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Jia Z, Huang Y, Liu J, Liu G, Li J, Xu H, Jiang Y, Zhang S, Wang Y, Chen G, Qiao G, Li Y. Single nucleotide polymorphisms associated with female breast cancer susceptibility in Chinese population. Gene 2023; 884:147676. [PMID: 37524136 DOI: 10.1016/j.gene.2023.147676] [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: 11/29/2022] [Revised: 05/09/2023] [Accepted: 07/28/2023] [Indexed: 08/02/2023]
Abstract
Breast cancer is a complex disease influenced by both external and internal factors, among which genetic factors play a critical role. Single-nucleotide polymorphisms (SNPs) are major contributors to the heritability of breast cancer, and their frequencies vary across ethnic groups. In this study, we aimed to investigate the association between 34 SNPs identified in previous genome-wide association studies (GWAS) and overall breast cancer risk, as well as breast cancer subtypes, in the Chinese female population. To accomplish this, we conducted an extensive association analysis using the high-throughput Sequenom MassARRAY® platform in a case-control study comprising 1848 breast cancer patients and 709 healthy controls. Our analysis, which utilized the SNPassoc package in R based on chi-squared (χ2) test and genetic model analysis, identified significant associations between breast cancer risk and SNP rs12493607 (TGFBR2, risk allele C, OR = 1.28 [1.11-1.47], P = 0.0005), as well as a less conservatively significant association with rs4784227 (CASC16, risk allele T, OR = 1.24 [1.08-1.42], P = 0.0017) and rs2046210 (ESR1, risk allele A, OR = 1.50 [1.16-1.95], P = 0.0016). Furthermore, our stratified analyses revealed that rs12493607 was significantly associated with invasive carcinoma, estrogen receptor (ER)-positive, progesterone receptor (PR)-positive, HER2-negative, and young (aged younger than 45) breast cancer. SNP rs4784227 and rs3803662 (CASC16) were associated with invasive carcinoma and ER-positive breast cancer, while rs2046210 was linked to ductal carcinoma in situ, ER-negative, PR-negative, HER2-positive, and elder (aged more than 45) breast cancers. SNPs rs10484919 (ESR1) and rs1038304 (CCDC170) showed links to HER2-positive breast cancer, and rs616488 (PEX14) with premenopausal breast cancer. In summary, our study shed light on the relationship between SNPs and breast cancer susceptibility within a vast Chinese cohort, supporting the development of polygenetic risk scores for the Chinese population. These findings provide valuable insights into the genetic basis of breast cancer and have important implications for risk prediction, early detection, and personalized treatment of this disease.
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Affiliation(s)
- Ziqi Jia
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yansong Huang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China; School of Clinical Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Jiaqi Liu
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Gang Liu
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Jiayi Li
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China; School of Clinical Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Hengyi Xu
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China; School of Clinical Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Yiwen Jiang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China; School of Clinical Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Song Zhang
- Department of Breast Surgery, Yantai Yuhuangding Hospital, The Affiliated Hospital of Qingdao University, Yantai 264000, China
| | - Yidan Wang
- Department of Breast Surgery, Yantai Yuhuangding Hospital, The Affiliated Hospital of Qingdao University, Yantai 264000, China
| | - Gang Chen
- Department of Breast Surgery, Yantai Yuhuangding Hospital, The Affiliated Hospital of Qingdao University, Yantai 264000, China
| | - Guangdong Qiao
- Department of Breast Surgery, Yantai Yuhuangding Hospital, The Affiliated Hospital of Qingdao University, Yantai 264000, China
| | - Yalun Li
- Department of Breast Surgery, Yantai Yuhuangding Hospital, The Affiliated Hospital of Qingdao University, Yantai 264000, China.
