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Bumrungthai S, Duangjit S, Passorn S, Pongpakdeesakul S, Butsri S, Janyakhantikul S. Comprehensive breast cancer risk analysis with whole exome sequencing and the prevalence of BRCA1 and ABCG2 mutations and oncogenic HPV. Biomed Rep 2024; 21:144. [PMID: 39170756 PMCID: PMC11337157 DOI: 10.3892/br.2024.1832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 07/02/2024] [Indexed: 08/23/2024] Open
Abstract
Breast cancer is the most prevalent cancer and also the leading cause of cancer death in women worldwide. A comprehensive understanding of breast cancer risk factors and their incidences is useful information for breast cancer prevention and control planning. The present study aimed to provide information on single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) in breast cancer, the allele frequency of two SNPs in breast cancer-related genes BRCA1 DNA repair associated (BRCA1; rs799917) and ATP binding cassette subfamily G member 2 (ABCG2; rs2231142), and the prevalence of human papillomavirus (HPV) infections in a normal population living in Phayao Province, Northern Thailand. One breast cancer and 10 healthy samples were investigated by whole exome sequencing (WES) and compared for genetic variation. The WES data contained SNPs in genes previously implicated in breast cancer and provided data on CNVs. The allele frequencies for SNPs rs799917 and rs2231142 were also examined. The SNP genotype frequencies were 35.88% CC, 46.54% CT, and 17.58% TT for rs799917 and 33.20% CC, 46.88% CA, and 19.92% AA for rs2231142. A total of 825 human whole blood samples were examined for HPV infection by PCR, and the pooled DNA was tested for HPV infection using metagenomic sequencing. No HPV infections were detected among all 825 samples or the pooled blood samples. The incidence of breast cancer among the tested samples was estimated based on acceptable breast cancer risk factors and demographic data and was 1.47%. The present study provided data on SNPs and CNVs in breast cancer-related genes. The associations between SNPs rs2231142 and rs799917 and breast cancer should be further investigated in a case-control study since heterozygous and homozygous variants are more common. Based on the detection of HPV infection in the blood samples, HPV may not be associated with breast cancer, at least in the Northern Thai population.
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Affiliation(s)
- Sureewan Bumrungthai
- Division of Biopharmaceutical Sciences, Faculty of Pharmaceutical Sciences, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
- Division of Microbiology and Parasitology, School of Medical Sciences, University of Phayao, Phayao 56000, Thailand
- Center for Pharmacogenomics and Clinical Translational Research, Faculty of Pharmaceutical Sciences, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Sureewan Duangjit
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmaceutical Sciences, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Supaporn Passorn
- Division of Biotechnology, School of Agriculture and Natural resources, University of Phayao, Phayao 56000, Thailand
| | - Sutida Pongpakdeesakul
- Division of Biotechnology, School of Agriculture and Natural resources, University of Phayao, Phayao 56000, Thailand
| | - Siriwoot Butsri
- Division of Biopharmaceutical Sciences, Faculty of Pharmaceutical Sciences, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
- Center for Pharmacogenomics and Clinical Translational Research, Faculty of Pharmaceutical Sciences, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Somwang Janyakhantikul
- Division of Biopharmaceutical Sciences, Faculty of Pharmaceutical Sciences, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
- Center for Pharmacogenomics and Clinical Translational Research, Faculty of Pharmaceutical Sciences, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
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Sun X, Verma SP, Jia G, Wang X, Ping J, Guo X, Shu XO, Chen J, Derkach A, Cai Q, Liang X, Long J, Offit K, Hun Oh J, Reiner AS, Watt GP, Woods M, Yang Y, Ambrosone CB, Ambs S, Chen Y, Concannon P, Garcia-Closas M, Gu J, Haiman CA, Hu JJ, Huo D, John EM, Knight JA, Li CI, Lynch CF, Mellemkjær L, Nathanson KL, Nemesure B, Olopade OI, Olshan AF, Pal T, Palmer JR, Press MF, Sanderson M, Sandler DP, Troester MA, Zheng W, Bernstein JL, Buas MF, Shu X. Case-Case Genome-Wide Analyses Identify Subtype-Informative Variants That Confer Risk for Breast Cancer. Cancer Res 2024; 84:2533-2548. [PMID: 38832928 PMCID: PMC11293972 DOI: 10.1158/0008-5472.can-23-3854] [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: 12/08/2023] [Revised: 03/15/2024] [Accepted: 05/31/2024] [Indexed: 06/06/2024]
Abstract
Breast cancer includes several subtypes with distinct characteristic biological, pathologic, and clinical features. Elucidating subtype-specific genetic etiology could provide insights into the heterogeneity of breast cancer to facilitate the development of improved prevention and treatment approaches. In this study, we conducted pairwise case-case comparisons among five breast cancer subtypes by applying a case-case genome-wide association study (CC-GWAS) approach to summary statistics data of the Breast Cancer Association Consortium. The approach identified 13 statistically significant loci and eight suggestive loci, the majority of which were identified from comparisons between triple-negative breast cancer (TNBC) and luminal A breast cancer. Associations of lead variants in 12 loci remained statistically significant after accounting for previously reported breast cancer susceptibility variants, among which, two were genome-wide significant. Fine mapping implicated putative functional/causal variants and risk genes at several loci, e.g., 3q26.31/TNFSF10, 8q22.3/NACAP1/GRHL2, and 8q23.3/LINC00536/TRPS1, for TNBC as compared with luminal cancer. Functional investigation further identified rs16867605 at 8q22.3 as a SNP that modulates the enhancer activity of GRHL2. Subtype-informative polygenic risk scores (PRS) were derived, and patients with a high subtype-informative PRS had an up to two-fold increased risk of being diagnosed with TNBC instead of luminal cancers. The CC-GWAS PRS remained statistically significant after adjusting for TNBC PRS derived from traditional case-control GWAS in The Cancer Genome Atlas and the African Ancestry Breast Cancer Genetic Consortium. The CC-GWAS PRS was also associated with overall survival and disease-specific survival among patients with breast cancer. Overall, these findings have advanced our understanding of the genetic etiology of breast cancer subtypes, particularly for TNBC. Significance: The discovery of subtype-informative genetic risk variants for breast cancer advances our understanding of the etiologic heterogeneity of breast cancer, which could accelerate the identification of targets and personalized strategies for prevention and treatment.
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Affiliation(s)
- Xiaohui Sun
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology, Zhejiang Chinese Medical University, Zhejiang, China
| | - Shiv Prakash Verma
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Guochong Jia
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xinjun Wang
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, 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
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jianhong Chen
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Andriy Derkach
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiaolin Liang
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - 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
| | - Jung Hun Oh
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anne S. Reiner
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gordon P. Watt
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Meghan Woods
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, 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, University of Virginia, Charlottesville, VA, USA
- UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, VA, USA
| | - Christine B. Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yu Chen
- Department of Population Health, New York University Grossman School of Medicine, New York, NY, USA
| | - Patrick Concannon
- Genetics Institute and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Montserrat Garcia-Closas
- Trans-Divisional Research Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jian Gu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jennifer J. Hu
- The University of Miami School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Esther M. John
- Department of Epidemiology & Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia A. Knight
- Prosserman Centre for Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Christopher I. Li
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Charles F. Lynch
- Department of Epidemiology, University of Iowa College of Public Health, Iowa City, IA, USA
| | - Lene Mellemkjær
- Diet, Cancer and Health, Danish Cancer Institute, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Katherine L. Nathanson
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Barbara Nemesure
- Stony Brook Medicine, Department of Family, Population, and Preventive Medicine, Stony Brook, NY, USA
| | | | - Andrew F. Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Tuya Pal
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Julie R. Palmer
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | - Michael F. Press
- Department of Pathology, Keck School of Medicine, USC/Norris Comprehensive Cancer Center, 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, Research Triangle Park, NC, USA
| | - Melissa A. Troester
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jonine L. Bernstein
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew F. Buas
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xiang Shu
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Shikholeslami SR, Keshavarzi F. Investigation of the association between the CASP8rs1045485 and SOD2 rs4880 single nucleotide polymorphisms (SNPs) with breast cancer. Cancer Treat Res Commun 2024; 40:100835. [PMID: 39038402 DOI: 10.1016/j.ctarc.2024.100835] [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: 06/18/2024] [Revised: 07/09/2024] [Accepted: 07/09/2024] [Indexed: 07/24/2024]
Abstract
INTRODUCTION Single nucleotide polymorphisms (SNPs) have been identified as prognostic markers that can influence the response to chemotherapy and, ultimately, the outcome of the disease. The objective of this study is to investigate the association between the rs1045485 and rs4880 variants and breast cancer. METHODS Ninety-nine cases and 81 healthy individuals (over 60 years old) were recruited from Iranian population. Genotyping of the rs1045485 and rs4880 polymorphisms was determined using the PCR-RFLP molecular method. The obtained results were then evaluated using the SPSS 23.0, odds ratios (ORs) with 95 % confidence intervals (95 %CIs). RESULTS The average age of the subjects was 50.17± 1.8 years, with age ranging from 40 to 76 years. Additionally, more patients were in stage and grade 2 of the disease. Furthermore, 51.73 %, 53.24 % and 41.48 % of patients tested positive for ER, PR and HER2 status, respectively. The odds ratios of the genotypes studied for each of the two variants were not statistically significant. Additionally, all models (dominant, codominant, recessive and over dominant) also indicated that this difference was not significant (p > 0.05). Investigation of the association between the CASP8rs1045485 and SOD2 rs4880 variants with clinicopathological status were not revealed a significant relationship. The Hardy-Weinberg test showed that the evaluated population was balanced (p > 0.05). CONCLUSION In the studied models of both polymorphisms, no significant correlation was found between the genotypes and the conditions of estrogen, progesterone and Her2 receptors, as well as the stage and grade of the disease.
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Affiliation(s)
| | - Fatemeh Keshavarzi
- Department of Biology, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran.
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Mabey B, Hughes E, Kucera M, Simmons T, Hullinger B, Pederson HJ, Yehia L, Eng C, Garber J, Gary M, Gordon O, Klemp JR, Mukherjee S, Vijai J, Offit K, Olopade OI, Pruthi S, Kurian A, Robson ME, Whitworth PW, Pal T, Ratzel S, Wagner S, Lanchbury JS, Taber KJ, Slavin TP, Gutin A. Validation of a clinical breast cancer risk assessment tool combining a polygenic score for all ancestries with traditional risk factors. Genet Med 2024; 26:101128. [PMID: 38829299 DOI: 10.1016/j.gim.2024.101128] [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: 11/02/2023] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 06/05/2024] Open
Abstract
PURPOSE We previously described a combined risk score (CRS) that integrates a multiple-ancestry polygenic risk score (MA-PRS) with the Tyrer-Cuzick (TC) model to assess breast cancer (BC) risk. Here, we present a longitudinal validation of CRS in a real-world cohort. METHODS This study included 130,058 patients referred for hereditary cancer genetic testing and negative for germline pathogenic variants in BC-associated genes. Data were obtained by linking genetic test results to medical claims (median follow-up 12.1 months). CRS calibration was evaluated by the ratio of observed to expected BCs. RESULTS Three hundred forty BCs were observed over 148,349 patient-years. CRS was well-calibrated and demonstrated superior calibration compared with TC in high-risk deciles. MA-PRS alone had greater discriminatory accuracy than TC, and CRS had approximately 2-fold greater discriminatory accuracy than MA-PRS or TC. Among those classified as high risk by TC, 32.6% were low risk by CRS, and of those classified as low risk by TC, 4.3% were high risk by CRS. In cases where CRS and TC classifications disagreed, CRS was more accurate in predicting incident BC. CONCLUSION CRS was well-calibrated and significantly improved BC risk stratification. Short-term follow-up suggests that clinical implementation of CRS should improve outcomes for patients of all ancestries through personalized risk-based screening and prevention.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Joseph Vijai
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kenneth Offit
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - Mark E Robson
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Tuya Pal
- Vanderbilt University Medical Center, Nashville, TN
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Gao G, McClellan J, Barbeira AN, Fiorica PN, Li JL, Mu Z, Olopade OI, Huo D, Im HK. A multi-tissue, splicing-based joint transcriptome-wide association study identifies susceptibility genes for breast cancer. Am J Hum Genet 2024; 111:1100-1113. [PMID: 38733992 PMCID: PMC11179262 DOI: 10.1016/j.ajhg.2024.04.010] [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: 10/09/2023] [Revised: 04/13/2024] [Accepted: 04/15/2024] [Indexed: 05/13/2024] Open
Abstract
Splicing-based transcriptome-wide association studies (splicing-TWASs) of breast cancer have the potential to identify susceptibility genes. However, existing splicing-TWASs test the association of individual excised introns in breast tissue only and thus have limited power to detect susceptibility genes. In this study, we performed a multi-tissue joint splicing-TWAS that integrated splicing-TWAS signals of multiple excised introns in each gene across 11 tissues that are potentially relevant to breast cancer risk. We utilized summary statistics from a meta-analysis that combined genome-wide association study (GWAS) results of 424,650 women of European ancestry. Splicing-level prediction models were trained in GTEx (v.8) data. We identified 240 genes by the multi-tissue joint splicing-TWAS at the Bonferroni-corrected significance level; in the tissue-specific splicing-TWAS that combined TWAS signals of excised introns in genes in breast tissue only, we identified nine additional significant genes. Of these 249 genes, 88 genes in 62 loci have not been reported by previous TWASs, and 17 genes in seven loci are at least 1 Mb away from published GWAS index variants. By comparing the results of our splicing-TWASs with previous gene-expression-based TWASs that used the same summary statistics and expression prediction models trained in the same reference panel, we found that 110 genes in 70 loci that are identified only by the splicing-TWASs. Our results showed that for many genes, expression quantitative trait loci (eQTL) did not show a significant impact on breast cancer risk, whereas splicing quantitative trait loci (sQTL) showed a strong impact through intron excision events.
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Affiliation(s)
- Guimin Gao
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Julian McClellan
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Alvaro N Barbeira
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Peter N Fiorica
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - James L Li
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Zepeng Mu
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Olufunmilayo I Olopade
- Section of Hematology and Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA; Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA.
| | - Hae Kyung Im
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA.
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Yari K, Hakimi A, Mohammadi M, Ammari-Allahyari M, Salari N, Ghasemi H. The Association of PTEN Gene Mutations with the Breast Cancer Risk: A Systematic Review and Meta-analysis. Biochem Genet 2024; 62:1617-1635. [PMID: 37658255 DOI: 10.1007/s10528-023-10464-z] [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: 12/06/2022] [Accepted: 07/18/2023] [Indexed: 09/03/2023]
Abstract
Breast cancer (BC) is the most common malignancy in women in western countries. A significant part of malignant cases is caused by genetic mutation. Mutations in the gene phosphatase and tensin homologue deleted on chromosome (PTEN) have been proven in various malignancies. The present study was conducted with the aim of investigating the prevalence of BC due to PTEN gene mutation, as well as estimating the chance of developing BC due to the occurrence of PTEN gene mutation. The present study was conducted using a systematic review method based on PRISMA 2020 statements. The search was done in PubMed, Web of Science (WOS), Scopus, and direct scientific databases. The search was performed using the keywords breast cancer, breast malignancy, PTEN, polymorphism, mutation, variant, and their equivalents. Statistical analysis was performed using the second version of Comprehensive Meta-Analysis Software. A total of 2138 articles were collected. After removing duplicate articles, checking the title and abstract, and then checking the full text of the documents, finally 64 articles were approved and entered the systematic review process. Analysis of these studies with a sample size of 231,179 showed the prevalence of breast cancer patients with PTEN mutations. The combined results of 64 studies showed that the prevalence of PTEN mutations has a 3.3 (95% CI 2.2-5) in BC patients, and an analysis of 6 studies showed that the odds ratio of developing BC due to PTEN mutation is 3.7 (95% CI 1.1-11.9). The results of this study show that mutation in the PTEN gene increases the chance of developing BC. However, it was found that a small part of patients gets BC due to the occurrence of mutation in this gene.
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Affiliation(s)
- Kheirollah Yari
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ali Hakimi
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Masoud Mohammadi
- Cellular and Molecular Research Center, Gerash University of Medical Sciences, Gerash, Iran
| | | | - Nader Salari
- Department of Biostatistics, School of Health, Kermanshah University of Medical Sciences, Kermanshah, Iran.
- Sleep Disorders Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Hooman Ghasemi
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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Passi G, Lieberman S, Zahdeh F, Murik O, Renbaum P, Beeri R, Linial M, May D, Levy-Lahad E, Schneidman-Duhovny D. Discovering predisposing genes for hereditary breast cancer using deep learning. Brief Bioinform 2024; 25:bbae346. [PMID: 39038933 PMCID: PMC11262808 DOI: 10.1093/bib/bbae346] [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: 01/16/2024] [Revised: 04/18/2024] [Accepted: 07/04/2024] [Indexed: 07/24/2024] Open
Abstract
Breast cancer (BC) is the most common malignancy affecting Western women today. It is estimated that as many as 10% of BC cases can be attributed to germline variants. However, the genetic basis of the majority of familial BC cases has yet to be identified. Discovering predisposing genes contributing to familial BC is challenging due to their presumed rarity, low penetrance, and complex biological mechanisms. Here, we focused on an analysis of rare missense variants in a cohort of 12 families of Middle Eastern origins characterized by a high incidence of BC cases. We devised a novel, high-throughput, variant analysis pipeline adapted for family studies, which aims to analyze variants at the protein level by employing state-of-the-art machine learning models and three-dimensional protein structural analysis. Using our pipeline, we analyzed 1218 rare missense variants that are shared between affected family members and classified 80 genes as candidate pathogenic. Among these genes, we found significant functional enrichment in peroxisomal and mitochondrial biological pathways which segregated across seven families in the study and covered diverse ethnic groups. We present multiple evidence that peroxisomal and mitochondrial pathways play an important, yet underappreciated, role in both germline BC predisposition and BC survival.
