented opportunity to detect pleiotropic associations; however, efficient pleiotropy test methods are still lacking. We here consider pleiotropy identification from a methodological perspective of high-dimensional composite null hypothesis and propose a powerful gene-based method called MAIUP. MAIUP is constructed based on the traditional intersection-union test with two sets of independent P-values as input and follows a novel idea that was originally proposed under the high-dimensional mediation analysis framework. The key improvement of MAIUP is that it takes the composite null nature of pleiotropy test into account by fitting a three-component mixture null distribution, which can ultimately generate well-calibrated P-values for effective control of family-wise error rate and false discover rate. Another attractive advantage of MAIUP is its ability to effectively address the issue of overlapping subjects commonly encountered in association studies. Simulation studies demonstrate that compared with other methods, only MAIUP can maintain correct type I error control and has higher power across a wide range of scenarios. We apply MAIUP to detect shared associated genes among 14 psychiatric disorders with summary statistics and discover many new pleiotropic genes that are otherwise not identified if failing to account for the issue of composite null hypothesis testing. Functional and enrichment analyses offer additional evidence supporting the validity of these identified pleiotropic genes associated with psychiatric disorders. Overall, MAIUP represents an efficient method for pleiotropy identification.
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Affiliation(s)
- Ting Wang
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Haojie Lu
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Ping Zeng
- Department of Biostatistics, School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China.,Center for Medical Statistics and Data Analysis, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China.,Key Laboratory of Human Genetics and Environmental Medicine, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
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Rammal S, Kourie HR, Jalkh N, Mehawej C, Chouery E, Moujaess E, Dabar G. Molecular pathogenesis of hereditary lung cancer: a literature review. Pharmacogenomics 2021; 22:791-803. [PMID: 34410147 DOI: 10.2217/pgs-2020-0150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Among all cancer types, pulmonary cancer has the highest mortality rate. Tobacco consumption remains the major risk factor for the development of lung cancer. However, many studies revealed a correlation between inherited genetic variants and predisposition to lung cancer, especially in nonsmokers. To date, genetic testing for the detection of germline mutations is not yet recommended in patients with lung cancer and testing is focused on somatic alterations given their implication in the treatment choice. Understanding the impact of genetic predisposition on the occurrence of lung cancer is essential to enable the introduction of accurate guidelines and recommendations that might reduce mortality. In this review paper, we describe familial lung cancer, and expose germline mutations that are linked to this type of cancer. We also report pathogenic genetic variants linked to syndromes associated with lung cancer.
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Affiliation(s)
- Souraya Rammal
- Faculty of Medicine, Saint Joseph University of Beirut, Beirut, Lebanon
| | - Hampig Raphael Kourie
- Hematology-Oncology Department, Faculty of Medicine, Saint Joseph University of Beirut, Beirut, Lebanon
| | - Nadine Jalkh
- Medical Genetics Unit, Faculty of Medicine, Saint Joseph University of Beirut, Beirut, Lebanon
| | - Cybel Mehawej
- Medical Genetics Unit, Faculty of Medicine, Saint Joseph University of Beirut, Beirut, Lebanon
| | - Eliane Chouery
- Medical Genetics Unit, Faculty of Medicine, Saint Joseph University of Beirut, Beirut, Lebanon
| | - Elissar Moujaess
- Hematology-Oncology Department, Faculty of Medicine, Saint Joseph University of Beirut, Beirut, Lebanon
| | - Georges Dabar
- Pulmonary & Critical Care Division, Hotel Dieu de France, Saint Joseph University of Beirut, Beirut, Lebanon
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39
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Kar SP, Considine DP, Tyrer JP, Plummer JT, Chen S, Dezem FS, Barbeira AN, Rajagopal PS, Rosenow WT, Moreno F, Bodelon C, Chang-Claude J, Chenevix-Trench G, deFazio A, Dörk T, Ekici AB, Ewing A, Fountzilas G, Goode EL, Hartman M, Heitz F, Hillemanns P, Høgdall E, Høgdall CK, Huzarski T, Jensen A, Karlan BY, Khusnutdinova E, Kiemeney LA, Kjaer SK, Klapdor R, Köbel M, Li J, Liebrich C, May T, Olsson H, Permuth JB, Peterlongo P, Radice P, Ramus SJ, Riggan MJ, Risch HA, Saloustros E, Simard J, Szafron LM, Titus L, Thompson CL, Vierkant RA, Winham SJ, Zheng W, Doherty JA, Berchuck A, Lawrenson K, Im HK, Manichaikul AW, Pharoah PD, Gayther SA, Schildkraut JM. Pleiotropy-guided transcriptome imputation from normal and tumor tissues identifies candidate susceptibility genes for breast and ovarian cancer. HGG ADVANCES 2021; 2:100042. [PMID: 34317694 PMCID: PMC8312632 DOI: 10.1016/j.xhgg.2021.100042] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 06/04/2021] [Indexed: 12/12/2022] Open
Abstract
Familial, sequencing, and genome-wide association studies (GWASs) and genetic correlation analyses have progressively unraveled the shared or pleiotropic germline genetics of breast and ovarian cancer. In this study, we aimed to leverage this shared germline genetics to improve the power of transcriptome-wide association studies (TWASs) to identify candidate breast cancer and ovarian cancer susceptibility genes. We built gene expression prediction models using the PrediXcan method in 681 breast and 295 ovarian tumors from The Cancer Genome Atlas and 211 breast and 99 ovarian normal tissue samples from the Genotype-Tissue Expression project and integrated these with GWAS meta-analysis data from the Breast Cancer Association Consortium (122,977 cases/105,974 controls) and the Ovarian Cancer Association Consortium (22,406 cases/40,941 controls). The integration was achieved through application of a pleiotropy-guided conditional/conjunction false discovery rate (FDR) approach in the setting of a TWASs. This identified 14 candidate breast cancer susceptibility genes spanning 11 genomic regions and 8 candidate ovarian cancer susceptibility genes spanning 5 genomic regions at conjunction FDR < 0.05 that were >1 Mb away from known breast and/or ovarian cancer susceptibility loci. We also identified 38 candidate breast cancer susceptibility genes and 17 candidate ovarian cancer susceptibility genes at conjunction FDR < 0.05 at known breast and/or ovarian susceptibility loci. The 22 genes identified by our cross-cancer analysis represent promising candidates that further elucidate the role of the transcriptome in mediating germline breast and ovarian cancer risk.