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Letsou W, Wang F, Moon W, Im C, Sapkota Y, Robison LL, Yasui Y. Refining the genetic risk of breast cancer with rare haplotypes and pattern mining. Life Sci Alliance 2023; 6:e202302183. [PMID: 37541849 PMCID: PMC10403637 DOI: 10.26508/lsa.202302183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/24/2023] [Accepted: 07/26/2023] [Indexed: 08/06/2023] Open
Abstract
Hundreds of common variants have been found to confer small but significant differences in breast cancer risk, supporting the widely accepted polygenic model of inherited predisposition. Using a novel closed-pattern mining algorithm, we provide evidence that rare haplotypes may refine the association of breast cancer risk with common germline alleles. Our method, called Chromosome Overlap, consists in iteratively pairing chromosomes from affected individuals and looking for noncontiguous patterns of shared alleles. We applied Chromosome Overlap to haplotypes of genotyped SNPs from female breast cancer cases from the UK Biobank at four loci containing common breast cancer-risk SNPs. We found two rare (frequency <0.1%) haplotypes bearing a GWAS hit at 11q13 (hazard ratio = 4.21 and 16.7) which replicated in an independent, European ancestry population at P < 0.05, and another at 22q12 (frequency <0.2%, hazard ratio = 2.58) which expanded the risk pool to noncarriers of a GWAS hit. These results suggest that rare haplotypes (or mutations) may underlie the "synthetic association" of breast cancer risk with at least some common variants.
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Affiliation(s)
- William Letsou
- Department of Biological & Chemical Sciences, New York Institute of Technology, Old Westbury, NY, USA
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Fan Wang
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wonjong Moon
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cindy Im
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- School of Public Health, University of Alberta, Edmonton, Canada
| | - Yadav Sapkota
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Leslie L Robison
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yutaka Yasui
- Department of Biological & Chemical Sciences, New York Institute of Technology, Old Westbury, NY, USA
- School of Public Health, University of Alberta, Edmonton, Canada
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Efficient and accurate frailty model approach for genome-wide survival association analysis in large-scale biobanks. Nat Commun 2022; 13:5437. [PMID: 36114182 PMCID: PMC9481565 DOI: 10.1038/s41467-022-32885-x] [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: 12/07/2021] [Accepted: 08/22/2022] [Indexed: 01/11/2023] Open
Abstract
With decades of electronic health records linked to genetic data, large biobanks provide unprecedented opportunities for systematically understanding the genetics of the natural history of complex diseases. Genome-wide survival association analysis can identify genetic variants associated with ages of onset, disease progression and lifespan. We propose an efficient and accurate frailty model approach for genome-wide survival association analysis of censored time-to-event (TTE) phenotypes by accounting for both population structure and relatedness. Our method utilizes state-of-the-art optimization strategies to reduce the computational cost. The saddlepoint approximation is used to allow for analysis of heavily censored phenotypes (>90%) and low frequency variants (down to minor allele count 20). We demonstrate the performance of our method through extensive simulation studies and analysis of five TTE phenotypes, including lifespan, with heavy censoring rates (90.9% to 99.8%) on ~400,000 UK Biobank participants with white British ancestry and ~180,000 individuals in FinnGen. We further analyzed 871 TTE phenotypes in the UK Biobank and presented the genome-wide scale phenome-wide association results with the PheWeb browser.
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Xu W, Zhong Y, Yang H, Gong Y, Dao J, Bao L. Association between the rs4784227-CASC16 polymorphism and the risk of breast cancer: A meta-analysis. Medicine (Baltimore) 2022; 101:e30218. [PMID: 36042591 PMCID: PMC9410658 DOI: 10.1097/md.0000000000030218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
OBJECTIVE Although several studies have identified an association between the rs4784227-cancer susceptibility candidate gene 16 (CASC16) polymorphism and breast cancer, the results remain inconclusive. Therefore, we conducted a meta-analysis to assess the relationship between the rs4784227-CASC16 polymorphism and breast cancer risk. METHODS Studies were searched in the PubMed, Web of Science, Embase, Google Scholar, and Cochran Library databases until June 10, 2021, to identify all potential literature on rs4784227-CASC16 polymorphism and breast cancer risk association. Fixed-effect or random-effect models were used to calculate odds ratios (ORs) and their corresponding 95% confidence intervals (95% CIs). Subgroup analyses, publication bias, and sensitivity analyses were also conducted. RESULTS Seventeen eligible studies involving 34,719 subjects (18,445 cases and 16,274 healthy controls) from 7 articles were included in the current meta-analysis. The pooled ORs regarding the association between the rs4784227-CASC16 polymorphism and breast cancer risk were statistically significant [T vs C: OR = 1.244, 95% CI = 1.202-1.287; TT vs CT + CC: OR = 1.407, 95% CI = 1.296-1.528; CC vs CT + TT: OR = 0.777, 95% CI = 0.745-0.811; TT vs CC: OR = 1.544, 95% CI = 1.419-1.681; CT vs CC: OR = 1.244, 95% CI = 1.189-1.301]. On subgroup analysis, the rs4784227-CASC16 T/C gene has a certain correlation with breast cancer susceptibility in Asian and North American populations, but no significant risk in the Australian population. CONCLUSION Our pooled analysis showed a significant association between the rs4784227- (T) allele and breast cancer susceptibility in Asian and North American populations, and intervention with this mutation might be a new therapeutic strategy for breast cancer. However, large-scale and well-designed studies are needed in different populations to further evaluate the role of the rs4784227-CASC16 polymorphism in breast cancer.