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Affiliation(s)
- Gal Passi
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Sari Lieberman
- The Fuld Family Medical Genetics Institute, Shaare Zedek Medical Center 12 Bayit St., Jerusalem 9103101, Israel
- The Eisenberg R&D Authority, Shaare Zedek Medical Center, 12 Bayit St., Jerusalem 9103101, Israel
- Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem PO Box 12271 Jerusalem 9112102, Israel
| | - Fouad Zahdeh
- The Fuld Family Medical Genetics Institute, Shaare Zedek Medical Center 12 Bayit St., Jerusalem 9103101, Israel
- The Eisenberg R&D Authority, Shaare Zedek Medical Center, 12 Bayit St., Jerusalem 9103101, Israel
| | - Omer Murik
- The Fuld Family Medical Genetics Institute, Shaare Zedek Medical Center 12 Bayit St., Jerusalem 9103101, Israel
- The Eisenberg R&D Authority, Shaare Zedek Medical Center, 12 Bayit St., Jerusalem 9103101, Israel
| | - Paul Renbaum
- The Fuld Family Medical Genetics Institute, Shaare Zedek Medical Center 12 Bayit St., Jerusalem 9103101, Israel
- The Eisenberg R&D Authority, Shaare Zedek Medical Center, 12 Bayit St., Jerusalem 9103101, Israel
| | - Rachel Beeri
- The Fuld Family Medical Genetics Institute, Shaare Zedek Medical Center 12 Bayit St., Jerusalem 9103101, Israel
- The Eisenberg R&D Authority, Shaare Zedek Medical Center, 12 Bayit St., Jerusalem 9103101, Israel
| | - Michal Linial
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Dalit May
- The Fuld Family Medical Genetics Institute, Shaare Zedek Medical Center 12 Bayit St., Jerusalem 9103101, Israel
- The Eisenberg R&D Authority, Shaare Zedek Medical Center, 12 Bayit St., Jerusalem 9103101, Israel
- Clalit Health Services, Jerusalem, Israel
| | - Ephrat Levy-Lahad
- The Fuld Family Medical Genetics Institute, Shaare Zedek Medical Center 12 Bayit St., Jerusalem 9103101, Israel
- The Eisenberg R&D Authority, Shaare Zedek Medical Center, 12 Bayit St., Jerusalem 9103101, Israel
- Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem PO Box 12271 Jerusalem 9112102, Israel
| | - Dina Schneidman-Duhovny
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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Zhang Y, Zhong K, Liang W, Liu R, Qu W, Lu Y. Causal associations between estradiol and mouth ulcers: A Mendelian randomization study. Medicine (Baltimore) 2024; 103:e37989. [PMID: 38669373 PMCID: PMC11049722 DOI: 10.1097/md.0000000000037989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 04/02/2024] [Indexed: 04/28/2024] Open
Abstract
People have difficulty in eating and speaking when they are suffering from mouth ulcers. Some studies suggest that estradiol is associated with the development and treatment of mouth ulcers, while some do not. To clarify the effect of estradiol on mouth ulcers, we performed 2-sample Mendelian randomization and multivariable Mendelian randomization (MVMR) analysis to evaluate their relationship. Data were obtained from the IEU OpenGWAS project and UK biobank, including male estradiol dataset (case/controls = 13,367/134,323), female estradiol dataset (case/controls = 37,461/126,524), mouth ulcers dataset (case/controls = 47,102/414,011). The causal associations were estimated by MR-Egger, weighted median, inverse-variance weighted (IVW) method, simple mode, and weighted mode. Cochran Q test, MR-Egger intercept test, MR-PRESSO tests, and leave-one-out analysis were used to examine sensitivity analyses. The MVMR controlling for depression, anxiety or panic attacks, severe stress and adjustment disorders was used to assess the effect of estradiol on mouth ulcers. Through screening, 13 single nucleotide polymorphisms (SNPs) of males and 2 SNPs of females in estradiol were used for harmonizing and MR analysis. The 2-sample MR analysis showed no causal association between estradiol of males and mouth ulcers (IVW, OR: 0.998, 95% confidence interval [95% CI]: 0.995-1.001, P = .18). Similar results were obtained between estradiol of females and mouth ulcers (IVW, OR: 1.000, 95% CI: 0.988-1.012, P = .97). No pleiotropy and heterogeneity were found and the results were robust (P > .05). After adjusting for the potential effects of confounders, estradiol of males and mouth ulcers still showed no causal association through MVMR analysis (P = .081). While MVMR analysis showed that the causal relationship between estradiol and mouth ulcers in women could not be statistical for the small number of SNPs. There was no evidence of a causal relationship between estradiol and mouth ulcers. The strategy of treating mouth ulcers with estradiol still needs to be confirmed by more studies.
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Affiliation(s)
- Yaqian Zhang
- Research Centre of Basic Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
| | - Kunting Zhong
- Research Centre of Basic Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
| | - Weiyu Liang
- Research Centre of Basic Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
| | - Ruihanqiu Liu
- Research Centre of Basic Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
| | - Weiling Qu
- Research Centre of Basic Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
| | - Yan Lu
- Research Centre of Basic Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China
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9
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Ponomarenko I, Pasenov K, Churnosova M, Sorokina I, Aristova I, Churnosov V, Ponomarenko M, Reshetnikova Y, Reshetnikov E, Churnosov M. Obesity-Dependent Association of the rs10454142 PPP1R21 with Breast Cancer. Biomedicines 2024; 12:818. [PMID: 38672173 PMCID: PMC11048332 DOI: 10.3390/biomedicines12040818] [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: 03/05/2024] [Revised: 03/30/2024] [Accepted: 04/02/2024] [Indexed: 04/28/2024] Open
Abstract
The purpose of this work was to find a link between the breast cancer (BC)-risk effects of sex hormone-binding globulin (SHBG)-associated polymorphisms and obesity. The study was conducted on a sample of 1498 women (358 BC; 1140 controls) who, depending on the presence/absence of obesity, were divided into two groups: obese (119 BC; 253 controls) and non-obese (239 BC; 887 controls). Genotyping of nine SHBG-associated single nucleotide polymorphisms (SNP)-rs17496332 PRMT6, rs780093 GCKR, rs10454142 PPP1R21, rs3779195 BAIAP2L1, rs440837 ZBTB10, rs7910927 JMJD1C, rs4149056 SLCO1B1, rs8023580 NR2F2, and rs12150660 SHBG-was executed, and the BC-risk impact of these loci was analyzed by logistic regression separately in each group of obese/non-obese women. We found that the BC-risk effect correlated by GWAS with the SHBG-level polymorphism rs10454142 PPP1R21 depends on the presence/absence of obesity. The SHBG-lowering allele C rs10454142 PPP1R21 has a risk value for BC in obese women (allelic model: CvsT, OR = 1.52, 95%CI = 1.10-2.11, and pperm = 0.013; additive model: CCvsTCvsTT, OR = 1.71, 95%CI = 1.15-2.62, and pperm = 0.011; dominant model: CC + TCvsTT, OR = 1.95, 95%CI = 1.13-3.37, and pperm = 0.017) and is not associated with the disease in women without obesity. SNP rs10454142 PPP1R21 and 10 proxy SNPs have adipose-specific regulatory effects (epigenetic modifications of promoters/enhancers, DNA interaction with 51 transcription factors, eQTL/sQTL effects on five genes (PPP1R21, RP11-460M2.1, GTF2A1L, STON1-GTF2A1L, and STON1), etc.), can be "likely cancer driver" SNPs, and are involved in cancer-significant pathways. In conclusion, our study detected an obesity-dependent association of the rs10454142 PPP1R21 with BC in women.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Mikhail Churnosov
- Department of Medical Biological Disciplines, Belgorod State National Research University, 308015 Belgorod, Russia; (I.P.); (K.P.); (M.C.); (I.S.); (I.A.); (V.C.); (M.P.); (Y.R.); (E.R.)
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10
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Ponomarenko I, Pasenov K, Churnosova M, Sorokina I, Aristova I, Churnosov V, Ponomarenko M, Reshetnikov E, Churnosov M. Sex-Hormone-Binding Globulin Gene Polymorphisms and Breast Cancer Risk in Caucasian Women of Russia. Int J Mol Sci 2024; 25:2182. [PMID: 38396861 PMCID: PMC10888713 DOI: 10.3390/ijms25042182] [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: 01/21/2024] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
In our work, the associations of GWAS (genome-wide associative studies) impact for sex-hormone-binding globulin (SHBG)-level SNPs with the risk of breast cancer (BC) in the cohort of Caucasian women of Russia were assessed. The work was performed on a sample of 1498 women (358 BC patients and 1140 control (non BC) subjects). SHBG correlated in previously GWAS nine polymorphisms such as rs780093 GCKR, rs17496332 PRMT6, rs3779195 BAIAP2L1, rs10454142 PPP1R21, rs7910927 JMJD1C, rs4149056 SLCO1B1, rs440837 ZBTB10, rs12150660 SHBG, and rs8023580 NR2F2 have been genotyped. BC risk effects of allelic and non-allelic SHBG-linked gene SNPs interactions were detected by regression analysis. The risk genetic factor for BC developing is an SHBG-lowering allele variant C rs10454142 PPP1R21 ([additive genetic model] OR = 1.31; 95%CI = 1.08-1.65; pperm = 0.024; power = 85.26%), which determines 0.32% of the cancer variance. Eight of the nine studied SHBG-related SNPs have been involved in cancer susceptibility as part of nine different non-allelic gene interaction models, the greatest contribution to which is made by rs10454142 PPP1R21 (included in all nine models, 100%) and four more SNPs-rs7910927 JMJD1C (five models, 55.56%), rs17496332 PRMT6 (four models, 44.44%), rs780093 GCKR (four models, 44.44%), and rs440837 ZBTB10 (four models, 44.44%). For SHBG-related loci, pronounced functionality in the organism (including breast, liver, fibroblasts, etc.) was predicted in silico, having a direct relationship through many pathways with cancer pathophysiology. In conclusion, our results demonstrated the involvement of SHBG-correlated genes polymorphisms in BC risk in Caucasian women in Russia.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Mikhail Churnosov
- Department of Medical Biological Disciplines, Belgorod State National Research University, 308015 Belgorod, Russia; (I.P.); (K.P.); (M.C.); (I.S.); (I.A.); (V.C.); (M.P.); (E.R.)
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11
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Valentini V, Bucalo A, Conti G, Celli L, Porzio V, Capalbo C, Silvestri V, Ottini L. Gender-Specific Genetic Predisposition to Breast Cancer: BRCA Genes and Beyond. Cancers (Basel) 2024; 16:579. [PMID: 38339330 PMCID: PMC10854694 DOI: 10.3390/cancers16030579] [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: 12/21/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Among neoplastic diseases, breast cancer (BC) is one of the most influenced by gender. Despite common misconceptions associating BC as a women-only disease, BC can also occur in men. Additionally, transgender individuals may also experience BC. Genetic risk factors play a relevant role in BC predisposition, with important implications in precision prevention and treatment. The genetic architecture of BC susceptibility is similar in women and men, with high-, moderate-, and low-penetrance risk variants; however, some sex-specific features have emerged. Inherited high-penetrance pathogenic variants (PVs) in BRCA1 and BRCA2 genes are the strongest BC genetic risk factor. BRCA1 and BRCA2 PVs are more commonly associated with increased risk of female and male BC, respectively. Notably, BRCA-associated BCs are characterized by sex-specific pathologic features. Recently, next-generation sequencing technologies have helped to provide more insights on the role of moderate-penetrance BC risk variants, particularly in PALB2, CHEK2, and ATM genes, while international collaborative genome-wide association studies have contributed evidence on common low-penetrance BC risk variants, on their combined effect in polygenic models, and on their role as risk modulators in BRCA1/2 PV carriers. Overall, all these studies suggested that the genetic basis of male BC, although similar, may differ from female BC. Evaluating the genetic component of male BC as a distinct entity from female BC is the first step to improve both personalized risk assessment and therapeutic choices of patients of both sexes in order to reach gender equality in BC care. In this review, we summarize the latest research in the field of BC genetic predisposition with a particular focus on similarities and differences in male and female BC, and we also discuss the implications, challenges, and open issues that surround the establishment of a gender-oriented clinical management for BC.
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Affiliation(s)
- Virginia Valentini
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.V.); (A.B.); (G.C.); (L.C.); (V.P.); (C.C.); (V.S.)
| | - Agostino Bucalo
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.V.); (A.B.); (G.C.); (L.C.); (V.P.); (C.C.); (V.S.)
| | - Giulia Conti
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.V.); (A.B.); (G.C.); (L.C.); (V.P.); (C.C.); (V.S.)
| | - Ludovica Celli
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.V.); (A.B.); (G.C.); (L.C.); (V.P.); (C.C.); (V.S.)
| | - Virginia Porzio
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.V.); (A.B.); (G.C.); (L.C.); (V.P.); (C.C.); (V.S.)
| | - Carlo Capalbo
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.V.); (A.B.); (G.C.); (L.C.); (V.P.); (C.C.); (V.S.)
- Medical Oncology Unit, Sant’Andrea University Hospital, 00189 Rome, Italy
| | - Valentina Silvestri
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.V.); (A.B.); (G.C.); (L.C.); (V.P.); (C.C.); (V.S.)
| | - Laura Ottini
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.V.); (A.B.); (G.C.); (L.C.); (V.P.); (C.C.); (V.S.)
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12
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Azadeh Jouneghani M, Keshavarzi F, Haghnazari N, Hooshmandi Z, Amini S. The Investigation of the Association Between the Bcl-2 3'-UTR rs1564483 Polymorphism and miR-296-3p in the Development of Breast and Gastric Cancers. Clin Med Insights Oncol 2023; 17:11795549231207835. [PMID: 37928451 PMCID: PMC10625176 DOI: 10.1177/11795549231207835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 09/27/2023] [Indexed: 11/07/2023] Open
Abstract
Background B-cell leukemia/lymphoma 2 (Bcl-2) gene regulates carcinogenesis by inhibiting apoptosis. This study evaluated the association of Bcl-2 3'-untranslated regions (3' UTR) rs1564483 polymorphism and miR-296-3p with the development of breast and gastric cancers. Methods A microarray analysis was performed on the Genomic Spatial Event (GSE)29431 and GSE161533 datasets for breast and gastric cancers. Blood samples were taken from 222 (111 patients and 111 controls) and 210 (84 patients and 126 controls) individuals for breast and gastric cancers, respectively. Genomic DNA was extracted from the blood samples and genotyping was performed using real-time polymerase chain reaction (RT-PCR), followed by examining the high-temperature melting curve. Statistical analysis was conducted to examine the potential correlation between the rs1564483 polymorphism and the risk of breast and gastric cancers concerning pathological characteristics. Results The results of the microarray showed that the Bcl-2 gene was up-regulated in gastric cancer (logFC [log fold change]: 0.65, adjusted P < .05). Clinical outcome showed no notable relationship between the rs1564483 polymorphism and breast cancer risk; however, for gastric cancer, it identified a large difference between healthy controls and patients for an allelic frequency of rs1564483 (P ⩽ .001). Moreover, an assay of different models (dominant, recessive, and co-dominant) showed a significant association between the AG genotype between control and gastric cases (Pearson chi-square test, P = .046). In addition, the prevalence of the AG genotype was greater in persons under the age of 45 and in patients with H. pylori infection (P ⩽ .001). The AG genotype was not related to smoking, although the AA genotype was associated with increased cancer incidence in smokers (P ⩽ .001). Conclusions In silico studies and calculations of the ΔG binding of micro ribonucleic acid (miRNA) hsa-miR-296-3p to the mutant and wild alleles of the rs15644833 single nucleotide polymorphism (SNP) have revealed that Bcl-2 mRNA expression in gastric cancer decreases, thus confirming the tumor suppressor role of the Bcl-2 gene.
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Affiliation(s)
| | - Fatemeh Keshavarzi
- Department of Biology, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran
| | - Nahid Haghnazari
- Department of Biology, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran
| | - Zahra Hooshmandi
- Department of Biology, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran
| | - Sabrieh Amini
- Department of Biology, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran
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13
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Ghadamgahi SR, Hosseinzadeh L, Ardalan Khales S, Nassiri M, Alidoust M, Etemadrezaei S, Khorshid Shamshiri A, Homaei Shandiz F, Pasdar A, Afzaljavan F. Potential Role of Zinc Finger 365 rs10822013 and rs10995190 in Mammographic Density, Sporadic Breast Cancer Risk, and Prognosis. IRANIAN JOURNAL OF MEDICAL SCIENCES 2023; 48:551-562. [PMID: 38094285 PMCID: PMC10715120 DOI: 10.30476/ijms.2023.96141.2767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 11/08/2022] [Accepted: 12/17/2022] [Indexed: 12/18/2023]
Abstract
Background Despite suggesting many genetic risk markers as the outcome of Genome-wide association studies (GWAS) for breast cancer, replicating the results in different populations has remained the main issue. In this regard, this study assessed the association of two variations in Zinc Finger 365 (ZNF365) in an Iranian population. Methods In a case-control study conducted at Mashhad University of Medical Sciences, Mashhad, Iran, between 2017 and 2020, ZNF365-rs10822013 and rs10995190 were genotyped using Allele-Specific PCR (AS-PCR). Breast density was assessed using mammography images. PHASE software module version 2 and SPSS version 16.0 were used for haplotype and statistical analyses. Quantitative and qualitative variables were compared between groups using independent t tests and Chi square tests, respectively. Binary logistic regression analysis was performed to calculate odds ratios. Multivariate analysis was then undertaken for the baseline variables, with a P<0.05 in the univariate analysis. The survival analysis was performed using the Kaplan-Meier method and the log-rank test. Results In this survey, 732 females, including 342 breast cancer patients and 390 healthy subjects, were enrolled. rs10822013-T allele (P=0.014), rs10995190-G allele (P=0.003), and TG haplotype (P=0.002) were significantly associated with the increased risk of breast cancer. Moreover, rs10995190-GG genotype (P=0.042) and C-G haplotype (P=0.019) revealed a significant association with better overall survival. However, considered polymorphisms and their haplotypes indicated no association with breast density and clinical features of breast cancer. Conclusion ZNF365 variants might be a potential risk marker of breast cancer in the Iranian population. The interaction between alleles in haplotypes may modulate the amount of the risk conferred by these variants. Further studies on different ethnic groups can validate these results.
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Affiliation(s)
- Seyed Reza Ghadamgahi
- Department of Genetics, School of Sciences, Azad University of Damghan, Damghan, Iran
| | - Leila Hosseinzadeh
- Lung Cancer and Immuno- Oncology Laboratory (LCIO), Jules Bordet Institute, Université Libre de Bruxelles, Brussels, Belgium
| | - Sahar Ardalan Khales
- Congenital Malformations Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Mohammadreza Nassiri
- Recombinant Protein Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Maryam Alidoust
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Science, Mashhad, Iran
| | | | - Asma Khorshid Shamshiri
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Science, Mashhad, Iran
| | | | - Alireza Pasdar
- Division of Applied Medicine, School of Medicine, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Fahimeh Afzaljavan
- Clinical Research Development Unit, Imam Reza Hospital, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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14
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Sarkis-Tannous D, Sukol RB, Sullivan E. Toward more personalized breast cancer risk assessment: The polygenic risk score. JAAPA 2023; 36:37-40. [PMID: 37751256 DOI: 10.1097/01.jaa.0000977692.63075.f3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
ABSTRACT Healthcare providers often are uncertain about how best to assess and manage breast cancer risk. Women at average risk wonder when to start mammography and how often to go. Women at increased risk might inquire about genetic testing, MRI screening, and preventive measures. Patients who carry gene mutations face higher stakes and more complex risk management choices, but only some are aware of their status. This article helps clinicians stratify breast cancer risk and discusses a newer genomic test, the polygenic risk score, that may enable more personalized risk management and decision-making.