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Affiliation(s)
- Siddhartha P. Kar
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Daniel P.C. Considine
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jonathan P. Tyrer
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Jasmine T. Plummer
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Science, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Stephanie Chen
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Science, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Felipe S. Dezem
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Science, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Alvaro N. Barbeira
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Padma S. Rajagopal
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Will T. Rosenow
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Fernando Moreno
- Department of Oncology, Hospital Clínico San Carlos, Madrid, Spain
| | - Clara Bodelon
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Anna deFazio
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, NSW, Australia
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Arif B. Ekici
- Institute of Human Genetics, University Hospital Erlangen, Erlangen, Germany
- Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen, Erlangen, Germany
| | - Ailith Ewing
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | - Ellen L. Goode
- Department of Quantitative Health Sciences, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Mikael Hartman
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Florian Heitz
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte/Evang., Essen, Germany
- Department of Gynecology, Center for Oncologic Surgery, Charité Campus Virchow-Klinikum, Berlin, Germany
| | - Peter Hillemanns
- Department of Gynecology and Obstetrics, Hannover Medical School, Hannover, Germany
| | - Estrid Høgdall
- Department of Virus, Lifestyle, and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
- Molecular Unit, Department of Pathology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Claus K. Høgdall
- The Juliane Marie Centre, Department of Gynecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Tomasz Huzarski
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
- Department of Genetics and Pathology, University of Zielona Góra, Zielona Góra, Poland
| | - Allan Jensen
- Department of Lifestyle, Reproduction, and Cancer, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Beth Y. Karlan
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Lambertus A. Kiemeney
- Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Susanne K. Kjaer
- Department of Virus, Lifestyle, and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Gynaecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Rüdiger Klapdor
- Department of Gynecology and Obstetrics, Hannover Medical School, Hannover, Germany
| | - Martin Köbel
- Department of Pathology and Laboratory Medicine, University of Calgary, Foothills Medical Center, Calgary, AB, Canada
| | - Jingmei Li
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Genome Institute of Singapore, Human Genetics, Singapore, Singapore
| | - Clemens Liebrich
- Department of Obstetrics and Gynecology, Klinikum Wolfsburg, Wolfsburg, Germany
| | - Taymaa May
- Division of Gynecologic Oncology, University Health Network, Princess Margaret Hospital, Toronto, ON, Canada
| | - Håkan Olsson
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Jennifer B. Permuth
- Departments of Cancer Epidemiology and Gastrointestinal Oncology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Paolo Peterlongo
- Genome Diagnostics Program, IFOM-The FIRC Institute of Molecular Oncology, Milan, Italy
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Susan J. Ramus
- School of Women’s and Children’s Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
- Adult Cancer Program, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Marjorie J. Riggan
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Harvey A. Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | | | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec - Université Laval Research Center, Québec City, QC, Canada
| | - Lukasz M. Szafron
- Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Linda Titus
- Muskie School of Public Service, University of Southern Maine, Portland, ME, USA
| | - Cheryl L. Thompson
- Department of Nutrition, Case Western Reserve University, Cleveland, OH, USA
| | - Robert A. Vierkant
- Department of Quantitative Health Sciences, Division of Clinical Trials and Biostatistics, Mayo Clinic, Rochester, MN, USA
| | - Stacey J. Winham
- Department of Quantitative Health Sciences, Division of Computational Biology, Mayo Clinic, Rochester, MN, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jennifer A. Doherty
- Huntsman Cancer Institute, Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - Andrew Berchuck
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Kate Lawrenson
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Science, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Women’s Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Hae Kyung Im
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Ani W. Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Paul D.P. Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Simon A. Gayther
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Science, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Joellen M. Schildkraut
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
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40
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Chen H, Majumdar A, Wang L, Kar S, Brown KM, Feng H, Turman C, Dennis J, Easton D, Michailidou K, Simard J, Bishop T, Cheng IC, Huyghe JR, Schmit SL, O’Mara TA, Spurdle AB, Gharahkhani P, Schumacher J, Jankowski J, Gockel I, Bondy ML, Houlston RS, Jenkins RB, Melin B, Lesseur C, Ness AR, Diergaarde B, Olshan AF, Amos CI, Christiani DC, Landi MT, McKay JD, Brossard M, Iles MM, Law MH, MacGregor S, Beesley J, Jones MR, Tyrer J, Winham SJ, Klein AP, Petersen G, Li D, Wolpin BM, Eeles RA, Haiman CA, Kote-Jarai Z, Schumacher FR, Brennan P, Chanock SJ, Gaborieau V, Purdue MP, Pharoah P, Hung RJ, Amundadottir LT, Kraft P, Pasaniuc B, Lindström S. Large-scale cross-cancer fine-mapping of the 5p15.33 region reveals multiple independent signals. HGG ADVANCES 2021; 2:100041. [PMID: 34355204 PMCID: PMC8336922 DOI: 10.1016/j.xhgg.2021.100041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/04/2021] [Indexed: 12/23/2022] Open
Abstract
Genome-wide association studies (GWASs) have identified thousands of cancer risk loci revealing many risk regions shared across multiple cancers. Characterizing the cross-cancer shared genetic basis can increase our understanding of global mechanisms of cancer development. In this study, we collected GWAS summary statistics based on up to 375,468 cancer cases and 530,521 controls for fourteen types of cancer, including breast (overall, estrogen receptor [ER]-positive, and ER-negative), colorectal, endometrial, esophageal, glioma, head/neck, lung, melanoma, ovarian, pancreatic, prostate, and renal cancer, to characterize the shared genetic basis of cancer risk. We identified thirteen pairs of cancers with statistically significant local genetic correlations across eight distinct genomic regions. Specifically, the 5p15.33 region, harboring the TERT and CLPTM1L genes, showed statistically significant local genetic correlations for multiple cancer pairs. We conducted a cross-cancer fine-mapping of the 5p15.33 region based on eight cancers that showed genome-wide significant associations in this region (ER-negative breast, colorectal, glioma, lung, melanoma, ovarian, pancreatic, and prostate cancer). We used an iterative analysis pipeline implementing a subset-based meta-analysis approach based on cancer-specific conditional analyses and identified ten independent cross-cancer associations within this region. For each signal, we conducted cross-cancer fine-mapping to prioritize the most plausible causal variants. Our findings provide a more in-depth understanding of the shared inherited basis across human cancers and expand our knowledge of the 5p15.33 region in carcinogenesis.
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Affiliation(s)
- Hongjie Chen
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Arunabha Majumdar
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Mathematics, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - Lu Wang
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Siddhartha Kar
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Kevin M. Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Helian Feng
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Constance Turman
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Douglas Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Jacques Simard
- Department of Molecular Medicine, Faculty of Medicine, Université Laval and Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
| | - Breast Cancer Association Consortium (BCAC)
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Mathematics, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
- Department of Molecular Medicine, Faculty of Medicine, Université Laval and Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
- College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE
- Comprehensive Clinical Trials Unit, University College London, London, UK
- Department of Visceral, Transplant, Thoracic, and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
- Department of Epidemiology and Population Health, Stanford University, Palo Alto, CA, USA
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Department of Laboratory Medicine and Pathology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, MN, USA
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- International Agency for Research on Cancer, World Health Organization, Lyon, France
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK
- Bristol Dental School, University of Bristol, Bristol, UK
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Genetic Epidemiology and Functional Genomics of Multifactorial Diseases Team, Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-1124, Université Paris Descartes, Paris, France
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbuaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
- School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Medical Oncology, Dana Farber Harvard Cancer Center, Boston, MA, USA
- Oncogenetics Team, Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, UK
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
- Seidman Cancer Center, University Hospitals, Cleveland, OH, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Timothy Bishop
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Iona C. Cheng
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA, USA
| | - Jeroen R. Huyghe
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stephanie L. Schmit
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Colorectal Transdisciplinary Study (CORECT)
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Mathematics, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
- Department of Molecular Medicine, Faculty of Medicine, Université Laval and Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
- College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE
- Comprehensive Clinical Trials Unit, University College London, London, UK
- Department of Visceral, Transplant, Thoracic, and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
- Department of Epidemiology and Population Health, Stanford University, Palo Alto, CA, USA
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Department of Laboratory Medicine and Pathology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, MN, USA
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- International Agency for Research on Cancer, World Health Organization, Lyon, France
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK
- Bristol Dental School, University of Bristol, Bristol, UK
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Genetic Epidemiology and Functional Genomics of Multifactorial Diseases Team, Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-1124, Université Paris Descartes, Paris, France
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbuaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
- School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Medical Oncology, Dana Farber Harvard Cancer Center, Boston, MA, USA
- Oncogenetics Team, Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, UK
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
- Seidman Cancer Center, University Hospitals, Cleveland, OH, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Colon Cancer Family Registry Study (CCFR)
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Mathematics, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
- Department of Molecular Medicine, Faculty of Medicine, Université Laval and Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
- College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE
- Comprehensive Clinical Trials Unit, University College London, London, UK
- Department of Visceral, Transplant, Thoracic, and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
- Department of Epidemiology and Population Health, Stanford University, Palo Alto, CA, USA
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Department of Laboratory Medicine and Pathology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, MN, USA
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- International Agency for Research on Cancer, World Health Organization, Lyon, France
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK
- Bristol Dental School, University of Bristol, Bristol, UK
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Genetic Epidemiology and Functional Genomics of Multifactorial Diseases Team, Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-1124, Université Paris Descartes, Paris, France
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbuaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
- School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Medical Oncology, Dana Farber Harvard Cancer Center, Boston, MA, USA
- Oncogenetics Team, Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, UK
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
- Seidman Cancer Center, University Hospitals, Cleveland, OH, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO)
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Mathematics, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
- Department of Molecular Medicine, Faculty of Medicine, Université Laval and Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
- College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE
- Comprehensive Clinical Trials Unit, University College London, London, UK
- Department of Visceral, Transplant, Thoracic, and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
- Department of Epidemiology and Population Health, Stanford University, Palo Alto, CA, USA
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Department of Laboratory Medicine and Pathology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, MN, USA
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- International Agency for Research on Cancer, World Health Organization, Lyon, France
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK
- Bristol Dental School, University of Bristol, Bristol, UK
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Genetic Epidemiology and Functional Genomics of Multifactorial Diseases Team, Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-1124, Université Paris Descartes, Paris, France
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbuaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
- School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Medical Oncology, Dana Farber Harvard Cancer Center, Boston, MA, USA