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Affiliation(s)
- Wenji Xu
- Department of Gastrointestinal and Plastic Surgery, Pu’er People’s Hospital, Yunnan
| | - Yao Zhong
- Department of Gastroenterology, Pu’er People’s Hospital, Yunnan
| | - Haihui Yang
- Department of Cardiology, Pu’er People’s Hospital, Yunnan
| | - Yuhan Gong
- Department of Nephrology, Pu’er People’s Hospital, Yunnan
| | - Jun Dao
- Department of Nephrology, Pu’er People’s Hospital, Yunnan
| | - Liping Bao
- Department of Nephrology, Pu’er People’s Hospital, Yunnan
- *Correspondence: Liping Bao, Department of Nephrology, Pu’er People’s Hospital, Yunnan, 44 Zhenxing Avenue, 665000, Pu’er, P.R.China (e-mail )
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Barnekow E, Liu W, Helgadottir HT, Michailidou K, Dennis J, Bryant P, Thutkawkorapin J, Wendt C, Czene K, Hall P, Margolin S, Lindblom A. A Swedish Genome-Wide Haplotype Association Analysis Identifies a Novel Breast Cancer Susceptibility Locus in 8p21.2 and Characterizes Three Loci on Chromosomes 10, 11 and 16. Cancers (Basel) 2022; 14:cancers14051206. [PMID: 35267517 PMCID: PMC8909613 DOI: 10.3390/cancers14051206] [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: 12/31/2021] [Revised: 02/17/2022] [Accepted: 02/24/2022] [Indexed: 02/04/2023] Open
Abstract
(1) Background: The heritability of breast cancer is partly explained but much of the genetic contribution remains to be identified. Haplotypes are often used as markers of ethnicity as they are preserved through generations. We have previously demonstrated that haplotype analysis, in addition to standard SNP association studies, could give novel and more detailed information on genetic cancer susceptibility. (2) Methods: In order to examine the association of a SNP or a haplotype to breast cancer risk, we performed a genome wide haplotype association study, using sliding window analysis of window sizes 1−25 and 50 SNPs, in 3200 Swedish breast cancer cases and 5021 controls. (3) Results: We identified a novel breast cancer susceptibility locus in 8p21.1 (OR 2.08; p 3.92 × 10−8), confirmed three known loci in 10q26.13, 11q13.3, 16q12.1-2 and further identified novel subloci within these three loci. Altogether 76 risk SNPs, 3302 risk haplotypes of window size 2−25 and 113 risk haplotypes of window size 50 at p < 5 × 10−8 on chromosomes 8, 10, 11 and 16 were identified. In the known loci haplotype analysis reached an OR of 1.48 in overall breast cancer and in familial cases OR 1.68. (4) Conclusions: Analyzing haplotypes, rather than single variants, could detect novel susceptibility loci even in small study populations but the method requires a fairly homogenous study population.
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Affiliation(s)
- Elin Barnekow
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, 11883 Stockholm, Sweden; (C.W.); (S.M.)