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Affiliation(s)
- Daad Sarkis-Tannous
- At the time this article was written, Daad Sarkis-Tannous, Roxanne B. Sukol, and Erika Sullivan were medical breast specialists at the Cleveland (Ohio) Clinic. Dr. Sukol is now retired. The authors have disclosed no potential conflicts of interest, financial or otherwise
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15
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Figlioli G, Billaud A, Wang Q, Bolla MK, Dennis J, Lush M, Kvist A, Adank MA, Ahearn TU, Antonenkova NN, Auvinen P, Behrens S, Bermisheva M, Bogdanova NV, Bojesen SE, Bonanni B, Brüning T, Camp NJ, Campbell A, Castelao JE, Cessna MH, Czene K, Devilee P, Dörk T, Eriksson M, Fasching PA, Flyger H, Gabrielson M, Gago-Dominguez M, García-Closas M, Glendon G, Gómez Garcia EB, González-Neira A, Grassmann F, Guénel P, Hahnen E, Hamann U, Hillemanns P, Hooning MJ, Hoppe R, Howell A, Humphreys K, Jakubowska A, Khusnutdinova EK, Kristensen VN, Lindblom A, Loizidou MA, Lubiński J, Mannermaa A, Maurer T, Mavroudis D, Newman WG, Obi N, Panayiotidis MI, Radice P, Rashid MU, Rhenius V, Ruebner M, Saloustros E, Sawyer EJ, Schmidt MK, Schmutzler RK, Shah M, Southey MC, Tomlinson I, Truong T, van Veen EM, Wendt C, Yang XR, Michailidou K, Dunning AM, Pharoah PDP, Easton DF, Andrulis IL, Evans DG, Hollestelle A, Chang-Claude J, Milne RL, Peterlongo P. Spectrum and Frequency of Germline FANCM Protein-Truncating Variants in 44,803 European Female Breast Cancer Cases. Cancers (Basel) 2023; 15:3313. [PMID: 37444426 DOI: 10.3390/cancers15133313] [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: 04/17/2023] [Revised: 05/30/2023] [Accepted: 06/02/2023] [Indexed: 07/15/2023] Open
Abstract
FANCM germline protein truncating variants (PTVs) are moderate-risk factors for ER-negative breast cancer. We previously described the spectrum of FANCM PTVs in 114 European breast cancer cases. In the present, larger cohort, we report the spectrum and frequency of four common and 62 rare FANCM PTVs found in 274 carriers detected among 44,803 breast cancer cases. We confirmed that p.Gln1701* was the most common PTV in Northern Europe with lower frequencies in Southern Europe. In contrast, p.Gly1906Alafs*12 was the most common PTV in Southern Europe with decreasing frequencies in Central and Northern Europe. We verified that p.Arg658* was prevalent in Central Europe and had highest frequencies in Eastern Europe. We also confirmed that the fourth most common PTV, p.Gln498Thrfs*7, might be a founder variant from Lithuania. Based on the frequency distribution of the carriers of rare PTVs, we showed that the FANCM PTVs spectra in Southwestern and Central Europe were much more heterogeneous than those from Northeastern Europe. These findings will inform the development of more efficient FANCM genetic testing strategies for breast cancer cases from specific European populations.
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Affiliation(s)
- Gisella Figlioli
- Genome Diagnostics Program, IFOM ETS-The AIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Amandine Billaud
- Genome Diagnostics Program, IFOM ETS-The AIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Qin Wang
- 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
| | - 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
| | - Anders Kvist
- Division of Oncology, Department of Clinical Sciences Lund, Lund University, 22185 Lund, Sweden
| | - Muriel A Adank
- The Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Family Cancer Clinic, 1066 CX Amsterdam, The Netherlands
| | - Thomas U Ahearn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Natalia N Antonenkova
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, 223040 Minsk, Belarus
| | - Päivi Auvinen
- Translational Cancer Research Area, University of Eastern Finland, 70210 Kuopio, Finland
- Institute of Clinical Medicine, Oncology, University of Eastern Finland, 70210 Kuopio, Finland
- Department of Oncology, Cancer Center, Kuopio University Hospital, 70210 Kuopio, Finland
| | - Sabine Behrens
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Marina Bermisheva
- Institute of Biochemistry and Genetics of the Ufa Federal Research Centre of the Russian Academy of Sciences, 450054 Ufa, Russia
| | - 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, Copenhagen University Hospital, Herlev and Gentofte Hospital, 2730 Herlev, Denmark
- Department of Clinical Biochemistry, Copenhagen University Hospital, Herlev and Gentofte 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
| | - Thomas Brüning
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University Bochum (IPA), 44789 Bochum, Germany
| | - Nicola J Camp
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh EH16 4UX, UK
| | - Jose E Castelao
- Oncology and Genetics Unit, Instituto de Investigación Sanitaria Galicia Sur (IISGS), Xerencia de Xestion Integrada de Vigo-SERGAS, 36312 Vigo, Spain
| | | | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Peter Devilee
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, 30625 Hannover, Germany
| | - Mikael Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, 91054 Erlangen, Germany
| | - Henrik Flyger
- Department of Breast Surgery, Copenhagen University Hospital, Herlev and Gentofte Hospital, 2730 Herlev, Denmark
| | - Marike Gabrielson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Manuela Gago-Dominguez
- Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS) Foundation, IDIS Cancer Genetics and Epidemiology Group, Genomic Medicine Group, Complejo Hospitalario Universitario de Santiago, SERGAS, 15706 Santiago de Compostela, Spain
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Gord Glendon
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Fred A. Litwin Center for Cancer Genetics, Toronto, ON M5G 1X5, Canada
- Laboratory Medicine Program, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Encarna B Gómez Garcia
- Department of Clinical Genetics, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands
| | - Anna González-Neira
- Human Genotyping Unit-CeGen, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Felix Grassmann
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Medicine, Institute for Clinical Research and Systems Medicine, Health and Medical University, 14467 Potsdam, Germany
| | - Pascal Guénel
- CESP U1018, Inserm "Exposome, Heredity, Cancer and Health" Team, UVSQ, University Paris-Saclay, Gustave Roussy, 94805 Villejuif, France
| | - Eric Hahnen
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Ute Hamann
- German Cancer Research Center (DKFZ), Molecular Genetics of Breast Cancer, 69120 Heidelberg, Germany
| | - Peter Hillemanns
- Gynaecology Research Unit, Hannover Medical School, 30625 Hannover, Germany
| | - Maartje J Hooning
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands
| | - Reiner Hoppe
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376 Stuttgart, Germany
- University of Tübingen, 72074 Tübingen, Germany
| | - Anthony Howell
- Division of Cancer Sciences, University of Manchester, Manchester M13 9PL, UK
| | - Keith Humphreys
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Anna Jakubowska
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University in Szczecin, 71-252 Szczecin, Poland
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University in Szczecin, 71-252 Szczecin, Poland
| | - Elza K Khusnutdinova
- Institute of Biochemistry and Genetics of the Ufa Federal Research Centre of the Russian Academy of Sciences, 450054 Ufa, Russia
- Department of Genetics and Fundamental Medicine, Ufa University of Science and Technology, 450076 Ufa, Russia
| | - 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
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Maria A Loizidou
- Department of Cancer Genetics, Therapeutics and Ultrastructural Pathology, The Cyprus Institute of Neurology & Genetics, 2371 Nicosia, Cyprus
| | - Jan Lubiński
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University in Szczecin, 71-252 Szczecin, Poland
| | - 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
- Kuopio University Hospital, Biobank of Eastern Finland, 70210 Kuopio, Finland
| | - Tabea Maurer
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Dimitrios Mavroudis
- Department of Medical Oncology, University Hospital of Heraklion, 711 10 Heraklion, Greece
| | - William G Newman
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9WL, UK
| | - Nadia Obi
- University Medical Center Hamburg-Eppendorf, Institute for Medical Biometry and Epidemiology, 20246 Hamburg, Germany
| | - Mihalis I Panayiotidis
- Department of Cancer Genetics, Therapeutics and Ultrastructural Pathology, The Cyprus Institute of Neurology & Genetics, 2371 Nicosia, Cyprus
| | - Paolo Radice
- Unit of 'Predictive Medicine: Molecular Bases of Genetic Risk', Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), 20133 Milan, Italy
| | - Muhammad U Rashid
- German Cancer Research Center (DKFZ), Molecular Genetics of Breast Cancer, 69120 Heidelberg, Germany
- Department of Basic Sciences, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH & RC), Lahore 54000, Pakistan
| | - Valerie Rhenius
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Matthias Ruebner
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, 91054 Erlangen, Germany
| | | | - Elinor J Sawyer
- King's College London, School of Cancer & Pharmaceutical Sciences, Comprehensive Cancer Centre, Guy's Campus, London SE1 9RT, UK
| | - Marjanka K Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, The Netherlands
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Rita K Schmutzler
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
- Center for Integrated Oncology (CIO), Faculty of Medicine and 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
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia
- Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC 3000, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC 3004, Australia
| | - Ian Tomlinson
- Cancer Research Centre, The University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Thérèse Truong
- CESP U1018, Inserm "Exposome, Heredity, Cancer and Health" Team, UVSQ, University Paris-Saclay, Gustave Roussy, 94805 Villejuif, France
| | - Elke M van Veen
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9WL, UK
| | - Camilla Wendt
- Department of Clinical Science and Education, Karolinska Institutet, Södersjukhuset, 118 83 Stockholm, Sweden
| | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
- Biostatistics Unit, The Cyprus Institute of Neurology & Genetics, 2371 Nicosia, Cyprus
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, 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
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, West Hollywood, CA 90069, USA
| | - 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
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Fred A. Litwin Center for Cancer Genetics, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - D Gareth Evans
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9WL, UK
| | - Antoinette Hollestelle
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands
| | - 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
| | - Roger L Milne
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3168, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Paolo Peterlongo
- Genome Diagnostics Program, IFOM ETS-The AIRC Institute of Molecular Oncology, 20139 Milan, Italy
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Cătană A, Trifa AP, Achimas-Cadariu PA, Bolba-Morar G, Lisencu C, Kutasi E, Chelaru VF, Muntean M, Martin DL, Antone NZ, Fetica B, Pop F, Militaru MS. Hereditary Breast Cancer in Romania-Molecular Particularities and Genetic Counseling Challenges in an Eastern European Country. Biomedicines 2023; 11:biomedicines11051386. [PMID: 37239058 DOI: 10.3390/biomedicines11051386] [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: 02/27/2023] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
In Romania, breast cancer (BC) is the most common malignancy in women. However, there is limited data on the prevalence of predisposing germline mutations in the population in the era of precision medicine, where molecular testing has become an indispensable tool in cancer diagnosis, prognosis, and therapeutics. Therefore, we conducted a retrospective study to determine the prevalence, mutational spectrum, and histopathological prediction factors for hereditary breast cancer (HBC) in Romania. A cohort of 411 women diagnosed with BC selected upon NCCN v.1.2020 guidelines underwent an 84-gene NGS-based panel testing for breast cancer risk assessment during 2018-2022 in the Department of Oncogenetics of the Oncological Institute of Cluj-Napoca, Romania. A total of 135 (33%) patients presented pathogenic mutations in 19 genes. The prevalence of genetic variants was determined, and demographic and clinicopathological characteristics were analyzed. We observed differences among BRCA and non-BRCA carriers regarding family history of cancer, age of onset, and histopathological subtypes. Triple-negative (TN) tumors were more often BRCA1 positive, unlike BRCA2 positive tumors, which were more often the Luminal B subtype. The most frequent non-BRCA mutations were found in CHEK2, ATM, and PALB2, and several recurrent variants were identified for each gene. Unlike other European countries, germline testing for HBC is still limited due to the high costs and is not covered by the National Health System (NSH), thus leading to significant discrepancies related to the screening and prophylaxis of cancer.
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Affiliation(s)
- Andreea Cătană
- Department of Molecular Sciences, Discipline of Medical Genetics, University of Medicine and Pharmacy Iuliu Hațieganu, Victor Babeș 8, 400347 Cluj-Napoca, Romania
- Breast Cancer Tumour Center, Institute of Oncology I. Chiricuță, Republicii Nr. 34-36, 400015 Cluj-Napoca, Romania
| | - Adrian P Trifa
- Breast Cancer Tumour Center, Institute of Oncology I. Chiricuță, Republicii Nr. 34-36, 400015 Cluj-Napoca, Romania
- Discipline of Medical Genetics, University of Medicine and Pharmacy Victor Babeș, Eftimie Murgu 2, 300041 Timișoara, Romania
| | - Patriciu A Achimas-Cadariu
- Breast Cancer Tumour Center, Institute of Oncology I. Chiricuță, Republicii Nr. 34-36, 400015 Cluj-Napoca, Romania
- Department of Oncology, Discipline of Surgery and Gynecological Oncology, University of Medicine and Pharmacy Iuliu Hațieganu, Republicii Nr. 34-36, 400015 Cluj-Napoca, Romania
| | - Gabriela Bolba-Morar
- Breast Cancer Tumour Center, Institute of Oncology I. Chiricuță, Republicii Nr. 34-36, 400015 Cluj-Napoca, Romania
| | - Carmen Lisencu
- Breast Cancer Tumour Center, Institute of Oncology I. Chiricuță, Republicii Nr. 34-36, 400015 Cluj-Napoca, Romania
| | - Eniko Kutasi
- Department of Molecular Sciences, Discipline of Medical Genetics, University of Medicine and Pharmacy Iuliu Hațieganu, Victor Babeș 8, 400347 Cluj-Napoca, Romania
| | - Vlad F Chelaru
- Department of Molecular Sciences, Discipline of Medical Genetics, University of Medicine and Pharmacy Iuliu Hațieganu, Victor Babeș 8, 400347 Cluj-Napoca, Romania
| | - Maximilian Muntean
- Breast Cancer Tumour Center, Institute of Oncology I. Chiricuță, Republicii Nr. 34-36, 400015 Cluj-Napoca, Romania
- Department of Oncology, Discipline of Surgery and Gynecological Oncology, University of Medicine and Pharmacy Iuliu Hațieganu, Republicii Nr. 34-36, 400015 Cluj-Napoca, Romania
| | - Daniela L Martin
- Breast Cancer Tumour Center, Institute of Oncology I. Chiricuță, Republicii Nr. 34-36, 400015 Cluj-Napoca, Romania
| | - Nicoleta Z Antone
- Breast Cancer Tumour Center, Institute of Oncology I. Chiricuță, Republicii Nr. 34-36, 400015 Cluj-Napoca, Romania
| | - Bogdan Fetica
- Breast Cancer Tumour Center, Institute of Oncology I. Chiricuță, Republicii Nr. 34-36, 400015 Cluj-Napoca, Romania
| | - Florina Pop
- Breast Cancer Tumour Center, Institute of Oncology I. Chiricuță, Republicii Nr. 34-36, 400015 Cluj-Napoca, Romania
| | - Mariela S Militaru
- Department of Molecular Sciences, Discipline of Medical Genetics, University of Medicine and Pharmacy Iuliu Hațieganu, Victor Babeș 8, 400347 Cluj-Napoca, Romania
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Godina C, Tryggvadottir H, Bosch A, Borgquist S, Belting M, Isaksson K, Jernström H. Caveolin-1 genotypes as predictor for locoregional recurrence and contralateral disease in breast cancer. Breast Cancer Res Treat 2023; 199:335-347. [PMID: 37017811 PMCID: PMC10175335 DOI: 10.1007/s10549-023-06919-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/18/2023] [Indexed: 04/06/2023]
Abstract
PURPOSE Caveolin-1 (CAV1) has been implicated in breast cancer oncogenesis and metastasis and may be a potential prognosticator, especially for non-distant events. CAV1 functions as a master regulator of membrane transport and cell signaling. Several CAV1 SNPs have been linked to multiple cancers, but the prognostic impact of CAV1 SNPs in breast cancer remains unclear. Here, we investigated CAV1 polymorphisms in relation to clinical outcomes in breast cancer. METHODS A cohort of 1017 breast cancer patients (inclusion 2002-2012, Sweden) were genotyped using Oncoarray by Ilumina. Patients were followed for up to 15 years. Five out of six CAV1 SNPs (rs10256914, rs959173, rs3807989, rs3815412, and rs8713) passed quality control and were used for haplotype construction. CAV1 genotypes and haplotypes in relation to clinical outcomes were assessed with Cox regression and adjusted for potential confounders (age, tumor characteristics, and adjuvant treatments). RESULTS Only one SNP was associated with lymph node status, no other SNPs or haplotypes were associated with tumor characteristics. The CAV1 rs3815412 CC genotype (5.8% of patients) was associated with increased risk of contralateral breast cancer, adjusted hazard ratio (HRadj) 4.26 (95% CI 1.86-9.73). Moreover, the TTACA haplotype (13% of patients) conferred an increased risk for locoregional recurrence HRadj 2.24 (95% CI 1.24-4.04). No other genotypes or haplotypes were associated with clinical outcome. CONCLUSION CAV1 polymorphisms were associated with increased risk for locoregional recurrence and contralateral breast cancer. These findings may identify patients that could derive benefit from more tailored treatment to prevent non-distant events, if confirmed.
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Affiliation(s)
- Christopher Godina
- Division of Oncology, Department of Clinical Sciences in Lund, Lund University and Skåne University Hospital, Barngatan 4, 221 85, Lund, Sweden
| | - Helga Tryggvadottir
- Division of Oncology, Department of Clinical Sciences in Lund, Lund University and Skåne University Hospital, Barngatan 4, 221 85, Lund, Sweden
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Lund and Malmö, Sweden
| | - Ana Bosch
- Division of Oncology, Department of Clinical Sciences in Lund, Lund University and Skåne University Hospital, Barngatan 4, 221 85, Lund, Sweden
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Lund and Malmö, Sweden
| | - Signe Borgquist
- Division of Oncology, Department of Clinical Sciences in Lund, Lund University and Skåne University Hospital, Barngatan 4, 221 85, Lund, Sweden
- Department of Oncology, Aarhus University and Aarhus University Hospital, Aarhus, Denmark
| | - Mattias Belting
- Division of Oncology, Department of Clinical Sciences in Lund, Lund University and Skåne University Hospital, Barngatan 4, 221 85, Lund, Sweden
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Lund and Malmö, Sweden
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Karolin Isaksson
- Division of Surgery, Department of Clinical Sciences in Lund, Lund University and Kristianstad Hospital, Lund and Kristianstad, Sweden
| | - Helena Jernström
- Division of Oncology, Department of Clinical Sciences in Lund, Lund University and Skåne University Hospital, Barngatan 4, 221 85, Lund, Sweden.