- Oncogenetics Team, Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, UK
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
- Seidman Cancer Center, University Hospitals, Cleveland, OH, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Tracy A. O’Mara
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Amanda B. Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Endometrial Cancer Association Consortium (ECAC)
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Mathematics, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
- Department of Molecular Medicine, Faculty of Medicine, Université Laval and Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
- College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE
- Comprehensive Clinical Trials Unit, University College London, London, UK
- Department of Visceral, Transplant, Thoracic, and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
- Department of Epidemiology and Population Health, Stanford University, Palo Alto, CA, USA
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Department of Laboratory Medicine and Pathology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, MN, USA
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- International Agency for Research on Cancer, World Health Organization, Lyon, France
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK
- Bristol Dental School, University of Bristol, Bristol, UK
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Genetic Epidemiology and Functional Genomics of Multifactorial Diseases Team, Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-1124, Université Paris Descartes, Paris, France
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbuaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
- School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Medical Oncology, Dana Farber Harvard Cancer Center, Boston, MA, USA
- Oncogenetics Team, Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, UK
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
- Seidman Cancer Center, University Hospitals, Cleveland, OH, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Puya Gharahkhani
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | - Janusz Jankowski
- College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE
- Comprehensive Clinical Trials Unit, University College London, London, UK
| | - Ines Gockel
- Department of Visceral, Transplant, Thoracic, and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
| | - Esophageal Cancer GWAS Consortium
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Mathematics, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
- Department of Molecular Medicine, Faculty of Medicine, Université Laval and Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
- College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE
- Comprehensive Clinical Trials Unit, University College London, London, UK
- Department of Visceral, Transplant, Thoracic, and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
- Department of Epidemiology and Population Health, Stanford University, Palo Alto, CA, USA
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Department of Laboratory Medicine and Pathology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, MN, USA
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- International Agency for Research on Cancer, World Health Organization, Lyon, France
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK
- Bristol Dental School, University of Bristol, Bristol, UK
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Genetic Epidemiology and Functional Genomics of Multifactorial Diseases Team, Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-1124, Université Paris Descartes, Paris, France
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbuaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
- School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Medical Oncology, Dana Farber Harvard Cancer Center, Boston, MA, USA
- Oncogenetics Team, Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, UK
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
- Seidman Cancer Center, University Hospitals, Cleveland, OH, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Melissa L. Bondy
- Department of Epidemiology and Population Health, Stanford University, Palo Alto, CA, USA
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Robert B. Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, MN, USA
| | - Beatrice Melin
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
| | - Glioma International Case Control Consortium (GICC)
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Mathematics, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
- Department of Molecular Medicine, Faculty of Medicine, Université Laval and Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
- College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE
- Comprehensive Clinical Trials Unit, University College London, London, UK
- Department of Visceral, Transplant, Thoracic, and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
- Department of Epidemiology and Population Health, Stanford University, Palo Alto, CA, USA
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Department of Laboratory Medicine and Pathology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, MN, USA
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- International Agency for Research on Cancer, World Health Organization, Lyon, France
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK
- Bristol Dental School, University of Bristol, Bristol, UK
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Genetic Epidemiology and Functional Genomics of Multifactorial Diseases Team, Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-1124, Université Paris Descartes, Paris, France
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbuaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
- School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Medical Oncology, Dana Farber Harvard Cancer Center, Boston, MA, USA
- Oncogenetics Team, Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, UK
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
- Seidman Cancer Center, University Hospitals, Cleveland, OH, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Corina Lesseur
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Andy R. Ness
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK
- Bristol Dental School, University of Bristol, Bristol, UK
| | - Brenda Diergaarde
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Andrew F. Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
| | - Head-Neck Cancer GWAS Consortium
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Mathematics, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
- Department of Molecular Medicine, Faculty of Medicine, Université Laval and Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
- College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE
- Comprehensive Clinical Trials Unit, University College London, London, UK
- Department of Visceral, Transplant, Thoracic, and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
- Department of Epidemiology and Population Health, Stanford University, Palo Alto, CA, USA
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Department of Laboratory Medicine and Pathology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, MN, USA
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- International Agency for Research on Cancer, World Health Organization, Lyon, France
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK
- Bristol Dental School, University of Bristol, Bristol, UK
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Genetic Epidemiology and Functional Genomics of Multifactorial Diseases Team, Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-1124, Université Paris Descartes, Paris, France
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbuaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
- School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Medical Oncology, Dana Farber Harvard Cancer Center, Boston, MA, USA
- Oncogenetics Team, Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, UK
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
- Seidman Cancer Center, University Hospitals, Cleveland, OH, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Christopher I. Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - David C. Christiani
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Maria T. Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - James D. McKay
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - International Lung Cancer Consortium (ILCCO)
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Mathematics, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
- Department of Molecular Medicine, Faculty of Medicine, Université Laval and Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
- College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE
- Comprehensive Clinical Trials Unit, University College London, London, UK
- Department of Visceral, Transplant, Thoracic, and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
- Department of Epidemiology and Population Health, Stanford University, Palo Alto, CA, USA
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Department of Laboratory Medicine and Pathology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, MN, USA
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- International Agency for Research on Cancer, World Health Organization, Lyon, France
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK
- Bristol Dental School, University of Bristol, Bristol, UK
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Genetic Epidemiology and Functional Genomics of Multifactorial Diseases Team, Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-1124, Université Paris Descartes, Paris, France
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbuaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
- School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Medical Oncology, Dana Farber Harvard Cancer Center, Boston, MA, USA
- Oncogenetics Team, Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, UK
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
- Seidman Cancer Center, University Hospitals, Cleveland, OH, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Myriam Brossard
- Genetic Epidemiology and Functional Genomics of Multifactorial Diseases Team, Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-1124, Université Paris Descartes, Paris, France
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbuaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Mark M. Iles
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
| | - Matthew H. Law
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia
| | - Stuart MacGregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Melanoma GWAS Consortium
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Mathematics, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
- Department of Molecular Medicine, Faculty of Medicine, Université Laval and Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
- College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE
- Comprehensive Clinical Trials Unit, University College London, London, UK
- Department of Visceral, Transplant, Thoracic, and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
- Department of Epidemiology and Population Health, Stanford University, Palo Alto, CA, USA
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Department of Laboratory Medicine and Pathology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, MN, USA
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- International Agency for Research on Cancer, World Health Organization, Lyon, France
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK
- Bristol Dental School, University of Bristol, Bristol, UK
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Genetic Epidemiology and Functional Genomics of Multifactorial Diseases Team, Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-1124, Université Paris Descartes, Paris, France
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbuaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
- School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Medical Oncology, Dana Farber Harvard Cancer Center, Boston, MA, USA
- Oncogenetics Team, Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, UK
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
- Seidman Cancer Center, University Hospitals, Cleveland, OH, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jonathan Beesley
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Michelle R. Jones
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jonathan Tyrer
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Stacey J. Winham
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
| | - Ovarian Cancer Association Consortium (OCAC)
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Mathematics, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
- Department of Molecular Medicine, Faculty of Medicine, Université Laval and Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
- College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE
- Comprehensive Clinical Trials Unit, University College London, London, UK
- Department of Visceral, Transplant, Thoracic, and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
- Department of Epidemiology and Population Health, Stanford University, Palo Alto, CA, USA
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Department of Laboratory Medicine and Pathology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, MN, USA
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- International Agency for Research on Cancer, World Health Organization, Lyon, France
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK
- Bristol Dental School, University of Bristol, Bristol, UK
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Genetic Epidemiology and Functional Genomics of Multifactorial Diseases Team, Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-1124, Université Paris Descartes, Paris, France
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbuaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
- School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Medical Oncology, Dana Farber Harvard Cancer Center, Boston, MA, USA
- Oncogenetics Team, Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, UK
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
- Seidman Cancer Center, University Hospitals, Cleveland, OH, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Alison P. Klein
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Gloria Petersen
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
| | - Donghui Li
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Brian M. Wolpin
- Department of Medical Oncology, Dana Farber Harvard Cancer Center, Boston, MA, USA
| | - Pancreatic Cancer Case-Control Consortium (PANC4)
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Mathematics, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
- Department of Molecular Medicine, Faculty of Medicine, Université Laval and Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
- College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE
- Comprehensive Clinical Trials Unit, University College London, London, UK
- Department of Visceral, Transplant, Thoracic, and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
- Department of Epidemiology and Population Health, Stanford University, Palo Alto, CA, USA
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Department of Laboratory Medicine and Pathology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, MN, USA
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- International Agency for Research on Cancer, World Health Organization, Lyon, France
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK
- Bristol Dental School, University of Bristol, Bristol, UK