- Department of Oncology, Södersjukhuset, 11883 Stockholm, Sweden;
- Correspondence: (E.B.); (A.L.); Tel.: +46-736-565-798 (E.B.); +46-852-485-248 (A.L.)
| | - Wen Liu
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17176 Stockholm, Sweden; (W.L.); (H.T.H.); (P.B.); (J.T.)
- Department of Neuroscience, Uppsala University, 75237 Uppsala, Sweden
| | - Hafdis T. Helgadottir
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17176 Stockholm, Sweden; (W.L.); (H.T.H.); (P.B.); (J.T.)
- Department of Clinical Genetics, Karolinska University Hospital, 17164 Stockholm, Sweden
| | - Kyriaki Michailidou
- The Cyprus Institute of Neurology & Genetics, Cyprus School of Molecular Medicine, 1683 Nicosia, Cyprus;
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB18RN, UK;
| | - Patrick Bryant
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17176 Stockholm, Sweden; (W.L.); (H.T.H.); (P.B.); (J.T.)
- Department of Biochemistry and Biophysics, Stockholm University, 17165 Stockholm, Sweden
- Science for Life Laboratory, 17165 Stockholm, Sweden
| | - Jessada Thutkawkorapin
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17176 Stockholm, Sweden; (W.L.); (H.T.H.); (P.B.); (J.T.)
- Department of Computer Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok 10330, Thailand
| | - Camilla Wendt
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, 11883 Stockholm, Sweden; (C.W.); (S.M.)
- Department of Oncology, Södersjukhuset, 11883 Stockholm, Sweden;
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17165 Stockholm, Sweden;
| | - Per Hall
- Department of Oncology, Södersjukhuset, 11883 Stockholm, Sweden;
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 17165 Stockholm, Sweden;
| | - Sara Margolin
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, 11883 Stockholm, Sweden; (C.W.); (S.M.)
- Department of Oncology, Södersjukhuset, 11883 Stockholm, Sweden;
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 17176 Stockholm, Sweden; (W.L.); (H.T.H.); (P.B.); (J.T.)
- Department of Clinical Genetics, Karolinska University Hospital, 17164 Stockholm, Sweden
- Correspondence: (E.B.); (A.L.); Tel.: +46-736-565-798 (E.B.); +46-852-485-248 (A.L.)
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Risk Association of TOX3 and MMP7 Gene Polymorphisms with Sporadic Breast Cancer in Mexican Women. Curr Oncol 2022; 29:1008-1017. [PMID: 35200585 PMCID: PMC8870835 DOI: 10.3390/curroncol29020086] [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: 10/08/2021] [Revised: 02/03/2022] [Accepted: 02/05/2022] [Indexed: 01/14/2023] Open
Abstract
Breast cancer (BC) has one of the highest incidences and mortality worldwide. Single nucleotide polymorphisms (SNPs) in TOX3 rs3803662 and MMP7 rs1943779 have been associated with susceptibility to BC. In this case-control study, we evaluated the association of rs3803662 (TOX3)/rs1943779 (MMP7) SNPs with clinical features, immunohistochemical reactivity, and risk association with BC in women from northeastern Mexico. We compared 212 BC cases and 212 controls. DNA was isolated from peripheral blood to perform the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay. We calculated genotype frequencies, odds ratios, and 95% confidence intervals. We found that CT (Cytocine-Thymine) and TT (Thymine -Thymine) genotypes, and T alleles of TOX3 rs3803662, were associated with BC risk (p = 0.034, p = 0.011, respectively). SNP TOX3 rs3803662 was associated with positive progesterone receptors (PR) and triple-negative BC (TNBC) but not with estrogen receptor (ER) or HER2 reactivity. CT and TT genotypes (p = 0.006) and T alleles (p = 0.002) of SNP MMP7 rs1943779 were associated with risk of BC. We found that T alleles of TOX3 rs3803662 and MMP7 rs1943779 SNPs are associated with BC risk. These findings contribute to personalized medicine in Mexican women.