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18
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Afzaljavan F, Vahednia E, Barati Bagherabad M, Vakili F, Moezzi A, Hosseini A, Homaei Shandiz F, Kooshyar MM, Nassiri M, Pasdar A. Genetic contribution of caspase-8 variants and haplotypes to breast cancer risk and prognosis: a case-control study in Iran. BMC Med Genomics 2023; 16:72. [PMID: 37016353 PMCID: PMC10071634 DOI: 10.1186/s12920-023-01484-0] [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: 05/27/2022] [Accepted: 03/09/2023] [Indexed: 04/06/2023] Open
Abstract
PURPOSE Multiple genome-wide and candidate-gene association studies have been conducted to search for common risk variants of breast cancer. Recent large meta-analyses and consolidating evidence have highlighted the role of the caspase-8 gene in breast cancer pathogenesis. Therefore, this study aimed to identify common variations and haplotypes associated with risk and overall survival of breast cancer with respect to underlying susceptibility variants in the CASP8 gene region in a group of the Iranian population. METHODS In a case-control study with a total of 1008 samples (455 cases and 553 controls), genotyping of 12 candidate polymorphisms, consisting of rs3834129, rs2037815, rs7608692, rs12990906, rs3769821, rs6435074, rs3754934, rs3817578, rs10931936, rs1045485, rs1045487, and rs13113, were performed using PCR-based methods, including ARMS-PCR, AS-PCR, RFLP-PCR, HRM-PCR, and TaqMan-PCR. RESULTS rs3834129, rs3754934, rs12990906, and rs10931936 were associated with the risk and overall survival of breast cancer. Several haplotypes were also identified an associated with a higher risk of breast cancer, including a three-SNP haplotype rs3817578-rs10931936-rs1045485 [p < 0.001, OR = 1.78(1.32-2.41)]. rs3754934-C allele showed an association with a lower risk of death in all patients [p = 0.022; HR = 0.46(0.23-0.89)] and in the hormone-receptor-positive group [p = 0.038; HR = 0.37(0.14-0.95)], as well as CC genotype in the hormone-receptor-positive group [p = 0.002; HR = 0.09(0.02-0.43)]. CONCLUSION The present study suggests a diagnostic and prognostic role of CASP8 gene variations in breast cancer. The risky haplotypes are likely to have one or more underlying breast cancer susceptibility alleles. Understanding the mode of action of these alleles will aid individual-level risk prediction. It also may help identify at-risk patients to provide them with better surveillance.
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Affiliation(s)
- Fahimeh Afzaljavan
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Elham Vahednia
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Matineh Barati Bagherabad
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Vakili
- Midwifery department, Faculty of Nursing and Midwifery, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Atefeh Moezzi
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Azar Hosseini
- Pharmacological Research Center of Medicinal Plants, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Mohammad Mahdi Kooshyar
- Department of Internal Medicine, Faculty of Medicine, Ghaem Medical Center, Mashhad University of Medical sciences, Mashhad, Iran
| | - Mohammadreza Nassiri
- Recombinant Protein Research Group, The Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Alireza Pasdar
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
- Bioinformatics Research Centre, Mashhad University of Medical Sciences, Mashhad, Iran.
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Qin Z, Li J, Tam B, Sinha S, Zhao B, Bhaskaran SP, Huang T, Wu X, Chian JS, Guo M, Kou SH, Lei H, Zhang L, Wang X, Lagniton PNP, Xiao F, Jiang X, Wang SM. Ethnic-specificity, evolution origin and deleteriousness of Asian BRCA variation revealed by over 7500 BRCA variants derived from Asian population. Int J Cancer 2023; 152:1159-1173. [PMID: 36385461 PMCID: PMC10098510 DOI: 10.1002/ijc.34359] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/23/2022] [Accepted: 11/08/2022] [Indexed: 11/18/2022]
Abstract
Pathogenic variation in BRCA1 and BRCA2 (BRCA) causes high risk of breast and ovarian cancer, and BRCA variation data are important markers for BRCA-related clinical cancer applications. However, comprehensive BRCA variation data are lacking from the Asian population despite its large population size, heterogenous genetic background and diversified living environment across the Asia continent. We performed a systematic study on BRCA variation in Asian population including extensive data mining, standardization, annotation and characterization. We identified 7587 BRCA variants from 685 592 Asian individuals in 40 Asia countries and regions, including 1762 clinically actionable pathogenic variants and 4915 functionally unknown variants (https://genemutation.fhs.um.edu.mo/Asian-BRCA/). We observed the highly ethnic-specific nature of Asian BRCA variants between Asian and non-Asian populations and within Asian populations, highlighting that the current European descendant population-based BRCA data is inadequate to reflect BRCA variation in the Asian population. We also provided archeological evidence for the evolutionary origin and arising time of Asian BRCA variation. We further provided structural-based evidence for the deleterious variants enriched within the functionally unknown Asian BRCA variants. The data from our study provide a current view of BRCA variation in the Asian population and a rich resource to guide clinical applications of BRCA-related cancer for the Asian population.
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Affiliation(s)
- Zixin Qin
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Jiaheng Li
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Benjamin Tam
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Siddharth Sinha
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Bojin Zhao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Shanmuga Priya Bhaskaran
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Teng Huang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Xiaobing Wu
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Jia Sheng Chian
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Maoni Guo
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Si Hoi Kou
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Huijun Lei
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Li Zhang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Xiaoyu Wang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Philip Naderev P Lagniton
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Fengxia Xiao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Xinyang Jiang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - San Ming Wang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
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20
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Wang SM. A global perspective on the ethnic-specific BRCA variation and its implication in clinical application. JOURNAL OF THE NATIONAL CANCER CENTER 2023; 3:14-20. [PMID: 39036311 PMCID: PMC11256725 DOI: 10.1016/j.jncc.2022.12.001] [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: 09/03/2022] [Revised: 11/25/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022] Open
Abstract
Pathogenic BRCA1 and BRCA2 (BRCA) variation is the genetic predisposition for high cancer risk affecting mostly breast and ovarian. BRCA variation information is widely used in clinical diagnosis, treatment, and prevention of BRCA-related cancer. The positive selection imposed on human BRCA leads to highly ethnic-specific BRCA variation to adapt different living environment on earth. Most of the human BRCA variants identified so far were from the European descendant populations and used as the standard reference for global human populations, whereas BRCA variation in other ethnic populations remains poorly characterized. This review addresses the origin of ethnic-specific BRCA variation, the importance of ethnic-specific BRCA variation in clinical application, the limitation of current BRCA variation data, and potential solutions to fill the gap.
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Affiliation(s)
- San Ming Wang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Center and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
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Association of the Estrogen Receptor 1 Polymorphisms rs2046210 and rs9383590 with the Risk, Age at Onset and Prognosis of Breast Cancer. Cells 2023; 12:cells12040515. [PMID: 36831182 PMCID: PMC9953811 DOI: 10.3390/cells12040515] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/16/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Estrogen receptor α (ERα), encoded by the ESR1 gene, is a key prognostic and predictive biomarker firmly established in routine diagnostics and as a therapeutic target of breast cancer, and it has a central function in breast cancer biology. Genetic variants at 6q25.1, containing the ESR1 gene, were found to be associated with breast cancer susceptibility. The rs2046210 and rs9383590 single nucleotide variants (SNVs) are located in the same putative enhancer region upstream of ESR1 and were separately identified as candidate causal variants responsible for these associations. Here, both SNVs were genotyped in a hospital-based case-control study of 409 female breast cancer patients and 422 female controls of a Central European (Austrian) study population. We analyzed the association of both SNVs with the risk, age at onset, clinically and molecularly relevant characteristics and prognosis of breast cancer. We also assessed the concordances between both SNVs and the associations of each SNV conditional on the other SNV. The minor alleles of both SNVs were found to be non-significantly associated with an increased breast cancer risk. Significant associations were found in specific subpopulations, particularly in patients with an age younger than 55 years. The minor homozygotes of rs2046210 and the minor homozygotes plus heterozygotes of rs9383590 exhibited a several-years-younger age at onset than the common homozygotes, which was more pronounced in ER-positive and luminal patients. Importantly, the observed associations of each SNV were not consistently nullified upon correction for the other SNV nor upon analyses in common homozygotes for the other SNV. We conclude that both SNVs remain independent candidate causal variants.
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22
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Robson M. Testing for Inherited Susceptibility to Breast Cancer. Hematol Oncol Clin North Am 2023; 37:17-31. [PMID: 36435609 DOI: 10.1016/j.hoc.2022.08.003] [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: 11/24/2022]
Abstract
When BRCA1 and BRCA2 were first identified, the initial models for delivering testing were shaped by concepts of genetic exceptionalism and a lack of data regarding therapeutic implications and the effectiveness of risk reduction. Since then, interventions have been effective, and treatment implications have become clear. The sensitivity of guideline-based testing is incomplete, leading to calls for universal testing. Completely universal testing, however, is not necessary to identify the great majority of BRCA1 or BRCA2 variants. Broader testing (both in terms of eligibility and genes tested) will identify more variants, particularly in moderate penetrance genes, but the clinical implications remain less clear for these variants.
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Affiliation(s)
- Mark Robson
- Breast Medicine Service, Department of Medicine, Memorial Hospital for Treatment of Cancer and Allied Disease, Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, 300 East 66th Street, Room 813, New York, NY 10065, USA.
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23
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Association of the Telomerase Reverse Transcriptase rs10069690 Polymorphism with the Risk, Age at Onset and Prognosis of Triple Negative Breast Cancer. Int J Mol Sci 2023; 24:ijms24031825. [PMID: 36768147 PMCID: PMC9916321 DOI: 10.3390/ijms24031825] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/04/2023] [Accepted: 01/13/2023] [Indexed: 01/19/2023] Open
Abstract
Telomerase reverse transcriptase (TERT) plays a key role in the maintenance of telomere DNA length. The rs10069690 single nucleotide variant, located in intron 4 of TERT, was found to be associated with telomere length and the risk of estrogen receptor-negative but not-positive breast cancer. This study aimed at analysis of the association of rs10069690 genotype and TERT expression with the risk, age at onset, prognosis, and clinically and molecularly relevant subtypes of breast cancer. Accordingly, rs10069690 was genotyped in a hospital-based case-control study of 403 female breast cancer patients and 246 female controls of a Central European (Austrian) study population, and the mRNA levels of TERT were quantified in 106 primary breast tumors using qRT-PCR. We found that in triple-negative breast cancer patients, the minor rs10069690 TT genotype tended to be associated with an increased breast cancer risk (OR, 1.87; 95% CI, 0.75-4.71; p = 0.155) and was significantly associated with 11.7 years younger age at breast cancer onset (p = 0.0002), whereas the CC genotype was associated with a poor brain metastasis-free survival (p = 0.009). Overall, our data show that the rs10069690 CC genotype and a high TERT expression tended to be associated with each other and with a poor prognosis. Our findings indicate a key role of rs10069690 in triple-negative breast cancer.
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An T, Chen Y, Chen Y, Ma L, Wang J, Zhao J. A machine learning-based approach to ERα bioactivity and drug ADMET prediction. Front Genet 2023; 13:1087273. [PMID: 36685926 PMCID: PMC9845410 DOI: 10.3389/fgene.2022.1087273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/01/2022] [Indexed: 01/05/2023] Open
Abstract
By predicting ERα bioactivity and mining the potential relationship between Absorption, Distribution, Metabolism, Excretion, Toxicity (ADMET) attributes in drug research and development, the development efficiency of specific drugs for breast cancer will be effectively improved and the misjudgment rate of R&D personnel will be reduced. The quantitative prediction model of ERα bioactivity and classification prediction model of Absorption, Distribution, Metabolism, Excretion, Toxicity properties were constructed. The prediction results of ERα bioactivity were compared by XGBoot, Light GBM, Random Forest and MLP neural network. Two models with high prediction accuracy were selected and fused to obtain ERα bioactivity prediction model from Mean absolute error (MAE), mean squared error (MSE) and R2. The data were further subjected to model-based feature selection and FDR/FPR-based feature selection, respectively, and the results were placed in a voting machine to obtain Absorption, Distribution, Metabolism, Excretion, Toxicity classification prediction model. In this study, 430 molecular descriptors were removed, and finally 20 molecular descriptors with the most significant effect on biological activity obtained by the dual feature screening combined optimization method were used to establish a compound molecular descriptor prediction model for ERα biological activity, and further classification and prediction of the Absorption, Distribution, Metabolism, Excretion, Toxicity properties of the drugs were made. Eighty variables were selected by the model ExtraTreesClassifier Classifie, and 40 variables were selected by the model GradientBoostingClassifier to complete the model-based feature selection. At the same time, the feature selection method based on FDR/FPR is also selected, and the three classification models obtained by the two methods are placed into the voting machine to obtain the final model. The experimental results showed that the model's evaluation indexes and roc diagram were excellent and could accurately predict ERα bioactivity and Absorption, Distribution, Metabolism, Excretion, Toxicity properties. The model constructed in this study has high accuracy, fast convergence and robustness, has a very high accuracy for Absorption, Distribution, Metabolism, Excretion, Toxicity and ERα classification prediction, has bright prospects in the biopharmaceutical field, and is an important method for energy conservation and yield increase in the future.
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Affiliation(s)
- Tianbo An
- College of Network Security, Changchun University, Changchun, Jilin, China,Institute of Education, Xiamen University, Xiamen, Fujian, China
| | - Yueren Chen
- College of Network Security, Changchun University, Changchun, Jilin, China
| | - Yefeng Chen
- College of Network Security, Changchun University, Changchun, Jilin, China
| | - Leyu Ma
- College of Network Security, Changchun University, Changchun, Jilin, China
| | - Jingrui Wang
- College of Network Security, Changchun University, Changchun, Jilin, China
| | - Jian Zhao
- College of Computer Science and Technology, Changchun University, Changchun, Jilin, China,*Correspondence: Jian Zhao,
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Kleinbielen T, Olasagasti F, Azcarate D, Beristain E, Viguri-Díaz A, Guerra-Merino I, García-Orad Á, de Pancorbo MM. In silico identification and in vitro expression analysis of breast cancer-related m 6A-SNPs. Epigenetics 2022; 17:2144-2156. [PMID: 35971775 PMCID: PMC9665143 DOI: 10.1080/15592294.2022.2111137] [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: 04/05/2022] [Accepted: 08/01/2022] [Indexed: 12/24/2022] Open
Abstract
Research on m6A-associated SNPs (m6A-SNPs) has emerged recently due to their possible critical roles in many key biological processes. In this sense, several investigations have identified m6A-SNPs in different diseases. In order to gain a more complete understanding of the role that m6A-SNPs can play in breast cancer, we performed an in silico analysis to identify the m6A-SNPs associated with breast cancer and to evaluate their possible effects. For this purpose, we downloaded SNPs related to breast cancer and a list of m6A-SNPs from public databases in order to identify which ones appear in both. Subsequently, we assessed the identified m6A-SNPs in silico by expression quantitative trait loci (eQTL) analysis and differential gene expression analysis. We genotyped the m6A-SNPs found in the in silico analysis in 35 patients with breast cancer, and we carried out a gene expression analysis experimentally on those that showed differences. Our results identified 981 m6A-SNPs related to breast cancer. Four m6A-SNPs showed an eQTL effect and only three were in genes that presented an altered gene expression. When the three m6A-SNPs were evaluated in the tissue sample of our breast cancer patients, only the m6A-SNP rs76563149 located in ZNF354A gene presented differences in allele frequencies and a low gene expression in breast cancer tissues, especially in luminal B HER2+ subtype. Future investigations of these m6A-SNPs should expand the study in different ethnic groups and increase the sample sizes to test their association with breast cancer and elucidate their molecular function.
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Affiliation(s)
- Tamara Kleinbielen
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU. Postal code: 01006. Vitoria-Gasteiz, Araba, Spain
- Department of Zoology and Animal Biology. University of the Basque Country (UPV/EHU). Postal code: 48940. Leioa, Bizkaia, Spain
- Bioaraba Health Research Institute. Postal Code: 01009, Vitoria-Gasteiz, Araba, Spain
| | - Felix Olasagasti
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU. Postal code: 01006. Vitoria-Gasteiz, Araba, Spain
- Bioaraba Health Research Institute. Postal Code: 01009, Vitoria-Gasteiz, Araba, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country, UPV/EHU. Postal code: 01006. Vitoria-Gasteiz, Araba, Spain
| | - Daniel Azcarate
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU. Postal code: 01006. Vitoria-Gasteiz, Araba, Spain
- Department of Zoology and Animal Biology. University of the Basque Country (UPV/EHU). Postal code: 48940. Leioa, Bizkaia, Spain
- Bioaraba Health Research Institute. Postal Code: 01009, Vitoria-Gasteiz, Araba, Spain
| | - Elena Beristain
- Bioaraba Health Research Institute. Postal Code: 01009, Vitoria-Gasteiz, Araba, Spain
- Molecular Genetics Laboratory, Araba University Hospital, Osakidetza Basque Health Service. Postal code: 01009. Vitoria-Gasteiz, Araba, Spain
| | - Amparo Viguri-Díaz
- Pathology Department, Araba University Hospital. Postal code: 01009. Vitoria-Gasteiz, Araba, Spain
| | - Isabel Guerra-Merino
- Bioaraba Health Research Institute. Postal Code: 01009, Vitoria-Gasteiz, Araba, Spain
- Pathology Department, Araba University Hospital. Postal code: 01009. Vitoria-Gasteiz, Araba, Spain
| | - África García-Orad
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU). Postal code: 48940. Leioa, Bizkaia, Spain
- BioCruces Bizkaia Health Research Institute. Postal code: 48903. Barakaldo, Bizkaia, Spain
| | - Marian M. de Pancorbo
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU. Postal code: 01006. Vitoria-Gasteiz, Araba, Spain
- Department of Zoology and Animal Biology. University of the Basque Country (UPV/EHU). Postal code: 48940. Leioa, Bizkaia, Spain
- Bioaraba Health Research Institute. Postal Code: 01009, Vitoria-Gasteiz, Araba, Spain
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26
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Hughes E, Wagner S, Pruss D, Bernhisel R, Probst B, Abkevich V, Simmons T, Hullinger B, Judkins T, Rosenthal E, Roa B, Domchek SM, Eng C, Garber J, Gary M, Klemp J, Mukherjee S, Offit K, Olopade OI, Vijai J, Weitzel JN, Whitworth P, Yehia L, Gordon O, Pederson H, Kurian A, Slavin TP, Gutin A, Lanchbury JS. Development and Validation of a Breast Cancer Polygenic Risk Score on the Basis of Genetic Ancestry Composition. JCO Precis Oncol 2022; 6:e2200084. [PMID: 36331239 PMCID: PMC9666117 DOI: 10.1200/po.22.00084] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 07/11/2022] [Accepted: 09/08/2022] [Indexed: 08/12/2023] Open
Abstract
PURPOSE Polygenic risk scores (PRSs) for breast cancer (BC) risk stratification have been developed primarily in women of European ancestry. Their application to women of non-European ancestry has lagged because of the lack of a formal approach to incorporate genetic ancestry and ancestry-dependent variant frequencies and effect sizes. Here, we propose a multiple-ancestry PRS (MA-PRS) that addresses these issues and may be useful in the development of equitable PRSs across other cancers and common diseases. MATERIALS AND METHODS Women referred for hereditary cancer testing were divided into consecutive cohorts for development (n = 189,230) and for independent validation (n = 89,126). Individual genetic composition as fractions of three reference ancestries (African, East Asian, and European) was determined from ancestry-informative single-nucleotide polymorphisms. The MA-PRS is a combination of three ancestry-specific PRSs on the basis of genetic ancestral composition. Stratification of risk was evaluated by multivariable logistic regression models controlling for family cancer history. Goodness-of-fit analysis compared expected with observed relative risks by quantiles of the MA-PRS distribution. RESULTS In independent validation, the MA-PRS was significantly associated with BC risk in the full cohort (odds ratio, 1.43; 95% CI, 1.40 to 1.46; P = 8.6 × 10-308) and within each major ancestry. The top decile of the MA-PRS consistently identified patients with two-fold increased risk of developing BC. Goodness-of-fit tests showed that the MA-PRS was well calibrated and predicted BC risk accurately in the tails of the distribution for both European and non-European women. CONCLUSION The MA-PRS uses genetic ancestral composition to expand the utility of polygenic risk prediction to non-European women. Inclusion of genetic ancestry in polygenic risk prediction presents an opportunity for more personalized treatment decisions for women of varying and mixed ancestries.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Susan M. Domchek
- Basser Center for BRCA, University of Pennsylvania, Philadelphia, PA
| | - Charis Eng
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH
| | | | | | - Jennifer Klemp
- The University of Kansas Cancer Center, The University of Kansas Medical Center, Kansas City, KS
| | | | - Kenneth Offit
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Joseph Vijai
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Lamis Yehia
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH
| | - Ora Gordon
- Providence Health and Services, Renton, WA
| | - Holly Pederson
- Medical Breast Services, Cleveland Clinic, Cleveland, OH
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Matrix Metalloproteinase Gene Polymorphisms Are Associated with Breast Cancer in the Caucasian Women of Russia. Int J Mol Sci 2022; 23:ijms232012638. [PMID: 36293492 PMCID: PMC9604098 DOI: 10.3390/ijms232012638] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/14/2022] [Accepted: 10/15/2022] [Indexed: 12/04/2022] Open
Abstract
We conducted this study to explore the association between matrix metalloproteinase (MMP) gene polymorphisms and breast cancer (BC) risk in the Caucasian women of Russia. In total, 358 affected (BC) and 746 unaffected (cancer-free) women were included in this case-control retrospective study. From BC-related genes in previous studies, ten single nucleotide polymorphisms (SNPs) in five MMP genes (MMP1, 2, 3, 8, 9) were genotyped. The BC risk was calculated by logistic regression (to evaluate the SNPs’ independent effects) and model-based multifactor dimensionality reduction (MB-MDR) (to identify SNP−SNP interactions) methods. The allelic variants’ distribution of c.836 A > G (rs17576) and c. 1721 C > G (rs2250889) MMP9 was significantly different between BC and cancer-free women: for G minor alleles, these SNPs manifested disorder protective effects (OR 0.82 and OR 0.67−0.71, respectively, pperm ≤ 0.035). Eleven haplotypes of six SNPs MMP9 were involved in BC risk (nine haplotypes) and protective (two haplotypes) effects. All 10 SNPs of the MMP genes examined were associated with BC within the 13 SNP−SNP interaction simulated models, with a pivotal role of the two-locus (rs17577 × rs3918242) MMP9 epistatic interaction (defined as 1.81% BC entropy within more than 60% of the genetic models). Under in silico bioinformatics, BC susceptibility MMP polymorphic loci are located in functionally active genome regions and impact genes expression and splicing “regulators” in the mammary gland. The biological pathways of BC MMP candidate genes are mainly realized due to metalloendopeptidase activity and extracellular matrix organization (structure, disassembly, metabolic process, etc.). In conclusion, our data show that MMP gene polymorphisms are related to BC susceptibility in the Caucasian women of Russia.