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Genetic Epidemiology and Functional Genomics of Multifactorial Diseases Team, Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-1124, Université Paris Descartes, Paris, France
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbuaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
- School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Medical Oncology, Dana Farber Harvard Cancer Center, Boston, MA, USA
- Oncogenetics Team, Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, UK
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
- Seidman Cancer Center, University Hospitals, Cleveland, OH, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Pancreatic Cancer Cohort Consortium (PanScan)
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Mathematics, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
- Department of Molecular Medicine, Faculty of Medicine, Université Laval and Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
- College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE
- Comprehensive Clinical Trials Unit, University College London, London, UK
- Department of Visceral, Transplant, Thoracic, and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
- Department of Epidemiology and Population Health, Stanford University, Palo Alto, CA, USA
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Department of Laboratory Medicine and Pathology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, MN, USA
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- International Agency for Research on Cancer, World Health Organization, Lyon, France
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK
- Bristol Dental School, University of Bristol, Bristol, UK
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Genetic Epidemiology and Functional Genomics of Multifactorial Diseases Team, Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-1124, Université Paris Descartes, Paris, France
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbuaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
- School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Medical Oncology, Dana Farber Harvard Cancer Center, Boston, MA, USA
- Oncogenetics Team, Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, UK
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
- Seidman Cancer Center, University Hospitals, Cleveland, OH, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Rosalind A. Eeles
- Oncogenetics Team, Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, UK
| | - Christopher A. Haiman
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Zsofia Kote-Jarai
- Oncogenetics Team, Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, UK
| | - Fredrick R. Schumacher
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
- Seidman Cancer Center, University Hospitals, Cleveland, OH, USA
| | - PRACTICAL consortium
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Mathematics, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
- Department of Molecular Medicine, Faculty of Medicine, Université Laval and Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
- College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE
- Comprehensive Clinical Trials Unit, University College London, London, UK
- Department of Visceral, Transplant, Thoracic, and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
- Department of Epidemiology and Population Health, Stanford University, Palo Alto, CA, USA
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Department of Laboratory Medicine and Pathology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, MN, USA
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- International Agency for Research on Cancer, World Health Organization, Lyon, France
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK
- Bristol Dental School, University of Bristol, Bristol, UK
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Genetic Epidemiology and Functional Genomics of Multifactorial Diseases Team, Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-1124, Université Paris Descartes, Paris, France
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbuaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
- School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Medical Oncology, Dana Farber Harvard Cancer Center, Boston, MA, USA
- Oncogenetics Team, Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, UK
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
- Seidman Cancer Center, University Hospitals, Cleveland, OH, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - CRUK
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Mathematics, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
- Department of Molecular Medicine, Faculty of Medicine, Université Laval and Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
- College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE
- Comprehensive Clinical Trials Unit, University College London, London, UK
- Department of Visceral, Transplant, Thoracic, and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
- Department of Epidemiology and Population Health, Stanford University, Palo Alto, CA, USA
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Department of Laboratory Medicine and Pathology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, MN, USA
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- International Agency for Research on Cancer, World Health Organization, Lyon, France
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK
- Bristol Dental School, University of Bristol, Bristol, UK
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Genetic Epidemiology and Functional Genomics of Multifactorial Diseases Team, Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-1124, Université Paris Descartes, Paris, France
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbuaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
- School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Medical Oncology, Dana Farber Harvard Cancer Center, Boston, MA, USA
- Oncogenetics Team, Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, UK
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
- Seidman Cancer Center, University Hospitals, Cleveland, OH, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - BPC3
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Mathematics, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
- Department of Molecular Medicine, Faculty of Medicine, Université Laval and Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
- College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE
- Comprehensive Clinical Trials Unit, University College London, London, UK
- Department of Visceral, Transplant, Thoracic, and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
- Department of Epidemiology and Population Health, Stanford University, Palo Alto, CA, USA
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Department of Laboratory Medicine and Pathology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, MN, USA
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- International Agency for Research on Cancer, World Health Organization, Lyon, France
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK
- Bristol Dental School, University of Bristol, Bristol, UK
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Genetic Epidemiology and Functional Genomics of Multifactorial Diseases Team, Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-1124, Université Paris Descartes, Paris, France
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbuaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
- School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Medical Oncology, Dana Farber Harvard Cancer Center, Boston, MA, USA
- Oncogenetics Team, Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, UK
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
- Seidman Cancer Center, University Hospitals, Cleveland, OH, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - CAPS
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Mathematics, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
- Department of Molecular Medicine, Faculty of Medicine, Université Laval and Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
- College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE
- Comprehensive Clinical Trials Unit, University College London, London, UK
- Department of Visceral, Transplant, Thoracic, and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
- Department of Epidemiology and Population Health, Stanford University, Palo Alto, CA, USA
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Department of Laboratory Medicine and Pathology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, MN, USA
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- International Agency for Research on Cancer, World Health Organization, Lyon, France
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK
- Bristol Dental School, University of Bristol, Bristol, UK
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Genetic Epidemiology and Functional Genomics of Multifactorial Diseases Team, Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-1124, Université Paris Descartes, Paris, France
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbuaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
- School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Medical Oncology, Dana Farber Harvard Cancer Center, Boston, MA, USA
- Oncogenetics Team, Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, UK
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
- Seidman Cancer Center, University Hospitals, Cleveland, OH, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - PEGASUS
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Mathematics, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
- Department of Molecular Medicine, Faculty of Medicine, Université Laval and Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
- College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE
- Comprehensive Clinical Trials Unit, University College London, London, UK
- Department of Visceral, Transplant, Thoracic, and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
- Department of Epidemiology and Population Health, Stanford University, Palo Alto, CA, USA
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Department of Laboratory Medicine and Pathology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, MN, USA
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- International Agency for Research on Cancer, World Health Organization, Lyon, France
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK
- Bristol Dental School, University of Bristol, Bristol, UK
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Genetic Epidemiology and Functional Genomics of Multifactorial Diseases Team, Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-1124, Université Paris Descartes, Paris, France
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbuaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
- School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Medical Oncology, Dana Farber Harvard Cancer Center, Boston, MA, USA
- Oncogenetics Team, Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, UK
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
- Seidman Cancer Center, University Hospitals, Cleveland, OH, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Paul Brennan
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Valerie Gaborieau
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK
| | - Mark P. Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Renal Cancer GWAS Consortium
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Mathematics, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
- Department of Molecular Medicine, Faculty of Medicine, Université Laval and Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Center for Human Genetics, University Hospital of Marburg, Marburg, Germany
- College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE
- Comprehensive Clinical Trials Unit, University College London, London, UK
- Department of Visceral, Transplant, Thoracic, and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
- Department of Epidemiology and Population Health, Stanford University, Palo Alto, CA, USA
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Department of Laboratory Medicine and Pathology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, MN, USA
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- International Agency for Research on Cancer, World Health Organization, Lyon, France
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK
- Bristol Dental School, University of Bristol, Bristol, UK
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Genetic Epidemiology and Functional Genomics of Multifactorial Diseases Team, Institut National de la Santé et de la Recherche Médicale (INSERM), UMRS-1124, Université Paris Descartes, Paris, France
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbuaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Leeds Institute for Data Analytics, University of Leeds, Leeds, UK
- School of Biomedical Sciences, Faculty of Health, and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Medical Oncology, Dana Farber Harvard Cancer Center, Boston, MA, USA
- Oncogenetics Team, Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, UK
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
- Seidman Cancer Center, University Hospitals, Cleveland, OH, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Paul Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Rayjean J. Hung
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbuaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Laufey T. Amundadottir
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Peter Kraft
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Bogdan Pasaniuc
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sara Lindström
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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Wang H, Liu H, Zhao L, Luo S, Akinyemiju T, Hwang S, Yue Y, Wei Q. Association of genetic variants of FBXO32 and FOXO6 in the FOXO pathway with breast cancer risk. Mol Carcinog 2021; 60:661-670. [PMID: 34197655 DOI: 10.1002/mc.23331] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 05/26/2021] [Accepted: 06/06/2021] [Indexed: 01/10/2023]
Abstract
Forkhead box class O (FOXO) transcription factors play a pivotal role in regulating a variety of biological processes, including organismal development, cell signaling, cell metabolism, and tumorigenesis. Therefore, we hypothesize that genetic variants in FOXO pathway genes are associated with breast cancer (BC) risk. To test this hypothesis, we conducted a large meta-analysis using 14 published genome-wide association study (GWAS) data sets in the Discovery, Biology, and Risk of Inherited Variants in Breast Cancer (DRIVE) study. We assessed associations between 5214 (365 genotyped in DRIVE and 4849 imputed) common single-nucleotide polymorphisms (SNPs) in 55 FOXO pathway genes and BC risk. After multiple comparison corrections by the Bayesian false-discovery probability method, we found five SNPs to be significantly associated with BC risk. In stepwise multivariate logistic regression analysis with adjustment for age, principal components, and previously published SNPs in the same data set, three independent SNPs (i.e., FBXO32 rs10093411 A>G, FOXO6 rs61229336 C>T, and FBXO32 rs62521280 C>T) remained to be significantly associated with BC risk (p = 0.0008, 0.0011, and 0.0017, respectively). Additional expression quantitative trait loci analysis revealed that the FBXO32 rs62521280 T allele was associated with decreased messenger RNA (mRNA) expression levels in breast tissue, while the FOXO6 rs61229336 T allele was found to be associated with decreased mRNA expression levels in the whole blood cells. Once replicated by other investigators, these genetic variants may serve as new biomarkers for BC risk.