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Coignard J, Lush M, Beesley J, O'Mara TA, Dennis J, Tyrer JP, Barnes DR, McGuffog L, Leslie G, Bolla MK, Adank MA, Agata S, Ahearn T, Aittomäki K, Andrulis IL, Anton-Culver H, Arndt V, Arnold N, Aronson KJ, Arun BK, Augustinsson A, Azzollini J, Barrowdale D, Baynes C, Becher H, Bermisheva M, Bernstein L, Białkowska K, Blomqvist C, Bojesen SE, Bonanni B, Borg A, Brauch H, Brenner H, Burwinkel B, Buys SS, Caldés T, Caligo MA, Campa D, Carter BD, Castelao JE, Chang-Claude J, Chanock SJ, Chung WK, Claes KBM, Clarke CL, Collée JM, Conroy DM, Czene K, Daly MB, Devilee P, Diez O, Ding YC, Domchek SM, Dörk T, Dos-Santos-Silva I, Dunning AM, Dwek M, Eccles DM, Eliassen AH, Engel C, Eriksson M, Evans DG, Fasching PA, Flyger H, Fostira F, Friedman E, Fritschi L, Frost D, Gago-Dominguez M, Gapstur SM, Garber J, Garcia-Barberan V, García-Closas M, García-Sáenz JA, Gaudet MM, Gayther SA, Gehrig A, Georgoulias V, Giles GG, Godwin AK, Goldberg MS, Goldgar DE, González-Neira A, Greene MH, Guénel P, Haeberle L, Hahnen E, Haiman CA, Håkansson N, Hall P, Hamann U, Harrington PA, Hart SN, He W, Hogervorst FBL, Hollestelle A, Hopper JL, Horcasitas DJ, Hulick PJ, Hunter DJ, Imyanitov EN, Jager A, Jakubowska A, James PA, Jensen UB, John EM, Jones ME, Kaaks R, Kapoor PM, Karlan BY, Keeman R, Khusnutdinova E, Kiiski JI, Ko YD, Kosma VM, Kraft P, Kurian AW, Laitman Y, Lambrechts D, Le Marchand L, Lester J, Lesueur F, Lindstrom T, Lopez-Fernández A, Loud JT, Luccarini C, Mannermaa A, Manoukian S, Margolin S, Martens JWM, Mebirouk N, Meindl A, Miller A, Milne RL, Montagna M, Nathanson KL, Neuhausen SL, Nevanlinna H, Nielsen FC, O'Brien KM, Olopade OI, Olson JE, Olsson H, Osorio A, Ottini L, Park-Simon TW, Parsons MT, Pedersen IS, Peshkin B, Peterlongo P, Peto J, Pharoah PDP, Phillips KA, Polley EC, Poppe B, Presneau N, Pujana MA, Punie K, Radice P, Rantala J, Rashid MU, Rennert G, Rennert HS, Robson M, Romero A, Rossing M, Saloustros E, Sandler DP, Santella R, Scheuner MT, Schmidt MK, Schmidt G, Scott C, Sharma P, Soucy P, Southey MC, Spinelli JJ, Steinsnyder Z, Stone J, Stoppa-Lyonnet D, Swerdlow A, Tamimi RM, Tapper WJ, Taylor JA, Terry MB, Teulé A, Thull DL, Tischkowitz M, Toland AE, Torres D, Trainer AH, Truong T, Tung N, Vachon CM, Vega A, Vijai J, Wang Q, Wappenschmidt B, Weinberg CR, Weitzel JN, Wendt C, Wolk A, Yadav S, Yang XR, Yannoukakos D, Zheng W, Ziogas A, Zorn KK, Park SK, Thomassen M, Offit K, Schmutzler RK, Couch FJ, Simard J, Chenevix-Trench G, Easton DF, Andrieu N, Antoniou AC. A case-only study to identify genetic modifiers of breast cancer risk for BRCA1/BRCA2 mutation carriers. Nat Commun 2021; 12:1078. [PMID: 33597508 PMCID: PMC7890067 DOI: 10.1038/s41467-020-20496-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 11/19/2020] [Indexed: 02/02/2023] Open
Abstract
Breast cancer (BC) risk for BRCA1 and BRCA2 mutation carriers varies by genetic and familial factors. About 50 common variants have been shown to modify BC risk for mutation carriers. All but three, were identified in general population studies. Other mutation carrier-specific susceptibility variants may exist but studies of mutation carriers have so far been underpowered. We conduct a novel case-only genome-wide association study comparing genotype frequencies between 60,212 general population BC cases and 13,007 cases with BRCA1 or BRCA2 mutations. We identify robust novel associations for 2 variants with BC for BRCA1 and 3 for BRCA2 mutation carriers, P < 10-8, at 5 loci, which are not associated with risk in the general population. They include rs60882887 at 11p11.2 where MADD, SP11 and EIF1, genes previously implicated in BC biology, are predicted as potential targets. These findings will contribute towards customising BC polygenic risk scores for BRCA1 and BRCA2 mutation carriers.