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The Modifying Effect of Obesity on the Association of Matrix Metalloproteinase Gene Polymorphisms with Breast Cancer Risk. Biomedicines 2022; 10:biomedicines10102617. [PMID: 36289879 PMCID: PMC9599943 DOI: 10.3390/biomedicines10102617] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/10/2022] [Accepted: 10/13/2022] [Indexed: 11/17/2022] Open
Abstract
Objective: We investigated the possible modifying effect of obesity on the association of matrix metalloproteinase (MMP) gene polymorphisms with breast cancer (BC) risk. Methods: A total of 1104 women divided into two groups according to their body mass index (BMI): BMI ≥ 30 (119 BC, and 190 control) and BMI < 30 (239 BC, and 556 control) were genotyped for specially selected (according to their association with BC in the previous study) 10 single-nucleotide polymorphisms (SNP) of MMP1, 2, 3, 8, and 9 genes. Logistic regression association analysis was performed in each studied group of women (with/without obesity). Functional annotation of BC-correlated MMP polymorphic variants was analyzed by in silico bioinformatics. Results: We observed significant differences in the involvement of MMP SNPs in BC in obese and non-obese women. Polymorphic loci MMP9 (c.836 A > G (rs17576) and c. 1721 C > G (rs2250889)) were BC-protective factors in obese women (OR 0.71, allelic model, and OR 0.55, additive model, respectively). Genotypes TT MMP2 (c.-1306 C > T,rs243865) and AA MMP9 (c. 1331-163 G > A,rs3787268) determined BC susceptibility in non-obese women (OR 0.31, and OR 2.36, respectively). We found in silico substantial multidirectional influences on gene expression in adipose tissue BC-related polymorphic loci: BC risk allele A-rs3787268 in non-obese women is associated with low expression NEURL2, PLTP, RP3-337O18.9, SPATA25, and ZSWIM1, whereas BC risk allele A-rs17576 in obese women is associated with high expression in the same genes in visceral and/or subcutaneous adipose. Conclusions: our study indicated that obesity has a significant modifying effect on the association of MMP genes with BC risk in postmenopausal women.
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Breast cancer polygenic risk scores are associated with short-term risk of poor prognosis breast cancer. Breast Cancer Res Treat 2022; 196:389-398. [PMID: 36138293 DOI: 10.1007/s10549-022-06739-5] [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: 06/15/2022] [Accepted: 09/04/2022] [Indexed: 11/02/2022]
Abstract
PURPOSE Polygenic risk scores (PRS) for breast cancer may help guide screening decisions. However, few studies have examined whether PRS are associated with risk of short-term or poor prognosis breast cancers. The study purpose was to evaluate the association of the 313 SNP breast cancer PRS with 2-year risk of poor prognosis breast cancer. METHODS We evaluated the association of breast cancer PRS with breast cancer overall, ER + and ER- breast cancer, and poor prognosis breast cancer diagnosed within 2 years of a negative mammogram among a cohort of 3657 women using logistic regression adjusted for age, breast density, race/ethnicity, year of screening, and genetic ancestry principal components. Breast cancers were considered poor prognosis if they were metastatic, positive lymph nodes, ER/PR + HER2- and > 2 cm, ER/PR/HER2-, or HER2 + and > 1 cm. RESULTS Of the 308 breast cancers, 137 (44%) were poor prognosis. The overall breast cancer PRS was significantly associated with breast cancer diagnosis within 2 years (OR 1.39, 95% CI 1.23-1.57, p < 0.001). The breast cancer PRS was also associated specifically with diagnosis of poor prognosis disease (OR 1.24, 95% CI 1.03-1.49, p = 0.018), but was more strongly associated with good prognosis cancer (OR 1.52 95% CI 1.29-1.80 p = 3.60 × 10-7) The ER + PRS was significantly associated with ER/PR + breast cancer (OR 1.41, 95% CI 1.24-1.61, p < 0.001) and the ER- PRS was significantly associated with ER- breast cancer (OR 1.48, 95% CI 1.08-2.02, p = 0.015). CONCLUSION Breast cancer PRS was independently and significantly associated with diagnosis of both breast cancer overall and poor prognosis breast cancer within 2 years of a negative mammogram, suggesting PRS may help guide decisions about screening intervals and supplemental screening.
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HSPA5 Could Be a Prognostic Biomarker Correlated with Immune Infiltration in Breast Cancer. DISEASE MARKERS 2022; 2022:7177192. [PMID: 36193502 PMCID: PMC9526594 DOI: 10.1155/2022/7177192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/17/2022] [Indexed: 11/22/2022]
Abstract
Background Breast cancer (BC) is a frequent disease in females. The heat shock 70 kDa protein 5 (HSPA5) has recently been discovered to have an important function in tumor growth. However, the biological significance of HSPA5 in BC is unknown. Material and Method. Firstly, The Cancer Genome Atlas (TCGA) database was applied to analyze the expressions of HSPA5 in different cancer types, especially in BC. Then, the LinkedOmics database was used to screen genes coexpressed with HSPA5 in BC, presented by protein-protein interaction (PPI) and analyzed by functional enrichment analyses. Next, the Kaplan-Meier plotter was adopted to study the prognostic significance of HSPA5 and the relation between HSPA5 expression and different clinical factors in BC. Finally, the Tumor Immune Estimation Resource (TIMER) method was adopted to explore the relation between immune infiltration and HSPA5 in BC. Result HSPA5 was highly expressed in most cancers, including BC. Genes coexpressed with HSPA5 were mainly related to endoplasmic reticulum unfolded protein response, melanosome, thyroid hormone synthesis, N-glycan biosynthesis, and so on. In the survival analysis, high HSPA5 expression indicated a poor prognosis in BC, and the expression of HSPA5 in BC was elevated after the incidence of BC, changing with different clinical factors. In the immune infiltration, HSPA5 was positively correlated with most immune cells. Conclusion HSPA5 is an oncogene in BC progression, and it is connected with the prognosis and the immune infiltration in BC. Our findings suggest that HSPA5 could be an immunotherapy target and a prognostic biomarker in BC.
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Loveday C, Garrett A, Law P, Hanks S, Poyastro-Pearson E, Adlard JW, Barwell J, Berg J, Brady AF, Brewer C, Chapman C, Cook J, Davidson R, Donaldson A, Douglas F, Greenhalgh L, Henderson A, Izatt L, Kumar A, Lalloo F, Miedzybrodzka Z, Morrison PJ, Paterson J, Porteous M, Rogers MT, Walker L, Eccles D, Evans DG, Snape K, Hanson H, Houlston RS, Turnbull C. Analysis of rare disruptive germline mutations in 2,135 enriched BRCA-negative breast cancers excludes additional high-impact susceptibility genes. Ann Oncol 2022; 33:1318-1327. [PMID: 36122798 DOI: 10.1016/j.annonc.2022.09.152] [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: 03/03/2022] [Revised: 08/15/2022] [Accepted: 09/01/2022] [Indexed: 11/01/2022] Open
Abstract
BACKGROUND Breast cancer has a significant heritable basis, of which approximately 60% remains unexplained. Testing for BRCA1/BRCA2 offers useful discrimination of breast cancer risk within families, and identification of additional breast cancer susceptibility genes could offer clinical utility. PATIENTS AND METHODS We included 2,135 invasive breast cancer cases recruited via the BOCS study, a retrospective UK study of familial breast cancer. ELIGIBILITY CRITERIA female, BRCA-negative, white European ethnicity, and one of: i) breast cancer family history, ii) bilateral disease, iii) young age of onset (<30 years), iv) concomitant ovarian cancer. We undertook exome sequencing of cases and performed gene-level burden testing of rare damaging variants against those from 51,377 ethnicity-matched population controls from gnomAD. RESULTS 159/2135 (7.4%) cases had a qualifying variant in an established breast cancer susceptibility gene, with minimal evidence of signal in other cancer susceptibility genes. Known breast cancer susceptibility genes PALB2, CHEK2 and ATM were the only genes to retain statistical significance after correcting for multiple testing. Due to the enrichment of hereditary cases in the series, we had good power (>80%) to detect a gene of BRCA1-like risk (odds ratio = 10.6) down to a population minor allele frequency of 4.6 x 10-5 (1 in 10,799, less than one tenth that of BRCA1)and of PALB2-like risk (odds ratio = 5.0) down to a population minor allele frequency of 2.8 x 10-4 (1 in 1,779, less than half that of PALB2). Power was lower for identification of novel moderate penetrance genes (odds ratio = 2-3) like CHEK2 and ATM. CONCLUSIONS This is the largest case-control whole-exome analysis of enriched breast cancer published to date. Whilst additional breast cancer susceptibility genes likely exist, those of high penetrance are likely to be of very low mutational frequency. Contention exists regarding the clinical utility of such genes.
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Affiliation(s)
- C Loveday
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - A Garrett
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - P Law
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - S Hanks
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - E Poyastro-Pearson
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - J W Adlard
- Yorkshire Regional Genetics Service, St James's University Hospital, Leeds, UK
| | - J Barwell
- Leicestershire Genetics Centre, University Hospitals of Leicester National Health Service (NHS) Trust, Leicester, UK
| | - J Berg
- Division of Medical Sciences, Human Genetics, University of Dundee, Dundee, UK
| | - A F Brady
- North West Thames Regional Genetics Service, Kennedy Galton Centre, London, UK
| | - C Brewer
- Peninsula Regional Genetics Service, Royal Devon & Exeter Hospital, Exeter, UK
| | - C Chapman
- West Midlands Regional Genetics Service, Birmingham Women's Hospital, Birmingham, UK
| | - J Cook
- Sheffield Regional Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - R Davidson
- West of Scotland Regional Genetics Service, Ferguson Smith Centre for Clinical Genetics, Glasgow, UK
| | - A Donaldson
- South Western Regional Genetics Service, University Hospitals of Bristol NHS Foundation Trust, Bristol, UK
| | - F Douglas
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - L Greenhalgh
- Cheshire and Merseyside Clinical Genetics Service, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | - A Henderson
- Northern Genetics Service (Cumbria), Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne, UK
| | - L Izatt
- South East Thames Regional Genetics Service, Guy's and St. Thomas NHS Foundation Trust, London, UK
| | - A Kumar
- North East Thames Regional Genetics Service, Great Ormond St. Hospital, London, UK
| | - F Lalloo
- University Department of Medical Genetics & Regional Genetics Service, St. Mary's Hospital, Manchester, UK
| | - Z Miedzybrodzka
- University of Aberdeen and North of Scotland Clinical Genetics Service, Aberdeen Royal Infirmary, Aberdeen, UK
| | - P J Morrison
- Belfast Health and Social Care (HSC) Trust & Department of Medical Genetics, Northern Ireland Regional Genetics Service, Queen's University Belfast, Belfast, UK
| | - J Paterson
- East Anglian Regional Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - M Porteous
- South East of Scotland Clinical Genetics Service, Western General Hospital, Edinburgh, UK
| | - M T Rogers
- All Wales Medical Genetics Service, University Hospital of Wales, Cardiff, UK
| | - L Walker
- Oxford Regional Genetics Service, Oxford Radcliffe Hospitals NHS Trust, Oxford, UK
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- Individual collaborators and their affiliations are listed in the Appendix
| | - D Eccles
- Faculty of Medicine, University of Southampton, Southampton University Hospitals NHS Trust, Southampton, UK
| | - D G Evans
- University Department of Medical Genetics & Regional Genetics Service, St. Mary's Hospital, Manchester, UK
| | - K Snape
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.; South West Thames Regional Genetics Service, St. George's Hospital, London, UK
| | - H Hanson
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.; South West Thames Regional Genetics Service, St. George's Hospital, London, UK
| | - R S Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - C Turnbull
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.; Royal Marsden NHS Foundation Hospital, London, UK.
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Gao G, Zhao F, Ahearn TU, Lunetta KL, Troester MA, Du Z, Ogundiran TO, Ojengbede O, Blot W, Nathanson KL, Domchek SM, Nemesure B, Hennis A, Ambs S, McClellan J, Nie M, Bertrand K, Zirpoli G, Yao S, Olshan AF, Bensen JT, Bandera EV, Nyante S, Conti DV, Press MF, Ingles SA, John EM, Bernstein L, Hu JJ, Deming-Halverson SL, Chanock SJ, Ziegler RG, Rodriguez-Gil JL, Sucheston-Campbell LE, Sandler DP, Taylor JA, Kitahara CM, O’Brien KM, Bolla MK, Dennis J, Dunning AM, Easton DF, Michailidou K, Pharoah PDP, Wang Q, Figueroa J, Biritwum R, Adjei E, Wiafe S, Ambrosone CB, Zheng W, Olopade OI, García-Closas M, Palmer JR, Haiman CA, Huo D. Polygenic risk scores for prediction of breast cancer risk in women of African ancestry: a cross-ancestry approach. Hum Mol Genet 2022; 31:3133-3143. [PMID: 35554533 PMCID: PMC9476624 DOI: 10.1093/hmg/ddac102] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/29/2022] [Accepted: 04/26/2022] [Indexed: 11/13/2022] Open
Abstract
Polygenic risk scores (PRSs) are useful for predicting breast cancer risk, but the prediction accuracy of existing PRSs in women of African ancestry (AA) remains relatively low. We aim to develop optimal PRSs for the prediction of overall and estrogen receptor (ER) subtype-specific breast cancer risk in AA women. The AA dataset comprised 9235 cases and 10 184 controls from four genome-wide association study (GWAS) consortia and a GWAS study in Ghana. We randomly divided samples into training and validation sets. We built PRSs using individual-level AA data by a forward stepwise logistic regression and then developed joint PRSs that combined (1) the PRSs built in the AA training dataset and (2) a 313-variant PRS previously developed in women of European ancestry. PRSs were evaluated in the AA validation set. For overall breast cancer, the odds ratio per standard deviation of the joint PRS in the validation set was 1.34 [95% confidence interval (CI): 1.27-1.42] with the area under receiver operating characteristic curve (AUC) of 0.581. Compared with women with average risk (40th-60th PRS percentile), women in the top decile of the PRS had a 1.98-fold increased risk (95% CI: 1.63-2.39). For PRSs of ER-positive and ER-negative breast cancer, the AUCs were 0.608 and 0.576, respectively. Compared with existing methods, the proposed joint PRSs can improve prediction of breast cancer risk in AA women.