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Affiliation(s)
- Haijiao Wang
- Department of Gynecology Oncology, The First Hospital of Jilin University, Changchun, Jilin, China.,Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA.,Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina, USA
| | - Hongliang Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA.,Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina, USA
| | - Lingling Zhao
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA.,Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina, USA.,Cancer Center, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Sheng Luo
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Tomi Akinyemiju
- Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina, USA
| | - Shelley Hwang
- Department of Surgery, Duke University School of Medicine, Durham, North Carolina, USA
| | - Ying Yue
- Department of Gynecology Oncology, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, USA.,Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina, USA.,Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.,Duke Global Health Institute, Duke University Medical Center, Durham, North Carolina, USA
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42
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Feng H, Mancuso N, Pasaniuc B, Kraft P. Multitrait transcriptome-wide association study (TWAS) tests. Genet Epidemiol 2021; 45:563-576. [PMID: 34082479 DOI: 10.1002/gepi.22391] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/26/2021] [Accepted: 04/05/2021] [Indexed: 12/19/2022]
Abstract
Multitrait tests can improve power to detect associations between individual single-nucleotide polymorphisms (SNPs) and several related traits. Here, we develop methods for multi-SNP transcriptome-wide association (TWAS) tests to test the association between predicted gene expression levels and multiple phenotypes. We show that the correlation in TWAS test statistics for multiple phenotypes has the same form as multitrait statistics for the single-SNP setting. Thus, established methods for combining single-SNP test statistics across multiple traits can be extended directly to the TWAS setting. We performed an extensive evaluation across eight multitrait methods in simulations that varied gene-phenotype effect sizes in addition to the underlying covariance structure among the phenotypes. We found that all multitrait TWAS tests have well-calibrated Type I error (except ASSET, which can have a slightly elevated or depressed Type I error rate). Our results show that multitrait TWAS can improve statistical power compared with multiple single-trait TWAS followed by Bonferroni correction. To illustrate our approach to real data, we conducted a multitrait TWAS of four circulating lipid traits from the Global Lipids Genetics Consortium. We found that our multitrait Wald TWAS approach identified 506 genes associated with lipid levels compared with 87 identified through Bonferroni-corrected single-trait TWAS. Overall, we find that our proposed multitrait TWAS framework outperforms single-trait approaches to identify new genetic associations, especially for functionally correlated phenotypes and phenotypes with overlapping genome-wide association studies samples, leading to insights into the genetic architecture of multiple phenotypes.
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Affiliation(s)
- Helian Feng
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Nicholas Mancuso
- Department of Preventive Medicine, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
- Division of Biostatistics, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Bogdan Pasaniuc
- Department of Human Genetics, University of California Los Angeles, Los Angeles, California, USA
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Peter Kraft
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
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Byun J, Han Y, Ostrom QT, Edelson J, Walsh KM, Pettit RW, Bondy ML, Hung RJ, McKay JD, Amos CI. The Shared Genetic Architectures Between Lung Cancer and Multiple Polygenic Phenotypes in Genome-Wide Association Studies. Cancer Epidemiol Biomarkers Prev 2021; 30:1156-1164. [PMID: 33771847 PMCID: PMC9108090 DOI: 10.1158/1055-9965.epi-20-1635] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/19/2021] [Accepted: 03/23/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Prior genome-wide association studies have identified numerous lung cancer risk loci and reveal substantial etiologic heterogeneity across histologic subtypes. Analyzing the shared genetic architecture underlying variation in complex traits can elucidate common genetic etiologies across phenotypes. Exploring pairwise genetic correlations between lung cancer and other polygenic traits can reveal the common genetic etiology of correlated phenotypes. METHODS Using cross-trait linkage disequilibrium score regression, we estimated the pairwise genetic correlation and heritability between lung cancer and multiple traits using publicly available summary statistics. Identified genetic relationships were also examined after excluding genomic regions known to be associated with smoking behaviors, a major risk factor for lung cancer. RESULTS We observed several traits showing moderate single nucleotide polymorphism-based heritability and significant genetic correlations with lung cancer. We observed highly significant correlations between the genetic architectures of lung cancer and emphysema/chronic bronchitis across all histologic subtypes, as well as among lung cancer occurring among smokers. Our analyses revealed highly significant positive correlations between lung cancer and paternal history of lung cancer. We also observed a strong negative correlation with parental longevity. We observed consistent directions in genetic patterns after excluding genomic regions associated with smoking behaviors. CONCLUSIONS This study identifies numerous phenotypic traits that share genomic architecture with lung carcinogenesis and are not fully accounted for by known smoking-associated genomic loci. IMPACT These findings provide new insights into the etiology of lung cancer by identifying traits that are genetically correlated with increased risk of lung cancer.
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Affiliation(s)
- Jinyoung Byun
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Younghun Han
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Quinn T Ostrom
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Jacob Edelson
- Department of Medicine, Center for Biomedical Informatics Research, Stanford University, Stanford, California
| | - Kyle M Walsh
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
| | - Rowland W Pettit
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas
| | - Melissa L Bondy
- Department of Epidemiology and Population Health, School of Medicine, Stanford University, Stanford, California
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Canada
| | - James D McKay
- Section of Genetics, International Agency for Research on Cancer, World Health Organization, Lyon, France
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Maguire S, Perraki E, Tomczyk K, Jones ME, Fletcher O, Pugh M, Winter T, Thompson K, Cooke R, Trainer A, James P, Bojesen S, Flyger H, Nevanlinna H, Mattson J, Friedman E, Laitman Y, Palli D, Masala G, Zanna I, Ottini L, Silvestri V, Hollestelle A, Hooning MJ, Novaković S, Krajc M, Gago-Dominguez M, Castelao JE, Olsson H, Hedenfalk I, Saloustros E, Georgoulias V, Easton DF, Pharoah P, Dunning AM, Bishop DT, Neuhausen SL, Steele L, Ashworth A, Garcia Closas M, Houlston R, Swerdlow A, Orr N. Common Susceptibility Loci for Male Breast Cancer. J Natl Cancer Inst 2021; 113:453-461. [PMID: 32785646 PMCID: PMC8023850 DOI: 10.1093/jnci/djaa101] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 05/14/2020] [Accepted: 07/10/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The etiology of male breast cancer (MBC) is poorly understood. In particular, the extent to which the genetic basis of MBC differs from female breast cancer (FBC) is unknown. A previous genome-wide association study of MBC identified 2 predisposition loci for the disease, both of which were also associated with risk of FBC. METHODS We performed genome-wide single nucleotide polymorphism genotyping of European ancestry MBC case subjects and controls in 3 stages. Associations between directly genotyped and imputed single nucleotide polymorphisms with MBC were assessed using fixed-effects meta-analysis of 1380 cases and 3620 controls. Replication genotyping of 810 cases and 1026 controls was used to validate variants with P values less than 1 × 10-06. Genetic correlation with FBC was evaluated using linkage disequilibrium score regression, by comprehensively examining the associations of published FBC risk loci with risk of MBC and by assessing associations between a FBC polygenic risk score and MBC. All statistical tests were 2-sided. RESULTS The genome-wide association study identified 3 novel MBC susceptibility loci that attained genome-wide statistical significance (P < 5 × 10-08). Genetic correlation analysis revealed a strong shared genetic basis with estrogen receptor-positive FBC. Men in the top quintile of genetic risk had a fourfold increased risk of breast cancer relative to those in the bottom quintile (odds ratio = 3.86, 95% confidence interval = 3.07 to 4.87, P = 2.08 × 10-30). CONCLUSIONS These findings advance our understanding of the genetic basis of MBC, providing support for an overlapping genetic etiology with FBC and identifying a fourfold high-risk group of susceptible men.