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Affiliation(s)
- Juliette Coignard
- Genetic Epidemiology of Cancer team, Inserm, U900, Paris, France
- Institut Curie Paris, Paris, France
- Mines ParisTech Fontainebleau, Paris, France
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- PSL University Paris, Paris, France
- Paris Sud University, Orsay, France
| | - Michael Lush
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jonathan Beesley
- Department of Genetics and Computational Biology QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Tracy A O'Mara
- Department of Genetics and Computational Biology QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Joe Dennis
- 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
| | - Daniel R Barnes
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Lesley McGuffog
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Goska Leslie
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Muriel A Adank
- Family Cancer Clinic, The Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Simona Agata
- Immunology and Molecular Oncology, Unit Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Thomas Ahearn
- Division of Cancer Epidemiology and Genetics National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - Kristiina Aittomäki
- Department of Clinical Genetics, Helsinki University Hospital University of Helsinki, Helsinki, Finland
| | - 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
| | - Hoda Anton-Culver
- Department of Epidemiology, Genetic Epidemiology Research Institute University of California Irvine, Irvine, CA, USA
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - 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
| | - Kristan J Aronson
- Department of Public Health Sciences, and Cancer Research Institute Queen's University, Kingston, ON, Canada
| | - Banu K Arun
- Department of Breast Medical Oncology University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Annelie Augustinsson
- Department of Cancer Epidemiology, Clinical Sciences Lund University, Lund, 22242, Sweden
| | - Jacopo Azzollini
- Unit of Medical Genetics, Department of Medical Oncology and Hematology Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Daniel Barrowdale
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Caroline Baynes
- Centre for Cancer Genetic Epidemiology, Department of Oncology University of Cambridge, Cambridge, UK
| | - Heiko Becher
- Institute for Medical Biometrics and Epidemiology University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marina Bermisheva
- Institute of Biochemistry and Genetics Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
| | - Leslie Bernstein
- Department of Population Sciences Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Katarzyna Białkowska
- Department of Genetics and Pathology Pomeranian Medical University Szczecin, Szczecin, Poland
| | - Carl Blomqvist
- Department of Oncology, Helsinki University Hospital University of Helsinki, Helsinki, Finland
- Department of Oncology Örebro University Hospital, Örebro, Sweden
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences University of Copenhagen, Copenhagen, Denmark
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Ake Borg
- Department of Oncology Lund University and Skåne University Hospital, Lund, Sweden
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- iFIT-Cluster of Excellence University of Tübingen, Tübingen, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Barbara Burwinkel
- Molecular Epidemiology Group, C080 German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Biology of Breast Cancer, University Womens Clinic Heidelberg University of Heidelberg, Heidelberg, Germany
| | - Saundra S Buys
- Department of Medicine Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - 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
| | - Daniele Campa
- Department of Biology University of Pisa, Pisa, Italy
- Division of Cancer Epidemiology German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Brian D Carter
- Behavioral and Epidemiology Research Group American Cancer Society Atlanta, Atlanta, GA, USA
| | - Jose E Castelao
- Oncology and Genetics Unit Instituto de Investigacion Sanitaria Galicia Sur (IISGS), Xerencia de Xestion Integrada de Vigo-SERGAS, Vigo, Spain
| | - 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
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA
| | | | - Christine L Clarke
- Westmead Institute for Medical Research University of Sydney, Sydney, NSW, Australia
| | - J Margriet Collée
- Department of Clinical Genetics Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Don M Conroy
- Centre for Cancer Genetic Epidemiology, Department of Oncology University of Cambridge, Cambridge, UK
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mary B Daly