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Affiliation(s)
- Guimin Gao
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Fangyuan Zhao
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Thomas U Ahearn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20850, USA
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Melissa A Troester
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Zhaohui Du
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Temidayo O Ogundiran
- Department of Surgery, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oladosu Ojengbede
- Centre for Population & Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - William Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Katherine L Nathanson
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Susan M Domchek
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Barbara Nemesure
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Anselm Hennis
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY 11794, USA
- University of the West Indies, Bridgetown, Bardados
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Julian McClellan
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Mark Nie
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA
| | | | - Gary Zirpoli
- Slone Epidemiology Center, Boston University, Boston, MA 02215, USA
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14203, USA
| | - Andrew F Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeannette T Bensen
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Elisa V Bandera
- Cancer Prevention and Control Program, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Sarah Nyante
- Department of Radiology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - David V Conti
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Michael F Press
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Sue A Ingles
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Esther M John
- Departments of Epidemiology & Population Health and of Medicine (Oncology) and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Leslie Bernstein
- Biomarkers of Early Detection and Prevention, Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Jennifer J Hu
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Sandra L Deming-Halverson
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20850, USA
| | - Regina G Ziegler
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20850, USA
| | - Jorge L Rodriguez-Gil
- Genomics, Development and Disease Section, Genetic Disease Research Branch, National Human Genome Research Institute, Bethesda, MD 20894, USA
| | - Lara E Sucheston-Campbell
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Cari M Kitahara
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Katie M O’Brien
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Manjeet K Bolla
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Joe Dennis
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Alison M Dunning
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Douglas F Easton
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology & Genetics, Nicosia 2371, Cyprus
| | - Paul D P Pharoah
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Qin Wang
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Jonine Figueroa
- Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh Medical School, Edinburgh EH16 5TJ, UK
- Cancer Research UK Edinburgh Centre, Edinburgh EH4 2XR, UK
| | | | | | - Seth Wiafe
- School of Public Health, Loma Linda University, Loma Linda, CA 92350, USA
| | | | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14203, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics & Global Health, The University of Chicago, Chicago, IL 60637, USA
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20850, USA
| | - Julie R Palmer
- Slone Epidemiology Center, Boston University, Boston, MA 02215, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Dezheng Huo
- Department of Public Health Sciences, The University of Chicago, Chicago, IL 60637, USA
- Center for Clinical Cancer Genetics & Global Health, The University of Chicago, Chicago, IL 60637, USA
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Hu GN, Wang Y, Tang CH, Jin LL, Huang BF, Wang Q, Shao JK, Wang CQ, Su CM. The impact of Angiopoietin-2 genetic polymorphisms on susceptibility for malignant breast neoplasms. Sci Rep 2022; 12:14522. [PMID: 36008514 PMCID: PMC9411117 DOI: 10.1038/s41598-022-18712-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 08/18/2022] [Indexed: 11/08/2022] Open
Abstract
Breast cancer causes morbidity and mortality among women worldwide, despite much research illuminating the genetic basis of this disease. Anti-angiogenesis therapies have been widely studied, although the association between angiopoietin-2 (ANGPT2) single nucleotide polymorphisms (SNPs) and breast cancer subtypes remains unclear. This case-control study included 464 patients with malignant breast neoplasms and 539 cancer-free females. We explored the effects of ANGPT2 SNPs on the susceptibility for a malignant breast neoplasm in a Chinese Han population. Five ANGPT2 SNPs (rs2442598, rs734701, rs1823375, 11,137,037, and rs12674822) were analyzed using TaqMan SNP genotyping. Carriers of the variant GG allele of rs1823375 were less likely than wild-type carriers to be diagnosed with clinically staged breast cancer, while females with human epidermal growth factor receptor 2 (HER2)-enriched disease carrying the CG or the CG+GG genotype at rs1823375 were significantly less likely than CC genotype carriers to be of lymph node status N1-N3. We also found that the T-T-C-A-T ANGPT2 haplotype significantly increased the risk for developing a malignant breast neoplasm by 1.385-fold (95% CI: 1.025-1.871; p < 0.05). Our study is the first to document a correlation between ANGPT2 polymorphisms and the development and progression of a malignant breast neoplasm in females of Chinese Han ethnicity.
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Affiliation(s)
- Gui-Nv Hu
- Department of Surgical Oncology, Affiliated Dongyang Hospital of Wenzhou Medical University, Dongyang, Zhejiang, China
| | - Yan Wang
- Department of Medical Oncology, Affiliated Dongyang Hospital of Wenzhou Medical University, Dongyang, Zhejiang, China
| | - Chih-Hsin Tang
- Department of Pharmacology, School of Medicine, China Medical University, Taichung, Taiwan
- Chinese Medicine Research Center, China Medical University, Taichung, Taiwan
- Department of Biotechnology, College of Health Science, Asia University, Taichung, Taiwan
| | - Lu-Lu Jin
- Department of Biomedical Sciences Laboratory, Affiliated Dongyang Hospital of Wenzhou Medical University, Dongyang, Zhejiang, China
| | - Bi-Fei Huang
- Department of Pathology, Affiliated Dongyang Hospital of Wenzhou Medical University, Dongyang, Zhejiang, 322100, China
| | - Qian Wang
- Department of Pathology, Affiliated Dongyang Hospital of Wenzhou Medical University, Dongyang, Zhejiang, 322100, China
| | - Jun-Kang Shao
- Department of Pathology, Affiliated Dongyang Hospital of Wenzhou Medical University, Dongyang, Zhejiang, 322100, China
| | - Chao-Qun Wang
- Department of Pathology, Affiliated Dongyang Hospital of Wenzhou Medical University, Dongyang, Zhejiang, 322100, China.
| | - Chen-Ming Su
- Department of Sports Medicine, China Medical University, Taichung, 406040, Taiwan.
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Fashina A, Busch T, Young M, Adamson O, Awotoye W, Alade A, Adeleke C, Hassan M, Oladayo AM, Gowans LJJ, Eshete M, Naicker T, Olotu J, Adeyemo WL, Butali A. Investigating the relationship between cancer and orofacial clefts using GWAS significant loci for cancers: A case-control and case-triad study. FRONTIERS IN ORAL HEALTH 2022; 3:915361. [PMID: 35990505 PMCID: PMC9388935 DOI: 10.3389/froh.2022.915361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 07/15/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundSeveral population-based case-control studies have reported concurrent presentation of cancer and congenital malformations. Many associations have been made between oral clefting and cancers, though some of these results are conflicting. Some studies have reported an increased risk of cancer among 1st-degree relatives of cleft cases and vice versa, and also an excess risk of cancers of the breast, lung, and brain among those with oral clefts. This study aimed to determine if the genetic polymorphisms found in some cancers are also associated with orofacial cleft in an African cohort.MethodsThe study was a case-control and case-triad study in which cases were 400 individuals clinically diagnosed with non-syndromic cleft lip and/or palate (CL/P), while controls were 450 individuals without CL/P. Samples were obtained from three African countries while DNA extraction, PCR, and genotyping were carried out at the University of Iowa, US. Eleven SNPs in genes coding for SWI/SNF subunits and 13 GWAS significant SNPs for cancers associated with orofacial cleft were selected. Case-control analysis, transmission disequilibrium test (TDT), and DFAM to combine the parent-offspring trio data and unrelated case/control data in a single analysis were carried out using PLINK.ResultsFor the case-control analyses that included all the clefts and for the CLP subtype, none of the SNPs were statistically significant. Statistically increased risk for the following SNPs rs34775372 (p = 0.02; OR = 1.54, CI:1.07–2.22), rs55658222 (p = 0.009; OR = 2.64, CI:1.28–5.45) and rs72728755 (p = 0.02; OR=2.27, CI:1.17–4.45) was observed with the CL only sub-group. None of these were significant after Bonferoni correction. In the TDT analyses, a significantly reduced risk with rs10941679 (p = 0.003; OR = 0.43, CI:0.24–0.75) was observed and this was significant after Bonferroni correction. The rs10941679 was also significant (p = 0.003) in the DFAM analyses as well even after Bonferroni correction.ConclusionThe results from this study represent an important starting point for understanding the concurrent presentation of some cancers in orofacial clefts, and cancer risks in cleft patients. The associations observed warrant further investigation in a larger cohort and will set the stage for a more mechanistic approach toward understanding the risk for cancers in families with clefts.
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Affiliation(s)
- Azeez Fashina
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos, Nigeria
- *Correspondence: Azeez Fashina
| | - Tamara Busch
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, United States
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, United States
| | - Mary Young
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, United States
| | - Olawale Adamson
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos, Nigeria
| | - Waheed Awotoye
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, United States
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, United States
| | - Azeez Alade
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, United States
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, United States
| | - Chinyere Adeleke
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, United States
| | - Mohaned Hassan
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, United States
| | - Abimbola M. Oladayo
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, United States
| | - Lord J. J. Gowans
- Komfo Anokye Teaching Hospital, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Mekonen Eshete
- Department of Surgery, School of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - Thirona Naicker
- School of Clinical Medicine, KwaZulu-Natal University, Durban, South Africa
| | - Joy Olotu
- Department of Anatomy, University of Port Harcourt, Port Harcourt, Nigeria
| | - Wasiu L. Adeyemo
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos, Nigeria
| | - Azeez Butali
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, United States
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, United States
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Role of Polygenic Risk Score in Cancer Precision Medicine of Non-European Populations: A Systematic Review. Curr Oncol 2022; 29:5517-5530. [PMID: 36005174 PMCID: PMC9406904 DOI: 10.3390/curroncol29080436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 11/17/2022] Open
Abstract
The development of new screening methods and diagnostic tests for traits, common diseases, and cancer is linked to the advent of precision genomic medicine, in which health care is individually adjusted based on a person’s lifestyle, environmental influences, and genetic variants. Based on genome-wide association study (GWAS) analysis, rapid and continuing progress in the discovery of relevant single nucleotide polymorphisms (SNPs) for traits or complex diseases has increased interest in the potential application of genetic risk models for routine health practice. The polygenic risk score (PRS) estimates an individual’s genetic risk of a trait or disease, calculated by employing a weighted sum of allele counts combined with non-genetic variables. However, 98.38% of PRS records held in public databases relate to the European population. Therefore, PRSs for multiethnic populations are urgently needed. We performed a systematic review to discuss the role of polygenic risk scores in advancing precision medicine for different cancer types in multiethnic non-European populations.
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Zavala VA, Casavilca-Zambrano S, Navarro-Vásquez J, Castañeda CA, Valencia G, Morante Z, Calderón M, Abugattas JE, Gómez H, Fuentes HA, Liendo-Picoaga R, Cotrina JM, Monge C, Neciosup SP, Huntsman S, Hu D, Sánchez SE, Williams MA, Núñez-Marrero A, Godoy L, Hechmer A, Olshen AB, Dutil J, Ziv E, Zabaleta J, Gelaye B, Vásquez J, Gálvez-Nino M, Enriquez-Vera D, Vidaurre T, Fejerman L. Association between Ancestry-Specific 6q25 Variants and Breast Cancer Subtypes in Peruvian Women. Cancer Epidemiol Biomarkers Prev 2022; 31:1602-1609. [PMID: 35654312 PMCID: PMC9662925 DOI: 10.1158/1055-9965.epi-22-0069] [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: 01/20/2022] [Revised: 03/07/2022] [Accepted: 05/23/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Breast cancer incidence in the United States is lower in Hispanic/Latina (H/L) compared with African American/Black or Non-Hispanic White women. An Indigenous American breast cancer-protective germline variant (rs140068132) has been reported near the estrogen receptor 1 gene. This study tests the association of rs140068132 and other polymorphisms in the 6q25 region with subtype-specific breast cancer risk in H/Ls of high Indigenous American ancestry. METHODS Genotypes were obtained for 5,094 Peruvian women with (1,755) and without (3,337) breast cancer. Associations between genotype and overall and subtype-specific risk for the protective variant were tested using logistic regression models and conditional analyses, including other risk-associated polymorphisms in the region. RESULTS We replicated the reported association between rs140068132 and breast cancer risk overall [odds ratio (OR), 0.53; 95% confidence interval (CI), 0.47-0.59], as well as the lower odds of developing hormone receptor negative (HR-) versus HR+ disease (OR, 0.77; 95% CI, 0.61-0.97). Models, including HER2, showed further heterogeneity with reduced odds for HR+HER2+ (OR, 0.68; 95% CI, 0.51-0.92), HR-HER2+ (OR, 0.63; 95% CI, 0.44-0.90) and HR-HER2- (OR, 0.77; 95% CI, 0.56-1.05) compared with HR+HER2-. Inclusion of other risk-associated variants did not change these observations. CONCLUSIONS The rs140068132 polymorphism is associated with decreased risk of breast cancer in Peruvians and is more protective against HR- and HER2+ diseases independently of other breast cancer-associated variants in the 6q25 region. IMPACT These results could inform functional analyses to understand the mechanism by which rs140068132-G reduces risk of breast cancer development in a subtype-specific manner. They also illustrate the importance of including diverse individuals in genetic studies.
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Affiliation(s)
- Valentina A. Zavala
- Department of Public Health Sciences, University of California Davis, Davis, California
| | | | | | | | | | - Zaida Morante
- Instituto Nacional de Enfermedades Neoplasicas, Lima, Peru
| | | | | | - Henry Gómez
- Instituto Nacional de Enfermedades Neoplasicas, Lima, Peru
| | | | | | | | - Claudia Monge
- Instituto Nacional de Enfermedades Neoplasicas, Lima, Peru
| | | | - Scott Huntsman
- Division of General Internal Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Donglei Hu
- Division of General Internal Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Sixto E. Sánchez
- Universidad Peruana de Ciencias Aplicadas, Lima, Peru and Asociación Civil Proyectos en Salud (PROESA), Lima, Peru
| | - Michelle A. Williams
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Angel Núñez-Marrero
- Department of Biochemistry, Cancer Biology Division, Ponce Research Institute, Ponce Health Sciences University, Ponce, Puerto Rico
| | - Lenin Godoy
- Department of Biochemistry, Cancer Biology Division, Ponce Research Institute, Ponce Health Sciences University, Ponce, Puerto Rico
| | - Aaron Hechmer
- Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Adam B. Olshen
- Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Julie Dutil
- Department of Biochemistry, Cancer Biology Division, Ponce Research Institute, Ponce Health Sciences University, Ponce, Puerto Rico
| | - Elad Ziv
- Division of General Internal Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Jovanny Zabaleta
- Department of Pediatrics and Stanley S. Scott Cancer Center LSUHSC, New Orleans, Louisiana
| | - Bizu Gelaye
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jule Vásquez
- Instituto Nacional de Enfermedades Neoplasicas, Lima, Peru
| | | | | | | | - Laura Fejerman
- Department of Public Health Sciences, University of California Davis, Davis, California
- UC Davis Comprehensive Cancer Center, University of California Davis, Davis, California
- Corresponding Author: Laura Fejerman, UC Davis Comprehensive Cancer Center, 451 Health Sciences Drive, Davis, CA 95616. Phone: 530-754-1690; E-mail:
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Brédart A, De Pauw A, Tüchler A, Lakeman IMM, Anota A, Rhiem K, Schmutzler R, van Asperen CJ, Devilee P, Stoppa-Lyonnet D, Kop JL, Dolbeault S. Genetic clinicians' confidence in BOADICEA comprehensive breast cancer risk estimates and counselees' psychosocial outcomes: a prospective study. Clin Genet 2022; 102:30-39. [PMID: 35508697 PMCID: PMC9322298 DOI: 10.1111/cge.14147] [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: 02/22/2022] [Revised: 04/27/2022] [Accepted: 05/01/2022] [Indexed: 11/29/2022]
Abstract
Counseling for familial breast cancer focuses on communicating the gene test result (GENE) to counselees, but risk prediction models have become more complex by including non‐genetic risk factors (NGRF) and polygenic risk scores (PRS). We examined genetic clinicians' confidence in counseling and counselees' psychosocial outcomes, using the BOADICEA risk prediction tool with different categories of risk factors as input. A prospective observational study in Dutch, French and German genetic clinics was performed including 22 clinicians, and 406 of 460 (88.3%) eligible cancer‐unaffected women at high breast cancer risk assessed at pre‐test and 350 (76.1%) at post‐test. We performed multilevel analyses accounting for the clinician, and counselees' characteristics. Overall, risk estimates category by GENE versus GENE+ NGRF, or GENE+NGRF+PRS differed in 11% and 25% of counselees, respectively. In multilevel analyses, clinicians felt less confident in counseling when the full model provided lower breast cancer risks than GENE (i.e., in 8% of cases). Older counselees expressed higher breast cancer risk perception and worries about the hereditary predisposition when the full model provided higher breast cancer risks than GENE only. Genetic clinicians appear confident with breast cancer risk comprehensive models, which seem only to affect perceptions of older counselees.
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Affiliation(s)
- Anne Brédart
- Institut Curie, Supportive Care Department, Psycho-oncology Unit, PSL University, 26 rue d'Ulm, 75005 Paris Cedex 05, Paris, France.,University of Paris, 71 avenue Edouard Vaillant, Boulogne-Billancourt, France
| | - Antoine De Pauw
- Institut Curie, Cancer genetic clinic, PSL University, University of Paris, 26 rue d'Ulm, Paris Cedex 05, France
| | - Anja Tüchler
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Hereditary Breast and Ovarian Cancer, Cologne, Germany, Kerpener Str. 62 50937 Cologne, University Hospital of Cologne, Cologne, Germany
| | - Inge M M Lakeman
- Leiden University Medical Centre, Department of Clinical Genetics, S4-P, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Amélie Anota
- Centre Léon Bérard, Department of Clinical Research and Innovation& Human and Social Sciences Department, 28 rue Laennec, 69373, Lyon; French National Platform Quality of Life and Cancer, Lyon, France
| | - Kerstin Rhiem
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Hereditary Breast and Ovarian Cancer, Cologne, Germany, Kerpener Str. 62 50937 Cologne, University Hospital of Cologne, Cologne, Germany
| | - Rita Schmutzler
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Hereditary Breast and Ovarian Cancer, Cologne, Germany, Kerpener Str. 62 50937 Cologne, University Hospital of Cologne, Cologne, Germany
| | - C J van Asperen
- Leiden University Medical Centre, Department of Clinical Genetics, S4-P, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Peter Devilee
- Leiden University Medical Centre, Department of Human Genetics, Department of Pathology, S4-P, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Dominique Stoppa-Lyonnet
- Institut Curie, Cancer genetic clinic, PSL University, University of Paris, 26 rue d'Ulm, Paris Cedex 05, France
| | - Jean-Luc Kop
- Université de Lorraine, 2LPN, 3 place Godefroy de Bouillon, 54 015 Nancy Cedex, Nancy, France
| | - Sylvie Dolbeault
- Institut Curie, Supportive Care Department, Psycho-oncology Unit, PSL University, 26 rue d'Ulm, 75005 Paris Cedex 05, Paris, France.,CESP, University Paris-Sud, UVSQ, INSERM, University Paris-Saclay, 16 avenue Paul Vaillant-Couturier, Villejuif cedex, France
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Investigation of the association of three ATM polymorphisms with breast cancer in Iranian women. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Kazemi SM, Esmaieli-bandboni A, Veisi Malekshahi Z, Shahbaz Sardood M, Hashemi M, Majidzadeh K, Kadkhodazadeh M, Esmaili R, Negahdari B. Vitamin D receptor gene polymorphisms and risk of breast cancer in Iranian women. Ann Med Surg (Lond) 2022; 73:103150. [PMID: 34917354 PMCID: PMC8666522 DOI: 10.1016/j.amsu.2021.103150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/02/2021] [Accepted: 12/02/2021] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVES Vitamin D deficiency is a driving force of common cancers like breast cancer. Vitamin D receptor (VDR) can play a tumor suppressor role by helping the precise function of vitamin D in cells such as modulation TGF-β signaling pathway. This study aimed to investigate the association of VDR gene variants and susceptibility to breast cancer in Iranian women. METHODS Genomic DNAs were isolated from blood samples of 161 women with breast cancer and 150 healthy women. After amplification of five positions of VDR gene, the prepared amplicons were digested with TaqI, ApaI, BsmI, Cdx2, and FokI restriction enzymes. RESULTS Subsequently, the digested products were electrophoresed on the 1.5% agarose gel. Odds ratios (ORs) for breast cancer were calculated for genotypes and estimated haplotypes. Binary logistic regression analysis showed FokI (rs2228570), BsmI (rs1544410), and ApaI (rs7975232) polymorphisms had the significant distribution in patients than to the normal group. Analysis of linkage disequilibrium for all pairs of SNPs showed that D'-value between SNP TaqI and SNP BsmI was significantly (p ≤ 0.05). We observed that four major haplotypes of ApaI, BsmI, FokI, Cdx2, and TaqI SNPs significantly were in high frequency than predicted frequency. Among these four haplotypes, CGTAT haplotype was in a higher significant association than others with breast cancer risk (p-value = 0.0001). CONCLUSION Our results showed that FokI, BsmI, and ApaI of VDR polymorphisms associated with the risk of breast cancer in Iranian population.