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Affiliation(s)
- Sarah Maguire
- The Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Eleni Perraki
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Katarzyna Tomczyk
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Michael E Jones
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - Olivia Fletcher
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Matthew Pugh
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Timothy Winter
- The Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, UK
| | - Kyle Thompson
- The Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, UK
| | - Rosie Cooke
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - kConFab Consortium
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Alison Trainer
- Parkville Familial Cancer Clinic, Sir Peter MacCallum Department of Oncology, University of Melbourne and Royal Melbourne Hospital, East Melbourne, Victoria, Australia
| | - Paul James
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Stig Bojesen
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
- The Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Johanna Mattson
- Department of Oncology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Eitan Friedman
- The Susanne Levy Gertner Oncogenetics Unit, Sheba Medical Centre, Tel Aviv, Israel
- The Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Yael Laitman
- The Susanne Levy Gertner Oncogenetics Unit, Sheba Medical Centre, Tel Aviv, Israel
- The Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Domenico Palli
- Cancer Risk Factors and Life-Style Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network-ISPRO, Florence, Italy
| | - Giovanna Masala
- Cancer Risk Factors and Life-Style Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network-ISPRO, Florence, Italy
| | - Ines Zanna
- Cancer Risk Factors and Life-Style Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network-ISPRO, Florence, Italy
| | - Laura Ottini
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | | | - Antoinette Hollestelle
- Department of Medical Oncology, Familial Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Maartje J Hooning
- Department of Medical Oncology, Familial Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Srdjan Novaković
- Department of Molecular Diagnostics, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Mateja Krajc
- Institute of Oncology Ljubljana, Cancer Genetics Clinic, Epidemiology and Cancer Registry, Ljubljana, Slovenia
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Foundation of Genomic Medicine, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS), Servicio Galego de Saúde (SERGAS), Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria Galicia Sur (IISGS), Xerencia de Xestion Integrada de Vigo-SERGAS, Oncology and Genetics Unit, Vigo, Spain
| | - Jose Esteban Castelao
- Genetic Oncology Unit, Complexo Hospitalario Universitario de Vigo (CHUVI), SERGAS, Vigo, Spain
| | - Hakan Olsson
- Division of Oncology, Department of Clinical Sciences, Lund, Lund University and Skåne University Hospital, Lund, Sweden
| | - Ingrid Hedenfalk
- Division of Oncology, Department of Clinical Sciences, Lund, Lund University and Skåne University Hospital, Lund, Sweden
| | | | - Vasilios Georgoulias
- Department of Medical Oncology, University General Hospital of Heraklion, Heraklion, Greece
| | - Douglas F Easton
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Paul Pharoah
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Alison M Dunning
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - D Timothy Bishop
- Division of Immunology, Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, UK
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Linda Steele
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Centre, San Francisco, CA, USA
| | | | - Richard Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Nick Orr
- The Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
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Qin N, Li Y, Wang C, Zhu M, Dai J, Hong T, Albanes D, Lam S, Tardon A, Chen C, Goodman G, Bojesen SE, Landi MT, Johansson M, Risch A, Wichmann HE, Bickeboller H, Rennert G, Arnold S, Brennan P, Field JK, Shete S, Le Marchand L, Melander O, Brunnstrom H, Liu G, Hung RJ, Andrew A, Kiemeney LA, Zienolddiny S, Grankvist K, Johansson M, Caporaso N, Woll P, Lazarus P, Schabath MB, Aldrich MC, Stevens VL, Jin G, Christiani DC, Hu Z, Amos CI, Ma H, Shen H. Comprehensive functional annotation of susceptibility variants identifies genetic heterogeneity between lung adenocarcinoma and squamous cell carcinoma. Front Med 2021; 15:275-291. [PMID: 32889700 PMCID: PMC8374896 DOI: 10.1007/s11684-020-0779-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 03/05/2020] [Indexed: 12/12/2022]
Abstract
Although genome-wide association studies have identified more than eighty genetic variants associated with non-small cell lung cancer (NSCLC) risk, biological mechanisms of these variants remain largely unknown. By integrating a large-scale genotype data of 15 581 lung adenocarcinoma (AD) cases, 8350 squamous cell carcinoma (SqCC) cases, and 27 355 controls, as well as multiple transcriptome and epigenomic databases, we conducted histology-specific meta-analyses and functional annotations of both reported and novel susceptibility variants. We identified 3064 credible risk variants for NSCLC, which were overrepresented in enhancer-like and promoter-like histone modification peaks as well as DNase I hypersensitive sites. Transcription factor enrichment analysis revealed that USF1 was AD-specific while CREB1 was SqCC-specific. Functional annotation and gene-based analysis implicated 894 target genes, including 274 specifics for AD and 123 for SqCC, which were overrepresented in somatic driver genes (ER = 1.95, P = 0.005). Pathway enrichment analysis and Gene-Set Enrichment Analysis revealed that AD genes were primarily involved in immune-related pathways, while SqCC genes were homologous recombination deficiency related. Our results illustrate the molecular basis of both well-studied and new susceptibility loci of NSCLC, providing not only novel insights into the genetic heterogeneity between AD and SqCC but also a set of plausible gene targets for post-GWAS functional experiments.
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Affiliation(s)
- Na Qin
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Yuancheng Li
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Cheng Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Nanjing Medical University, Nanjing, 211166, China
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, 211166, China
| | - Meng Zhu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Juncheng Dai
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Nanjing Medical University, Nanjing, 211166, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, 211166, China
- China International Cooperation Center for Environment and Human Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Tongtong Hong
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892-9304, USA
| | - Stephen Lam
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, BC, V5Z 1L3, Canada
| | - Adonina Tardon
- Faculty of Medicine, University of Oviedo and CIBERESP, Oviedo, 33006, Spain
| | - Chu Chen
- Program in Epidemiology, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109-1024, USA
| | - Gary Goodman
- Public Health Sciences Division, Swedish Cancer Institute, Seattle, WA, 98026, USA
| | - Stig E Bojesen
- Department of Clinical Biochemistry, Copenhagen University Hospital, Copenhagen, DK-1017, Denmark
| | | | - Mattias Johansson
- Genetic Epidemiology Group, International Agency for Research on Cancer, Lyon, 69372, France
| | - Angela Risch
- Cancer Center Cluster Salzburg at PLUS, Department of Molecular Biology, University of Salzburg, Heidelberg, 5020, Austria
| | - H-Erich Wichmann
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Epidemiology, Ludwig Maximilians University, Munich, Bavaria, 80539, Germany
| | - Heike Bickeboller
- Department of Genetic Epidemiology, University Medical Center Goettingen, Goettingen, 37075, Germany
| | - Gadi Rennert
- Technion Faculty of Medicine, Carmel Medical Center, Haifa, 3448516, Israel
| | - Susanne Arnold
- Markey Cancer Center, University of Kentucky, Lexington, KY, 40506-0054, USA
| | - Paul Brennan
- Genetic Epidemiology Group, International Agency for Research on Cancer, Lyon, 69372, France
| | - John K Field
- Department of Molecular and Clinical Cancer Medicine, Roy Castle Lung Cancer Research Programme, The University of Liverpool Institute of Translational Medicine, Liverpool, L69 7ZX, UK
| | - Sanjay Shete
- Department of Epidemiology, The University of Texas, MD Anderson Cancer Center, Houston, TX, 77079, USA
| | - Loic Le Marchand
- Department of Epidemiology, University of Hawaii Cancer Center, Honolulu, HI, 96813, USA
| | - Olle Melander
- Department of Clinical Sciences, Lund University, BMC F12, 221 84, Lund, Sweden
| | - Hans Brunnstrom
- Department of Clinical Sciences, Lund University, BMC F12, 221 84, Lund, Sweden
| | - Geoffrey Liu
- Epidemiology Division, Princess Margaret Cancer Center, Toronto, ON, M4Y 2H8, Canada
| | - Rayjean J Hung
- Epidemiology Division, Lunenfeld-Tanenbuaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Angeline Andrew
- Department of Neurology, Dartmouth-Hitchcock Medical Center, Lebanon, NH, 03756, USA
| | - Lambertus A Kiemeney
- Department of Health Evidence, Radboud University Medical Center, Nijmegen, 9101 6500, HB, Germany
| | - Shan Zienolddiny
- National Institute of Occupational Health (STAMI), Oslo, Pb 5330, Norway
| | - Kjell Grankvist
- Department of Medical Biosciences, Umeå University, Umea, 901 87, Sweden
| | - Mikael Johansson
- Department of Radiation Sciences, Umeå University, Umea, 901 87, Sweden
| | - Neil Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, 20850, USA
| | - Penella Woll
- Academic Unit of Clinical Oncology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Philip Lazarus
- College of Pharmacy, Washington State University, Spokane, WA, 99210, USA
| | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 12902, USA
| | - Melinda C Aldrich
- Department of Thoracic Surgery, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Victoria L Stevens
- Department of Epidemiology Research Program, American Cancer Society, Atlanta, GA, 30303, USA
| | - Guangfu Jin
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Nanjing Medical University, Nanjing, 211166, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, 211166, China
- China International Cooperation Center for Environment and Human Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - David C Christiani
- China International Cooperation Center for Environment and Human Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
- Department of Environmental Health, Harvard School of Public Health, Department of Medicine, Harvard Medical School/Massachusetts General Hospital, Boston, MA, 02115, USA
| | - Zhibin Hu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Nanjing Medical University, Nanjing, 211166, China
- China International Cooperation Center for Environment and Human Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Christopher I Amos
- Baylor College of Medicine, Institute for Clinical and Translational Research, Houston, TX, 21202, USA
| | - Hongxia Ma
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Nanjing Medical University, Nanjing, 211166, China.