- Department of Clinical Genetics Fox Chase Cancer Center Philadelphia, Philadelphia, PA, USA
| | - Peter Devilee
- Department of Pathology Leiden University Medical Center, Leiden, The Netherlands
- Department of Human Genetics Leiden University Medical Center, Leiden, The Netherlands
| | - Orland Diez
- Oncogenetics Group Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Clinical and Molecular Genetics Area University Hospital Vall d'Hebron, Barcelona, Spain
| | - Yuan Chun Ding
- Department of Population Sciences Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Susan M Domchek
- Basser Center for BRCA, Abramson Cancer Center University of Pennsylvania, Philadelphia, PA, USA
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Isabel Dos-Santos-Silva
- Department of Non-Communicable Disease Epidemiology London School of Hygiene and Tropical Medicine, London, UK
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology University of Cambridge, Cambridge, UK
| | - Miriam Dwek
- School of Life Sciences University of Westminster, London, UK
| | - Diana M Eccles
- Faculty of Medicine University of Southampton, Southampton, UK
| | - A Heather Eliassen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Epidemiology Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology University of Leipzig, Leipzig, Germany
| | - Mikael Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - D Gareth Evans
- Genomic Medicine, Division of Evolution and Genomic Sciences The University of Manchester, Manchester Academic Health Science Centre, Manchester Universities Foundation Trust, St Mary's Hospital, Manchester, UK
- Genomic Medicine, North West Genomics hub Manchester Academic Health Science Centre, Manchester Universities Foundation Trust, St Mary's Hospital, Manchester, UK
| | - Peter A Fasching
- David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology University of California at Los Angeles, Los Angeles, CA, USA
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center ER-EMN University Hospital Erlangen, Friedrich-Alexander-University, Erlangen-Nuremberg, Erlangen, Germany
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital Copenhagen University Hospital, Herlev, Denmark
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, INRASTES National Centre for Scientific Research íDemokritosí, Athens, Greece
| | - 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
| | - Lin Fritschi
- School of Public Health Curtin University, Perth, Western Australia, Australia
| | - Debra Frost
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Foundation of Genomic Medicine Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain
- Moores Cancer Center University of California, San Diego La Jolla, CA, USA
| | - Susan M Gapstur
- Behavioral and Epidemiology Research Group American Cancer Society Atlanta, Atlanta, GA, USA
| | - Judy Garber
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Vanesa Garcia-Barberan
- Medical Oncology Department, Hospital Clínico San Carlos Instituto de Investigación Sanitaria San Carlos (IdISSC), Centro Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - José A García-Sáenz
- Medical Oncology Department, Hospital Clínico San Carlos Instituto de Investigación Sanitaria San Carlos (IdISSC), Centro Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Mia M Gaudet
- Behavioral and Epidemiology Research Group American Cancer Society Atlanta, Atlanta, GA, USA
| | - Simon A Gayther
- Center for Bioinformatics and Functional Genomics and the Cedars Sinai Genomics Core Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Andrea Gehrig
- Department of Human Genetics University Würzburg, Würzburg, Germany
| | | | - Graham G Giles
- Cancer Epidemiology Division Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health Monash University, Clayton, VIC, Australia
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Mark S Goldberg
- Department of Medicine, McGill University, Montréal, QC, Canada
- Division of Clinical Epidemiology, Royal Victoria Hospital McGill University Montréal, Montréal, QC, Canada
| | - David E Goldgar
- Huntsman Cancer Institute and Department of Dermatology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Anna González-Neira
- Human Cancer Genetics Programme Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Mark H Greene
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics National Cancer Institute, Bethesda, MD, USA
| | - Pascal Guénel
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP) INSERM, University Paris-Sud, University Paris-Saclay, Villejuif, France
| | - Lothar Haeberle
- Department of Gynaecology and Obstetrics, University Hospital Erlangen Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Eric Hahnen
- Center for Hereditary 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