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Affiliation(s)
- Seyedeh Maryam Kazemi
- Department of Genetics, Tehran Medical Sciences Branch, Islamic Azad University, Tehran, Iran
- Toxicology and Chemotherapy Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Aghil Esmaieli-bandboni
- Department of Medical Genetics, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Ziba Veisi Malekshahi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Shahbaz Sardood
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehrdad Hashemi
- Department of Genetics, Tehran Medical Sciences Branch, Islamic Azad University, Tehran, Iran
| | - Keivan Majidzadeh
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | | | - Rezvan Esmaili
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Babak Negahdari
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
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Gong C, Zhou M, Hu Y, Ren Z, Ren J, Yao M. Elastic net-based identification of GAMT as potential diagnostic marker for early-stage gastric cancer. Biochem Biophys Res Commun 2021; 591:7-12. [PMID: 34990904 DOI: 10.1016/j.bbrc.2021.12.055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 12/15/2021] [Indexed: 12/24/2022]
Abstract
Early-stage gastric cancer (GC) is asymptomatic. How to diagnose the early-stage GC is challenging. The sensitivity and specificity of diagnosing signatures for early-stage patients are still poor. Elastic-net-based analysis was used to identify potential diagnostic signatures of early-stage GC. The expression level of candidate gene was evaluated by immunohistochemistry staining. The potential function of candidate gene was verified by overexpressing in vitro. Consensus genes (including GAMT) were identified using the different strengths of the penalty. Surprisingly, GAMT was still identified even if some multicollinear variables were deleted directly. IHC staining showed that there are no GAMT-positive signals in the cell nuclei of all tumor tissues, while GAMT does express in nuclei of adjacent normal tissue. There are 16.33% positive cell nuclei in paracancerous tissues. In addition, the number of larger-area colonies of overexpression-GAMT group, empty-vector group, and AGS group is 70±29.21, 151.33±15.95, and 111.67±22.03, respectively. Number of larger colonies in group with overexpression of GAMT is significantly less than control groups. Elastic-net-penalty-based workflow is a effective tool to identify diagnostic biomarker for early-stage solid tumor. GAMT has strong potential to be the diagnostic biomarker for the early-stage GC.
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Affiliation(s)
- Congcong Gong
- School of Food Science and Technology, South China University of Technology, Guangzhou, 510641, Guangdong, China
| | - Mao Zhou
- Department of Anesthesiology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, Guangdong, China
| | - Yang Hu
- The First Affiliated Hospital of Guangzhou Medical University, China
| | - Zhengyu Ren
- School of Pharmaceutical Science, University of South China, Hengyang, Hunan, 421001, China
| | - Jiaoyan Ren
- School of Food Science and Technology, South China University of Technology, Guangzhou, 510641, Guangdong, China
| | - Maojin Yao
- The First Affiliated Hospital of Guangzhou Medical University, China.
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Brédart A, De Pauw A, Anota A, Tüchler A, Dick J, Müller A, Kop JL, Rhiem K, Schmutzler R, Devilee P, Stoppa-Lyonnet D, Dolbeault S. Information needs on breast cancer genetic and non-genetic risk factors in relatives of women with a BRCA1/2 or PALB2 pathogenic variant. Breast 2021; 60:38-44. [PMID: 34455229 PMCID: PMC8403756 DOI: 10.1016/j.breast.2021.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/29/2021] [Accepted: 08/21/2021] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES Comprehensive breast cancer (BC) risk models integrating effects of genetic (GRF) and non-genetic risk factors (NGRF) may refine BC prevention recommendations. We explored the perceived information received on BC risk factors, and related characteristics, in female relatives of women with a BRCA1/2 or PALB2 pathogenic variant, undergoing BC risk assessment using the CanRisk© prediction tool. METHODS Of 200 consecutive cancer-free women approached after the initial genetic consultation, 161 (80.5%) filled in questionnaires on their perception of information received and wished further information on BC risk factors (e.g., being a carrier of a moderate risk altered gene, personal genetic profile, lifestyles). Multilevel multivariate linear models were performed accounting for the clinician who met the counselee and exploring the effect of counselees' socio-demographic, familial and psychological characteristics on the perceived extent of information received. RESULTS Perceived no/little information received and wish for further information were more frequent for NGRF (>50%) than for GRF, especially high-risk genes (<20%). Perceived amount of information received and desire for further information were inversely correlated (p=<0.0001). Higher education level related to lower perceived levels of information received on GRF. Younger counselees' age (β = 0.13, p = 0.02) and less frequent engagement coping (e.g., inclination to solicit information) (β = 0.24, p = 0.02) related to lower perceived information received about NGRF. Other assessed counselees' features were not found to be associated to GRF and NGRF information perception. CONCLUSIONS Awareness of counselees' perceived lack of information on BC risk factors indicates a need to enhance evidence-based information on BC NGRF especially.
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Affiliation(s)
- Anne Brédart
- Institut Curie, Supportive Care Department, Psycho-oncology Unit, PSL University, 26 rue d'Ulm, Paris, 75005 Paris Cedex 05, France; University of Paris, 71 Avenue Edouard Vaillant, Boulogne-Billancourt, 92774, France.
| | - Antoine De Pauw
- Institut Curie, Cancer Genetic Clinic, PSL University, 26 rue d'Ulm, 75005 Paris Cedex 05, France
| | - Amélie Anota
- Centre Léon Bérard, Department of Clinical Research and Innovation& Human and Social Sciences Department, 28 rue Laennec, Lyon; French National Platform Quality of Life and Cancer, Lyon, 69373, France
| | - Anja Tüchler
- Center for Familial Breast and Ovarian and Cancer for Integrated Oncology (CIO), Kerpener Str. 62 50937 Cologne, University Hospital of Cologne, Cologne, Germany
| | - Julia Dick
- Center for Familial Breast and Ovarian and Cancer for Integrated Oncology (CIO), Kerpener Str. 62 50937 Cologne, University Hospital of Cologne, Cologne, Germany
| | - Anita Müller
- Institut Curie, Supportive Care Department, Psycho-oncology Unit, PSL University, 26 rue d'Ulm, Paris, 75005 Paris Cedex 05, France; VCR, École de Psychologues Praticiens de l'Institut Catholique de Paris, 23 Rue du Montparnasse, 75006, Paris, France
| | - Jean-Luc Kop
- Université de Lorraine, 2LPN, 3 Place Godefroy de Bouillon, Nancy, 54 015 Nancy Cedex, France
| | - Kerstin Rhiem
- Center for Familial Breast and Ovarian and Cancer for Integrated Oncology (CIO), Kerpener Str. 62 50937 Cologne, University Hospital of Cologne, Cologne, Germany
| | - Rita Schmutzler
- Center for Familial Breast and Ovarian and Cancer for Integrated Oncology (CIO), Kerpener Str. 62 50937 Cologne, University Hospital of Cologne, Cologne, Germany
| | - Peter Devilee
- Leiden University Medical Centre, Department of Human Genetics, Department of Pathology, S4-P, P.O. Box 9600, 2300, RC, Leiden, the Netherlands
| | - Dominique Stoppa-Lyonnet
- Institut Curie, Cancer Genetic Clinic, PSL University, 26 rue d'Ulm, 75005 Paris Cedex 05, France
| | - Sylvie Dolbeault
- Institut Curie, Supportive Care Department, Psycho-oncology Unit, PSL University, 26 rue d'Ulm, Paris, 75005 Paris Cedex 05, France; CESP, University Paris-Sud, UVSQ, INSERM, University Paris-Saclay, 16 Avenue Paul Vaillant-Couturier, 94807, Villejuif Cedex, France
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Calvo Chozas A, Mahjani B, Rönnegård L. Family history of breast cancer is associated with elevated risk of prostate cancer: evidence for shared genetic risks. Hum Hered 2021; 87:000521215. [PMID: 34847553 DOI: 10.1159/000521215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 11/25/2021] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Although breast and prostate cancers arise in different organs and are more frequent in the opposite sex, multiple studies have reported an association between their family history. Analysis of single nucleotide polymorphism data, based on distant relatives, has revealed a small positive genetic correlation between these cancers explained by common variants. The estimate of genetic correlation based on close relatives reveals the extent to which shared genetic risks are explained by both common and rare variants. This estimate is unknown for breast and prostate cancer. METHOD We estimated the relative risks, heritability, and genetic correlation of breast cancer and prostate cancer, based on the Minnesota Breast and Prostate Cancer Study, a family study of 141 families ascertained for breast cancer. RESULTS Heritability of breast cancer was 0.34 (95% credible interval: 0.23-0.49) and 0.65 (95% credible interval: 0.36-0.97) for prostate cancer, and the genetic correlation was 0.23. In terms of odds ratios, these values correspond to a 1.3 times higher odds of breast cancer among probands, given that the brother has prostate cancer. CONCLUSION This study shows the inherent relation between prostate cancer and breast cancer; an incident of one in a family increases the risk of developing the other. The large difference between estimates of genetic correlation from distant and close relatives, if replicated, suggests that rare variants contribute to the shared genetic risk of breast and prostate cancer. However, the difference could steam from genotype-by-family effects shared between the two types of cancers.
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Hayat M, Chen WC, Brandenburg JT, Babb de Villiers C, Ramsay M, Mathew CG. Genetic Susceptibility to Breast Cancer in Sub-Saharan African Populations. JCO Glob Oncol 2021; 7:1462-1471. [PMID: 34623906 PMCID: PMC8509920 DOI: 10.1200/go.21.00089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Mahtaab Hayat
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Wenlong Carl Chen
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,National Cancer Registry, National Health Laboratory Service, Johannesburg, South Africa.,Non-communicable Diseases Research Division, Wits Health Consortium (PTY) Ltd, Johannesburg, South Africa
| | - Jean-Tristan Brandenburg
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Chantal Babb de Villiers
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Christopher G Mathew
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
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Molaei Ramshe S, Ghaedi H, Omrani MD, Geranpayeh L, Alipour B, Ghafouri-Fard S. Up-regulation of FOXN3-AS1 in invasive ductal carcinoma of breast cancer patients. Heliyon 2021; 7:e08179. [PMID: 34703931 PMCID: PMC8526775 DOI: 10.1016/j.heliyon.2021.e08179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 06/12/2021] [Accepted: 10/11/2021] [Indexed: 11/04/2022] Open
Abstract
Oncogenic and tumor-suppressive roles of long non-coding RNA make them an appropriate target for expression analysis in cancer studies. In this study, we selected two lncRNAs (EMX2OS and FOXN3-AS1) that are resided near the GWAS-identified SNPs for breast cancer (rs2901157 and rs141061110). These transcripts have been identified in different cancer types as either oncogenes or tumor suppressors. In the present investigation, we aimed to quantify the expression level of EMX2OS and FOXN3-AS1 in 44 breast cancer samples and normal adjacent tissues (ANCTs). The FOXN3-AS1 expression level was significantly increased in breast cancer samples compared with ANCTs (P value = 0.02), Also its amounts could distinguish two sets of samples with an accuracy of 70% (P value = 0.009). We have found an association between FOXN3-AS1 expression and tumor size (P value = 0.02). On the other hand, no significant differences were found in the EMX2OS expression level between two sets of samples (P value = 0.44); however, EMX2OS expression level has a significant association with the age of the patients (P value = 0.03). According to our result, FOXN3-AS1 can be demonstrated as a probable diagnostic marker in breast cancer so we suggest further functional studies to find the precise role of these lncRNAs in breast cancer progression.
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Affiliation(s)
- Samira Molaei Ramshe
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Ghaedi
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mir Davood Omrani
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Behnam Alipour
- Department of Laboratory Sciences, Faculty of Paramedicine, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Lakeman IMM, van den Broek AJ, Vos JAM, Barnes DR, Adlard J, Andrulis IL, Arason A, Arnold N, Arun BK, Balmaña J, Barrowdale D, Benitez J, Borg A, Caldés T, Caligo MA, Chung WK, Claes KBM, Collée JM, Couch FJ, Daly MB, Dennis J, Dhawan M, Domchek SM, Eeles R, Engel C, Evans DG, Feliubadaló L, Foretova L, Friedman E, Frost D, Ganz PA, Garber J, Gayther SA, Gerdes AM, Godwin AK, Goldgar DE, Hahnen E, Hake CR, Hamann U, Hogervorst FBL, Hooning MJ, Hopper JL, Hulick PJ, Imyanitov EN, Isaacs C, Izatt L, Jakubowska A, James PA, Janavicius R, Jensen UB, Jiao Y, John EM, Joseph V, Karlan BY, Kets CM, Konstantopoulou I, Kwong A, Legrand C, Leslie G, Lesueur F, Loud JT, Lubiński J, Manoukian S, McGuffog L, Miller A, Gomes DM, Montagna M, Mouret-Fourme E, Nathanson KL, Neuhausen SL, Nevanlinna H, Yie JNY, Olah E, Olopade OI, Park SK, Parsons MT, Peterlongo P, Piedmonte M, Radice P, Rantala J, Rennert G, Risch HA, Schmutzler RK, Sharma P, Simard J, Singer CF, Stadler Z, Stoppa-Lyonnet D, Sutter C, Tan YY, Teixeira MR, Teo SH, Teulé A, Thomassen M, Thull DL, Tischkowitz M, Toland AE, Tung N, van Rensburg EJ, Vega A, Wappenschmidt B, Devilee P, van Asperen CJ, Bernstein JL, Offit K, Easton DF, Rookus MA, Chenevix-Trench G, Antoniou AC, Robson M, Schmidt MK. The predictive ability of the 313 variant-based polygenic risk score for contralateral breast cancer risk prediction in women of European ancestry with a heterozygous BRCA1 or BRCA2 pathogenic variant. Genet Med 2021; 23:1726-1737. [PMID: 34113011 PMCID: PMC8460445 DOI: 10.1038/s41436-021-01198-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 04/26/2021] [Indexed: 11/25/2022] Open
Abstract
PURPOSE To evaluate the association between a previously published 313 variant-based breast cancer (BC) polygenic risk score (PRS313) and contralateral breast cancer (CBC) risk, in BRCA1 and BRCA2 pathogenic variant heterozygotes. METHODS We included women of European ancestry with a prevalent first primary invasive BC (BRCA1 = 6,591 with 1,402 prevalent CBC cases; BRCA2 = 4,208 with 647 prevalent CBC cases) from the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), a large international retrospective series. Cox regression analysis was performed to assess the association between overall and ER-specific PRS313 and CBC risk. RESULTS For BRCA1 heterozygotes the estrogen receptor (ER)-negative PRS313 showed the largest association with CBC risk, hazard ratio (HR) per SD = 1.12, 95% confidence interval (CI) (1.06-1.18), C-index = 0.53; for BRCA2 heterozygotes, this was the ER-positive PRS313, HR = 1.15, 95% CI (1.07-1.25), C-index = 0.57. Adjusting for family history, age at diagnosis, treatment, or pathological characteristics for the first BC did not change association effect sizes. For women developing first BC < age 40 years, the cumulative PRS313 5th and 95th percentile 10-year CBC risks were 22% and 32% for BRCA1 and 13% and 23% for BRCA2 heterozygotes, respectively. CONCLUSION The PRS313 can be used to refine individual CBC risks for BRCA1/2 heterozygotes of European ancestry, however the PRS313 needs to be considered in the context of a multifactorial risk model to evaluate whether it might influence clinical decision-making.
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Affiliation(s)
- Inge M M Lakeman
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Alexandra J van den Broek
- Division of Molecular Pathology, The Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Juliën A M Vos
- Division of Molecular Pathology, The Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Daniel R Barnes
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Julian Adlard
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds, UK
| | - Irene L Andrulis
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Adalgeir Arason
- Department of Pathology, Landspitali University Hospital, Reykjavik, Iceland
- BMC (Biomedical Centre), Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Norbert Arnold
- Department of Gynaecology and Obstetrics, University Hospital of Schleswig-Holstein, Campus Kiel, Christian-Albrechts University Kiel, Kiel, Germany
- Institute of Clinical Molecular Biology, University Hospital of Schleswig-Holstein, Campus Kiel, Christian-Albrechts University Kiel, Kiel, Germany
| | - Banu K Arun
- Department of Breast Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Judith Balmaña
- Hereditary cancer Genetics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
- Department of Medical Oncology, Vall d'Hebron Barcelona Hospital Campus, University Hospital of Vall d'Hebron, Barcelona, Spain
| | - Daniel Barrowdale
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Javier Benitez
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ake Borg
- Department of Oncology, Lund University and Skåne University Hospital, Lund, Sweden
| | - Trinidad Caldés
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Maria A Caligo
- SOD Genetica Molecolare. University Hospital, Pisa, Italy
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA
| | | | - J Margriet Collée
- Department of Clinical Genetics, Erasmus University Medical Center, CA, Rotterdam, The Netherlands
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Mary B Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Mallika Dhawan
- Cancer Genetics and Prevention Program, University of California San Francisco, San Francisco, CA, USA
| | - Susan M Domchek
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Ros Eeles
- Oncogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, UK
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, 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, 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, UK
| | - Lidia Feliubadaló
- Hereditary Cancer Program, ONCOBELL-IDIBELL-IGTP, Catalan Institute of Oncology, CIBERONC, Barcelona, Spain
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Eitan Friedman
- The Susanne Levy Gertner Oncogenetics Unit, Chaim Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - Debra Frost
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Patricia A Ganz
- Schools of Medicine and Public Health, Division of Cancer Prevention & Control Research, Jonsson Comprehensive Cancer Centre, UCLA, Los Angeles, CA, USA
| | - Judy Garber
- Cancer Risk and Prevention Clinic, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Simon A Gayther
- Center for Bioinformatics and Functional Genomics and the Cedars Sinai Genomics Core. Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - David E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Eric Hahnen
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | | | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frans B L Hogervorst
- Family Cancer Clinic, The Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Maartje J Hooning
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Peter J Hulick
- Center for Medical Genetics, NorthShore University HealthSystem, Evanston, IL, USA
- The University of Chicago Pritzker School of Medicine, Chicago, IL, USA
| | | | - Claudine Isaacs
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Louise Izatt
- Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, Szczecin, Poland
| | - Paul A James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Center, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - Ramunas Janavicius
- Hematology, Oncology and Transfusion Medicine Center, Department of Molecular and Regenerative Medicine, Vilnius University Hospital Santariskiu Clinics, Vilnius, Lithuania
- State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
| | - Uffe Birk Jensen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Yue Jiao
- Genetic Epidemiology of Cancer team, Paris, France
- Institut Curie, Paris, France
- Mines ParisTech, Fontainebleau, France
| | - Esther M John
- Department of Epidemiology & Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Vijai Joseph
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Beth Y Karlan
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Carolien M Kets
- Family Cancer Clinic, The Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research 'Demokritos', Athens, Greece
| | - Ava Kwong
- Hong Kong Hereditary Breast Cancer Family Registry, Cancer Genetics Centre, Happy Valley, Hong Kong
- Department of Surgery, The University of Hong Kong, Pok Fu Lam, Hong Kong
- Department of Surgery, Hong Kong Sanatorium and Hospital, Happy Valley, Hong Kong
| | | | - Goska Leslie
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Fabienne Lesueur
- Genetic Epidemiology of Cancer team, Paris, France
- Institut Curie, Paris, France
- Mines ParisTech, Fontainebleau, France
| | - Jennifer T Loud
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jan Lubiński
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Lesley McGuffog
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Austin Miller
- NRG Oncology, Statistics and Data Management Center, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Denise Molina Gomes
- Service de Biologie de la reproduction, Cytogénétique et Génétique Médicale, CHI Poissy-Saint Germain, Poissy, France
| | - Marco Montagna
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | | | - Katherine L Nathanson
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Joanne Ngeow Yuen Yie
- Cancer Genetics Service, National Cancer Centre, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Edith Olah
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | | | - Sue K Park
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
| | - Michael T Parsons
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Paolo Peterlongo
- Genome Diagnostics Program, IFOM-the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Marion Piedmonte
- NRG Oncology, Statistics and Data Management Center, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | | | - Gad Rennert
- Clalit National Cancer Control Center, Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - Harvey A Risch
- Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | - Rita K Schmutzler
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Priyanka Sharma
- Department of Internal Medicine, Division of Medical Oncology, University of Kansas Medical Center, Westwood, KS, USA
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, Québec City, QC, Canada
| | - Christian F Singer
- Dept of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Zsofia Stadler
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dominique Stoppa-Lyonnet
- Service de Génétique, Institut Curie, Paris, France
- Department of Tumour Biology, INSERM U830, Paris, France
- Université Paris Descartes, Paris, France
| | - Christian Sutter
- Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
| | - Yen Yen Tan
- Dept of OB/GYN, Medical University of Vienna, Vienna, Austria
| | - Manuel R Teixeira
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
- Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Soo Hwang Teo
- Breast Cancer Research Programme, Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Alex Teulé
- Hereditary Cancer Program, ONCOBELL-IDIBELL-IGTP, Catalan Institute of Oncology, CIBERONC, Barcelona, Spain
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odence C, Denmark
| | - Darcy L Thull
- Department of Medicine, Magee-Womens Hospital, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Marc Tischkowitz
- Program in Cancer Genetics, Departments of Human Genetics and Oncology, McGill University, Montréal, QC, Canada
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge. Vol Box 134, Level 6 Addenbrooke's Treatment Centre, Addenbrooke's Hosptital, Cambridge, UK
| | - Amanda E Toland
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Nadine Tung
- Department of Medical Oncology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | | | - Ana Vega
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain
| | - Barbara Wappenschmidt
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Christi J van Asperen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jonine L Bernstein
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Kenneth Offit
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Douglas F Easton
- 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
| | - Matti A Rookus
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute-Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Mark Robson
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marjanka K Schmidt
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.