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, 211166, China.
- China International Cooperation Center for Environment and Human Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.
| | - Hongbing Shen
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Nanjing Medical University, Nanjing, 211166, China.
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, 211166, China.
- China International Cooperation Center for Environment and Human Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.
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Fanfani V, Citi L, Harris AL, Pezzella F, Stracquadanio G. The Landscape of the Heritable Cancer Genome. Cancer Res 2021; 81:2588-2599. [PMID: 33731442 DOI: 10.1158/0008-5472.can-20-3348] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/15/2021] [Accepted: 03/02/2021] [Indexed: 12/24/2022]
Abstract
Genome-wide association studies (GWAS) have found hundreds of single-nucleotide polymorphisms (SNP) associated with increased risk of cancer. However, the amount of heritable risk explained by SNPs is limited, leaving most of the cancer heritability unexplained. Tumor sequencing projects have shown that causal mutations are enriched in genic regions. We hypothesized that SNPs located in protein coding genes and nearby regulatory regions could explain a significant proportion of the heritable risk of cancer. To perform gene-level heritability analysis, we developed a new method, called Bayesian Gene Heritability Analysis (BAGHERA), to estimate the heritability explained by all genotyped SNPs and by those located in genic regions using GWAS summary statistics. BAGHERA was specifically designed for low heritability traits such as cancer and provides robust heritability estimates under different genetic architectures. BAGHERA-based analysis of 38 cancers reported in the UK Biobank showed that SNPs explain at least 10% of the heritable risk for 14 of them, including late onset malignancies. We then identified 1,146 genes, called cancer heritability genes (CHG), explaining a significant proportion of cancer heritability. CHGs were involved in hallmark processes controlling the transformation from normal to cancerous cells. Importantly, 60 of them also harbored somatic driver mutations, and 27 are tumor suppressors. Our results suggest that germline and somatic mutation information could be exploited to identify subgroups of individuals at higher risk of cancer in the broader population and could prove useful to establish strategies for early detection and cancer surveillance. SIGNIFICANCE: This study describes a new statistical method to identify genes associated with cancer heritability in the broader population, creating a map of the heritable cancer genome with gene-level resolution.See related commentary by Bader, p. 2586.
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Affiliation(s)
- Viola Fanfani
- Institute of Quantitative Biology, Biochemistry, and Biotechnology, SynthSys, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Luca Citi
- School of Computer Science and Electronic Engineering, University of Essex, Colchester, United Kingdom
| | - Adrian L Harris
- Molecular Oncology Laboratories, Department of Oncology, The Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Francesco Pezzella
- Department of Clinical Laboratory Sciences, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Giovanni Stracquadanio
- Institute of Quantitative Biology, Biochemistry, and Biotechnology, SynthSys, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom.
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47
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Lesseur C, Ferreiro-Iglesias A, McKay JD, Bossé Y, Johansson M, Gaborieau V, Landi MT, Christiani DC, Caporaso NC, Bojesen SE, Amos CI, Shete S, Liu G, Rennert G, Albanes D, Aldrich MC, Tardon A, Chen C, Triantafillos L, Field JK, Teare MD, Kiemeney LA, Diergaarde B, Ferris RL, Zienolddiny S, Lam S, Olshan AF, Weissler MC, Lacko M, Risch A, Bickeböller H, Ness AR, Thomas S, Le Marchand L, Schabath MB, Wünsch-Filho V, Tajara EH, Andrew AS, Clifford GM, Lazarus P, Grankvist K, Johansson M, Arnold S, Melander O, Brunnström H, Boccia S, Cadoni G, Timens W, Obeidat M, Xiao X, Houlston RS, Hung RJ, Brennan P. Genome-wide association meta-analysis identifies pleiotropic risk loci for aerodigestive squamous cell cancers. PLoS Genet 2021; 17:e1009254. [PMID: 33667223 PMCID: PMC7968735 DOI: 10.1371/journal.pgen.1009254] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 03/17/2021] [Accepted: 11/05/2020] [Indexed: 11/20/2022] Open
Abstract
Squamous cell carcinomas (SqCC) of the aerodigestive tract have similar etiological risk factors. Although genetic risk variants for individual cancers have been identified, an agnostic, genome-wide search for shared genetic susceptibility has not been performed. To identify novel and pleotropic SqCC risk variants, we performed a meta-analysis of GWAS data on lung SqCC (LuSqCC), oro/pharyngeal SqCC (OSqCC), laryngeal SqCC (LaSqCC) and esophageal SqCC (ESqCC) cancers, totaling 13,887 cases and 61,961 controls of European ancestry. We identified one novel genome-wide significant (Pmeta<5x10-8) aerodigestive SqCC susceptibility loci in the 2q33.1 region (rs56321285, TMEM273). Additionally, three previously unknown loci reached suggestive significance (Pmeta<5x10-7): 1q32.1 (rs12133735, near MDM4), 5q31.2 (rs13181561, TMEM173) and 19p13.11 (rs61494113, ABHD8). Multiple previously identified loci for aerodigestive SqCC also showed evidence of pleiotropy in at least another SqCC site, these include: 4q23 (ADH1B), 6p21.33 (STK19), 6p21.32 (HLA-DQB1), 9p21.33 (CDKN2B-AS1) and 13q13.1(BRCA2). Gene-based association and gene set enrichment identified a set of 48 SqCC-related genes rel to DNA damage and epigenetic regulation pathways. Our study highlights the importance of cross-cancer analyses to identify pleiotropic risk loci of histology-related cancers arising at distinct anatomical sites.
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Affiliation(s)
- Corina Lesseur
- Section of Genetics, Genetic Epidemiology Group, International Agency for Research on Cancer, World Health Organization, Lyon, France
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Aida Ferreiro-Iglesias
- Section of Genetics, Genetic Epidemiology Group, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - James D. McKay
- Section of Genetics, Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Yohan Bossé
- Department of Molecular Medicine, Institut universitaire de cardiologie et de pneumologie de Québec, Laval University, Quebec City, Canada
| | - Mattias Johansson
- Section of Genetics, Genetic Epidemiology Group, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Valerie Gaborieau
- Section of Genetics, Genetic Epidemiology Group, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - David C. Christiani
- Department of Environmental Health, Harvard TH Chan School of Public Health, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Neil C. Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Stig E. Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen, Denmark
| | - Christopher I. Amos
- Department of Medicine, Baylor college of Medicine, Houston, Texas, United States of America
| | - Sanjay Shete
- Department of Biostatistics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Geoffrey Liu
- Lunenfeld-Tanenbaum Research Institute of Sinai Health System, University of Toronto, Toronto, Canada
| | - Gadi Rennert
- Clalit National Cancer Control Center, Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Melinda C. Aldrich
- Department of Thoracic Surgery, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Adonina Tardon
- Faculty of Medicine, University of Oviedo and CIBERESP, Oviedo, Spain
| | - Chu Chen
- Department of Epidemiology, University of Washington School of Public Health and Community Medicine, Seattle, Washington, United States of America
| | | | - John K. Field
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Marion Dawn Teare
- School of Health and Related Research, University Of Sheffield, Sheffield, United Kingdom
| | | | - Brenda Diergaarde
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Robert L. Ferris
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | | | - Stephen Lam
- British Columbia Cancer Agency, Vancouver, Canada
| | - Andrew F. Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Mark C. Weissler
- Department of Otolaryngology/Head and Neck Surgery, UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Martin Lacko
- Department of Otorhinolaryngology, Head and Neck Surgery, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Angela Risch
- University of Salzburg, Department of Biosciences and Cancer Cluster Salzburg, Salzburg, Austria
- Division of Epigenomics, DKFZ – German Cancer Research Center, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Göttingen, Germany
| | - Andy R. Ness
- National Institute for Health Research (NIHR) Bristol Biomedical Research Centre, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
- Bristol Dental School, University of Bristol, Bristol, United Kingdom
| | - Steve Thomas
- Bristol Dental School, University of Bristol, Bristol, United Kingdom
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Matthew B. Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | | | - Eloiza H. Tajara
- Department of Molecular Biology, School of Medicine of São José do Rio Preto, São José do Rio Preto, Brazil
| | - Angeline S. Andrew
- Biomedical Data Science, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Gary M. Clifford
- Infections Section, Infections and Cancer Epidemiology Group, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Philip Lazarus
- Department of Pharmaceutical Sciences, College of Pharmacy, Washington State University, Spokane, Washington, United States of America
| | - Kjell Grankvist
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | | | - Susanne Arnold
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky, United States of America
| | - Olle Melander
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
- Department of Internal Medicine, Skåne University Hospital, Malmö, Sweden
| | - Hans Brunnström
- Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Stefania Boccia
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, Roma, Italia
- Department of Woman and Child Health and Public Health - Public Health Area, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italia
| | - Gabriella Cadoni
- Dipartimento Patologia Testa Collo e Organi di Senso, Istituto di Clinica Otorinolaringoiatrica, Università Cattolica del Sacro Cuore, Roma, Italia
- Dipartimento di Scienze dell’Invecchiamento, Neurologiche, Ortopediche e della Testa-Collo, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italia
| | - Wim Timens
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- GRIAC Research Institute, University of Groningen, Groningen, The Netherlands
| | - Ma’en Obeidat
- Centre for Heart Lung Innovation, St Paul’s Hospital, The University of British Columbia, Vancouver, Canada
| | - Xiangjun Xiao
- Department of Medicine, Baylor college of Medicine, Houston, Texas, United States of America
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
| | - Rayjean J. Hung
- Prosserman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
| | - Paul Brennan
- Section of Genetics, Genetic Epidemiology Group, International Agency for Research on Cancer, World Health Organization, Lyon, France
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48
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Graff RE, Cavazos TB, Thai KK, Kachuri L, Rashkin SR, Hoffman JD, Alexeeff SE, Blatchins M, Meyers TJ, Leong L, Tai CG, Emami NC, Corley DA, Kushi LH, Ziv E, Van Den Eeden SK, Jorgenson E, Hoffmann TJ, Habel LA, Witte JS, Sakoda LC. Cross-cancer evaluation of polygenic risk scores for 16 cancer types in two large cohorts. Nat Commun 2021; 12:970. [PMID: 33579919 PMCID: PMC7880989 DOI: 10.1038/s41467-021-21288-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 01/19/2021] [Indexed: 02/07/2023] Open
Abstract
Even distinct cancer types share biological hallmarks. Here, we investigate polygenic risk score (PRS)-specific pleiotropy across 16 cancers in European ancestry individuals from the Genetic Epidemiology Research on Adult Health and Aging cohort (16,012 cases, 50,552 controls) and UK Biobank (48,969 cases, 359,802 controls). Within cohorts, each PRS is evaluated in multivariable logistic regression models against all other cancer types. Results are then meta-analyzed across cohorts. Ten positive and one inverse cross-cancer associations are found after multiple testing correction. Two pairs show bidirectional associations; the melanoma PRS is positively associated with oral cavity/pharyngeal cancer and vice versa, whereas the lung cancer PRS is positively associated with oral cavity/pharyngeal cancer, and the oral cavity/pharyngeal cancer PRS is inversely associated with lung cancer. Overall, we validate known, and uncover previously unreported, patterns of pleiotropy that have the potential to inform investigations of risk prediction, shared etiology, and precision cancer prevention strategies.
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Affiliation(s)
- Rebecca E Graff
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA.,Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Taylor B Cavazos
- Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, CA, USA
| | - Khanh K Thai
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Linda Kachuri
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Sara R Rashkin
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Joshua D Hoffman
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Stacey E Alexeeff
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Maruta Blatchins
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Travis J Meyers
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Lancelote Leong
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Caroline G Tai
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Nima C Emami
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA.,Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, CA, USA
| | - Douglas A Corley
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Lawrence H Kushi
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Elad Ziv
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Stephen K Van Den Eeden
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Thomas J Hoffmann
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA.,Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Laurel A Habel
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA. .,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA. .,Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA. .,Department of Urology, University of California San Francisco, San Francisco, CA, USA.
| | - Lori C Sakoda
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA. .,Department of Health System Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, CA, USA.
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49
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Majumdar A, Burch KS, Haldar T, Sankararaman S, Pasaniuc B, Gauderman WJ, Witte JS. A two-step approach to testing overall effect of gene-environment interaction for multiple phenotypes. Bioinformatics 2021; 36:5640-5648. [PMID: 33453114 DOI: 10.1093/bioinformatics/btaa1083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 12/09/2020] [Accepted: 12/17/2020] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION While gene-environment (GxE) interactions contribute importantly to many different phenotypes, detecting such interactions requires well-powered studies and has proven difficult. To address this, we combine two approaches to improve GxE power: simultaneously evaluating multiple phenotypes and using a two-step analysis approach. Previous work shows that the power to identify a main genetic effect can be improved by simultaneously analyzing multiple related phenotypes. For a univariate phenotype, two-step methods produce higher power for detecting a GxE interaction compared to single step analysis. Therefore, we propose a two-step approach to test for an overall GxE effect for multiple phenotypes. RESULTS Using simulations we demonstrate that, when more than one phenotype has GxE effect (i.e., GxE pleiotropy), our approach offers substantial gain in power (18%-43%) to detect an aggregate-level GxE effect for a multivariate phenotype compared to an analogous two-step method to identify GxE effect for a univariate phenotype. We applied the proposed approach to simultaneously analyze three lipids, LDL, HDL and Triglyceride with the frequency of alcohol consumption as environmental factor in the UK Biobank. The method identified two loci with an overall GxE effect on the vector of lipids, one of which was missed by the competing approaches. AVAILABILITY We provide an R package MPGE implementing the proposed approach which is available from CRAN: https://cran.r-project.org/web/packages/MPGE/index.html.
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Affiliation(s)
- Arunabha Majumdar
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Kathryn S Burch
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Sriram Sankararaman
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
| | - Bogdan Pasaniuc
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.,Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, USA
| | - W James Gauderman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
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50
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Viet NH, Trung NQ, Dong LT, Trung LQ, Espinoza JL. Genetic variants in NKG2D axis and susceptibility to Epstein-Barr virus-induced nasopharyngeal carcinoma. J Cancer Res Clin Oncol 2021; 147:713-723. [PMID: 33392659 DOI: 10.1007/s00432-020-03475-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/18/2020] [Indexed: 12/31/2022]
Abstract
BACKGROUND Nasopharyngeal carcinoma (NPC) is a rare epithelial carcinoma arising from the nasopharyngeal region. The pathogenesis of NPC is linked to Epstein-Barr virus (EBV) infection, although genetics and lifestyle factors appears to be also implicated. NKG2D is an immunoreceptor expressed by NK and T-cell subsets that recognizes MICA protein and other ligands on tumor cells. NKG2D interaction with MICA plays a role in the immunosurveillance to viruses and cancer. METHODS We investigated potential associations between functional polymorphisms in NKG2D and MICA genes with NPC susceptibility. We conducted a case-control study including 255 Vietnamese patients with EBV + non-differentiated NPC and 220 healthy controls. RESULTS We observed a significant association between the LNK/LNK genotype of rs1049174 (a variant associated with lower NKG2D receptor expression and reduced NK cell cytotoxicity) and increased susceptibility to NPC (adjusted OR = 1.66, 95% CI 1.07-2.59; p = 0.024). Similarly, the AA genotype of MICA rs2596542 was significantly associated with NPC (adjusted OR = 2.12; 95% CI 1.22-3.81; p = 0.009). In addition, tumor specimens of NPC patients with the AA genotype displayed a higher expression level of MICA proteins and showed higher EBV titers compared with tumor tissues from patients with the GG or GA genotypes. Higher EBV copy numbers were also observed in tumors with the A allele of MICA rs1051792 (also known as MICA-129 Met/Val) compared with those with the G allele; however, MICA rs1051792 variants were not associated with NPC susceptibility. These results suggest that genetic variants in components of the NKG2D axis may influence the individual susceptibility to EBV-induced NPC.
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Affiliation(s)
- Nguyen Hoang Viet
- Faculty of Medical Technology, Hanoi Medical University, Hanoi, Vietnam.,Center for Gene-Protein Research, Hanoi Medical University, Hanoi, Vietnam
| | - Nguyen Quang Trung
- Department of Otorhinolaryngology, Hanoi Medical University, Hanoi, Vietnam
| | - Le Thanh Dong
- Faculty of Medical Technology, Hanoi Medical University, Hanoi, Vietnam
| | - Ly Quoc Trung
- Faculty of Medicine and Pharmacy, Soc Trang Community College, Soc Trang, Vietnam
| | - J Luis Espinoza
- Faculty of Health Sciences, Kanazawa University, Kodatsuno 5-11-80, Kanazawa, 920-0942, Japan.
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