- Division of Molecular Pathology, The Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands.
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute-Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands.
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XPF -673C>T variation is associated with the susceptibility to breast cancer. Cancer Epidemiol 2021; 74:102007. [PMID: 34416547 DOI: 10.1016/j.canep.2021.102007] [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: 03/16/2021] [Revised: 08/02/2021] [Accepted: 08/08/2021] [Indexed: 11/22/2022]
Abstract
PURPOSE XPF variations might decrease the DNA repair capacity and further contribute to cancer development. This study aimed to investigate the association of XPF polymorphisms with risk of developing breast cancer. METHODS TCGA, the Human Protein Atlas and Kaplan-Meier plotter were used to analyze the expression of XPF in breast cancer tissues and its effect on the survival of breast cancer patients. The expression of XPF in breast cancer tissues was detected by qRT-PCR. This case-control study included 467 breast cancer patients and 467 healthy controls. The genotype of genetic variation was detected by polymerase chain reaction restriction fragment length polymorphism. Odds ratios and 95 % confidence intervals were calculated. Correlations between XPF variation and clinicopathological parameters were assessed through Kendall's Tau-b test. The relationship between XPF gene function variation and XPF gene expression was analyzed by GTEx. RESULTS The expression of XPF in breast cancer tissues is higher than that in normal tissues. Breast cancer patients with high XPF expression have a higher relapse free survival rate (HR = 0.88, 95 % CI = 0.80-0.97), but have no effect on the overall survival rate (logrank P = 0.28). XPF -673C > T variant can reduce the risk of breast cancer patients (OR = 0.35, 95 %CI = 0.20-0.63 for codominant mode; OR = 0.66, 95 %CI = 0.51-0.85 for dominant model; OR = 0.40, 95 %CI = 0.23-0.70 for recessive model). The XPF 11985 GG genotype reduced the risk of early breast cancer (OR = 0.49, 95 %CI = 0.24-0.97), but not the risk of advanced breast cancer (OR = 1.20, 95 % CI = 0.58-2.48). XPF 11985A > G variant can also reduce the risk of ERBB2 expression in patients (OR = 0.50, 95 %CI = 0.27-0.94). There is no correlation between XPF -673C > T/XPF11985A > G variants and ER and PR. XPF -673C > T variant can reduce XPF expression (P < 0.05). CONCLUSIONS Genetic variations of XPF gene may affect its expression and the risk of breast cancer in the Chinese population.
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Gao C, Polley EC, Hart SN, Huang H, Hu C, Gnanaolivu R, Lilyquist J, Boddicker NJ, Na J, Ambrosone CB, Auer PL, Bernstein L, Burnside ES, Eliassen AH, Gaudet MM, Haiman C, Hunter DJ, Jacobs EJ, John EM, Lindström S, Ma H, Neuhausen SL, Newcomb PA, O'Brien KM, Olson JE, Ong IM, Patel AV, Palmer JR, Sandler DP, Tamimi R, Taylor JA, Teras LR, Trentham-Dietz A, Vachon CM, Weinberg CR, Yao S, Weitzel JN, Goldgar DE, Domchek SM, Nathanson KL, Couch FJ, Kraft P. Risk of Breast Cancer Among Carriers of Pathogenic Variants in Breast Cancer Predisposition Genes Varies by Polygenic Risk Score. J Clin Oncol 2021; 39:2564-2573. [PMID: 34101481 PMCID: PMC8330969 DOI: 10.1200/jco.20.01992] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 02/19/2021] [Accepted: 04/20/2021] [Indexed: 12/11/2022] Open
Abstract
PURPOSE This study assessed the joint association of pathogenic variants (PVs) in breast cancer (BC) predisposition genes and polygenic risk scores (PRS) with BC in the general population. METHODS A total of 26,798 non-Hispanic white BC cases and 26,127 controls from predominately population-based studies in the Cancer Risk Estimates Related to Susceptibility consortium were evaluated for PVs in BRCA1, BRCA2, ATM, CHEK2, PALB2, BARD1, BRIP1, CDH1, and NF1. PRS based on 105 common variants were created using effect estimates from BC genome-wide association studies; the performance of an overall BC PRS and estrogen receptor-specific PRS were evaluated. The odds of BC based on the PVs and PRS were estimated using penalized logistic regression. The results were combined with age-specific incidence rates to estimate 5-year and lifetime absolute risks of BC across percentiles of PRS by PV status and first-degree family history of BC. RESULTS The estimated lifetime risks of BC among general-population noncarriers, based on 10th and 90th percentiles of PRS, were 9.1%-23.9% and 6.7%-18.2% for women with or without first-degree relatives with BC, respectively. Taking PRS into account, more than 95% of BRCA1, BRCA2, and PALB2 carriers had > 20% lifetime risks of BC, whereas, respectively, 52.5% and 69.7% of ATM and CHEK2 carriers without first-degree relatives with BC, and 78.8% and 89.9% of those with a first-degree relative with BC had > 20% risk. CONCLUSION PRS facilitates personalization of BC risk among carriers of PVs in predisposition genes. Incorporating PRS into BC risk estimation may help identify > 30% of CHEK2 and nearly half of ATM carriers below the 20% lifetime risk threshold, suggesting the addition of PRS may prevent overscreening and enable more personalized risk management approaches.
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Affiliation(s)
- Chi Gao
- Harvard T.H. Chan School of Public Health, Boston, MA
| | | | | | - Hongyan Huang
- Harvard T.H. Chan School of Public Health, Boston, MA
| | | | | | | | | | - Jie Na
- Mayo Clinic, Rochester, MN
| | | | - Paul L. Auer
- UWM Joseph J. Zilber School of Public Health, Milwaukee, WI
| | | | | | - A. Heather Eliassen
- Harvard T.H. Chan School of Public Health, Boston, MA
- Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Mia M. Gaudet
- Department of Population Science, American Cancer Society, Atlanta, GA
| | - Christopher Haiman
- Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - David J. Hunter
- Harvard T.H. Chan School of Public Health, Boston, MA
- University of Oxford, Oxford, United Kingdom
| | - Eric J. Jacobs
- Department of Population Science, American Cancer Society, Atlanta, GA
| | | | - Sara Lindström
- Department of Epidemiology, University of Washington, Seattle, WA
- Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Huiyan Ma
- Beckman Research Institute of City of Hope, Duarte, CA
| | | | - Polly A. Newcomb
- Department of Epidemiology, University of Washington, Seattle, WA
- Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | | | | | - Alpa V. Patel
- Department of Population Science, American Cancer Society, Atlanta, GA
| | - Julie R. Palmer
- Boston University School of Medicine and Slone Epidemiology Center, Boston, MA
| | - Dale P. Sandler
- National Institute of Environmental Health Sciences, Durham, NC
| | - Rulla Tamimi
- Population Health Sciences Department, Weill Cornell Medicine, New York, NY
| | - Jack A. Taylor
- National Institute of Environmental Health Sciences, Durham, NC
| | - Lauren R. Teras
- Department of Population Science, American Cancer Society, Atlanta, GA
| | | | | | | | - Song Yao
- Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | | | | | - Susan M. Domchek
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | | | | | - Peter Kraft
- Harvard T.H. Chan School of Public Health, Boston, MA
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48
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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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49
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Adedokun B, Du Z, Gao G, Ahearn TU, Lunetta KL, Zirpoli G, Figueroa J, John EM, Bernstein L, Zheng W, Hu JJ, Ziegler RG, Nyante S, Bandera EV, Ingles SA, Press MF, Deming-Halverson SL, Rodriguez-Gil JL, Yao S, Ogundiran TO, Ojengbede O, Blot W, Troester MA, Nathanson KL, Hennis A, Nemesure B, Ambs S, Fiorica PN, Sucheston-Campbell LE, Bensen JT, Kushi LH, Torres-Mejia G, Hu D, Fejerman L, Bolla MK, Dennis J, Dunning AM, Easton DF, Michailidou K, Pharoah PDP, Wang Q, Sandler DP, Taylor JA, O'Brien KM, Kitahara CM, Falusi AG, Babalola C, Yarney J, Awuah B, Addai-Wiafe B, Chanock SJ, Olshan AF, Ambrosone CB, Conti DV, Ziv E, Olopade OI, Garcia-Closas M, Palmer JR, Haiman CA, Huo D. Cross-ancestry GWAS meta-analysis identifies six breast cancer loci in African and European ancestry women. Nat Commun 2021; 12:4198. [PMID: 34234117 PMCID: PMC8263739 DOI: 10.1038/s41467-021-24327-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 06/02/2021] [Indexed: 02/06/2023] Open
Abstract
Our study describes breast cancer risk loci using a cross-ancestry GWAS approach. We first identify variants that are associated with breast cancer at P < 0.05 from African ancestry GWAS meta-analysis (9241 cases and 10193 controls), then meta-analyze with European ancestry GWAS data (122977 cases and 105974 controls) from the Breast Cancer Association Consortium. The approach identifies four loci for overall breast cancer risk [1p13.3, 5q31.1, 15q24 (two independent signals), and 15q26.3] and two loci for estrogen receptor-negative disease (1q41 and 7q11.23) at genome-wide significance. Four of the index single nucleotide polymorphisms (SNPs) lie within introns of genes (KCNK2, C5orf56, SCAMP2, and SIN3A) and the other index SNPs are located close to GSTM4, AMPD2, CASTOR2, and RP11-168G16.2. Here we present risk loci with consistent direction of associations in African and European descendants. The study suggests that replication across multiple ancestry populations can help improve the understanding of breast cancer genetics and identify causal variants.
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Affiliation(s)
- Babatunde Adedokun
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Zhaohui Du
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Guimin Gao
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Thomas U Ahearn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Gary Zirpoli
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | - Jonine Figueroa
- Usher Institute and CRUK Edinburgh Centre, University of Edinburgh, Edinburgh, UK
| | - Esther M John
- Departments of Epidemiology & Population Health and of Medicine (Oncology) and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Leslie Bernstein
- Biomarkers of Early Detection and Prevention, Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Jennifer J Hu
- Department of Public Health Sciences, University of Miami, Miami, FL, USA
| | - Regina G Ziegler
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Sarah Nyante
- Department of Radiology, University of North Carolina, Chapel Hill, NC, USA
| | - Elisa V Bandera
- Cancer Prevention and Control Program, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Sue A Ingles
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Michael F Press
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sandra L Deming-Halverson
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Jorge L Rodriguez-Gil
- Genomics, Development and Disease Section, Genetic Disease Research Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Temidayo O Ogundiran
- Department of Surgery, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oladosu Ojengbede
- Center for Population and Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - William Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Melissa A Troester
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Katherine L Nathanson
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anselm Hennis
- University of the West Indies, Bridgetown, Barbados
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Barbara Nemesure
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, National Cancer Institute, Bethesda, MD, USA
| | - Peter N Fiorica
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Lara E Sucheston-Campbell
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Jeannette T Bensen
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Lawrence H Kushi
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Gabriela Torres-Mejia
- Center for Population Health Research, Instituto Nacional de Salud Publica, Cuernavaca, Mexico
| | - Donglei Hu
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Laura Fejerman
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Douglas F Easton
- 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
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - 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
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Katie M O'Brien
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Cari M Kitahara
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Adeyinka G Falusi
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Chinedum Babalola
- Department of Pharmaceutical Chemistry, University of Ibadan, Ibadan, Oyo, Nigeria
| | | | | | | | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Andrew F Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - David V Conti
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Elad Ziv
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, IL, USA
| | | | - Julie R Palmer
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | - Christopher A Haiman
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Dezheng Huo
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, IL, USA.
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA.
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50
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Borde J, Ernst C, Wappenschmidt B, Niederacher D, Weber-Lassalle K, Schmidt G, Hauke J, Quante AS, Weber-Lassalle N, Horváth J, Pohl-Rescigno E, Arnold N, Rump A, Gehrig A, Hentschel J, Faust U, Dutrannoy V, Meindl A, Kuzyakova M, Wang-Gohrke S, Weber BHF, Sutter C, Volk AE, Giannakopoulou O, Lee A, Engel C, Schmidt MK, Antoniou AC, Schmutzler RK, Kuchenbaecker K, Hahnen E. Performance of Breast Cancer Polygenic Risk Scores in 760 Female CHEK2 Germline Mutation Carriers. J Natl Cancer Inst 2021; 113:893-899. [PMID: 33372680 PMCID: PMC8246885 DOI: 10.1093/jnci/djaa203] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 09/17/2020] [Accepted: 12/08/2020] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Genome-wide association studies suggest that the combined effects of breast cancer (BC)-associated single nucleotide polymorphisms (SNPs) can improve BC risk stratification using polygenic risk scores (PRSs). The performance of PRSs in genome-wide association studies-independent clinical cohorts is poorly studied in individuals carrying mutations in moderately penetrant BC predisposition genes such as CHEK2. METHODS A total of 760 female CHEK2 mutation carriers were included; 561 women were affected with BC, of whom 74 developed metachronous contralateral BC (mCBC). For PRS calculations, 2 SNP sets covering 77 (SNP set 1, developed for BC risk stratification in women unselected for their BRCA1/2 germline mutation status) and 88 (SNP set 2, developed for BC risk stratification in female BRCA1/2 mutation carriers) BC-associated SNPs were used. All statistical tests were 2-sided. RESULTS Both SNP sets provided concordant PRS results at the individual level (r = 0.91, P < 2.20 × 10-16). Weighted cohort Cox regression analyses revealed statistically significant associations of PRSs with the risk for first BC. For SNP set 1, a hazard ratio of 1.71 per SD of the PRS was observed (95% confidence interval = 1.36 to 2.15, P = 3.87 × 10-6). PRSs identify a subgroup of CHEK2 mutation carriers with a predicted lifetime risk for first BC that exceeds the surveillance thresholds defined by international guidelines. Association of PRS with mCBC was examined via Cox regression analysis (SNP set 1 hazard ratio = 1.23, 95% confidence interval = 0.86 to 1.78, P = .26). CONCLUSIONS PRSs may be used to personalize risk-adapted preventive measures for women with CHEK2 mutations. Larger studies are required to assess the role of PRSs in mCBC predisposition.
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Affiliation(s)
- Julika Borde
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Corinna Ernst
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Barbara Wappenschmidt
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Dieter Niederacher
- Department of Gynecology and Obstetrics, University Hospital Duesseldorf, Heinrich-Heine University Duesseldorf, Duesseldorf, Germany
| | - Konstantin Weber-Lassalle
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Gunnar Schmidt
- Institute of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Jan Hauke
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Anne S Quante
- Department of Gynecology and Obstetrics, Technical University Munich, University Hospital Rechts der Isar, Munich, Germany
| | - Nana Weber-Lassalle
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Judit Horváth
- Institute for Human Genetics, University Hospital Muenster, Muenster, Germany
| | - Esther Pohl-Rescigno
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Norbert Arnold
- Institute of Clinical Molecular Biology, Department of Gynaecology and Obstetrics, University Hospital of Schleswig-Holstein, Campus Kiel, Christian-Albrechts University Kiel, Kiel, Germany
| | - Andreas Rump
- Institute for Clinical Genetics, Technische Universitaet Dresden, Dresden, Germany
| | - Andrea Gehrig
- Institute of Human Genetics, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Julia Hentschel
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | - Ulrike Faust
- Institute of Medical Genetics and Applied Genomics, University Hospital Tuebingen, Tuebingen, Germany
| | - Véronique Dutrannoy
- Institute of Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Alfons Meindl
- Department of Gynecology and Obstetrics, Ludwig-Maximilians-University Munich, University Hospital Munich, Munich, Germany
| | - Maria Kuzyakova
- Institute of Human Genetics, University Medical Center, Georg August University, Goettingen, Germany
| | - Shan Wang-Gohrke
- Department of Gynaecology and Obstetrics, University Hospital Ulm, Ulm, Germany
| | - Bernhard H. F Weber
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
- Institute of Clinical Human Genetics, University Hospital Regensburg, Regensburg, Germany
| | - Christian Sutter
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Alexander E Volk
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Olga Giannakopoulou
- Division of Psychiatry, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Andrew Lee
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Marjanka K Schmidt
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Antonis C Antoniou
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Rita K Schmutzler
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Karoline Kuchenbaecker
- Division of Psychiatry, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Eric Hahnen
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
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