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine University of Southern California, Los Angeles, CA, USA
| | | | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - Ute Hamann
- Molecular Genetics of Breast Cancer German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patricia A Harrington
- Centre for Cancer Genetic Epidemiology, Department of Oncology University of Cambridge, Cambridge, UK
| | - Steven N Hart
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Wei He
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Frans B L Hogervorst
- Family Cancer Clinic, The Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Antoinette Hollestelle
- Department of Medical Oncology, Family Cancer Clinic 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
| | - Darling J Horcasitas
- New Mexico Oncology Hematology Consultants, University of New Mexico, Albuquerque, NM, USA
| | - Peter J Hulick
- Center for Medical Genetics NorthShore University HealthSystem, Evanston, IL, USA
- The University of Chicago Pritzker School of Medicine Chicago, Chicago, IL, USA
| | - David J Hunter
- Department of Epidemiology Harvard TH Chan School of Public Health, Boston, MA, USA
- Program in Genetic Epidemiology and Statistical Genetics Harvard TH Chan School of Public Health Boston, Boston, MA, USA
- Nuffield Department of Population Health University of Oxford, Oxford, UK
| | | | - Agnes Jager
- Department of Medical Oncology, Family Cancer Clinic Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Anna Jakubowska
- Department of Genetics and Pathology Pomeranian Medical University Szczecin, Szczecin, Poland
- Independent Laboratory of Molecular Biology and Genetic Diagnostics Pomeranian Medical University, Szczecin, Poland
| | - Paul A James
- Sir Peter MacCallum Department of Oncology The University of Melbourne, Melbourne, VIC, Australia
- Parkville Familial Cancer Centre Peter MacCallum Cancer Center, Melbourne, VIC, Australia
| | - Uffe Birk Jensen
- Department of Clinical Genetics Aarhus, University Hospital, Aarhus, Denmark
| | - Esther M John
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael E Jones
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - Rudolf Kaaks
- Division of Cancer Epidemiology German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pooja Middha Kapoor
- Division of Cancer Epidemiology German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Genetics and Epidemiology The Institute of Cancer Research, London, UK
| | - Beth Y Karlan
- Faculty of Medicine University of Heidelberg, Heidelberg, Germany
- David Geffen School of Medicine, Department of Obstetrics and Gynecology University of California at Los Angeles, Los Angeles, CA, USA
| | - Renske Keeman
- Womenís Cancer Program at the Samuel Oschin Comprehensive Cancer Institute Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
- Division of Molecular Pathology The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Johanna I Kiiski
- Department of Genetics and Fundamental Medicine Bashkir State Medical University, Ufa, Russia
| | - Yon-Dschun Ko
- Department of Obstetrics and Gynecology, Helsinki University Hospital University of Helsinki, Helsinki, Finland
| | - Veli-Matti Kosma
- Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH Johanniter Krankenhaus, Bonn, Germany
- Translational Cancer Research Area University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine University of Eastern Finland, Kuopio, Finland
| | - Peter Kraft
- Department of Epidemiology Harvard TH Chan School of Public Health, Boston, MA, USA
- Program in Genetic Epidemiology and Statistical Genetics Harvard TH Chan School of Public Health Boston, Boston, MA, USA
| | - Allison W Kurian
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - Yael Laitman
- The Susanne Levy Gertner Oncogenetics Unit Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Diether Lambrechts
- VIB Center for Cancer Biology, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Human Genetics University of Leuven, Leuven, Belgium
| | - Loic Le Marchand
- Epidemiology Program University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Jenny Lester
- Faculty of Medicine University of Heidelberg, Heidelberg, Germany
- David Geffen School of Medicine, Department of Obstetrics and Gynecology University of California at Los Angeles, Los Angeles, CA, USA
| | - Fabienne Lesueur
- Genetic Epidemiology of Cancer team, Inserm, U900, Paris, France
- Institut Curie Paris, Paris, France
- Mines ParisTech Fontainebleau, Paris, France
- PSL University Paris, Paris, France
| | - Tricia Lindstrom
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Adria Lopez-Fernández
- High Risk and Cancer Prevention Group Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Jennifer T Loud
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics National Cancer Institute, Bethesda, MD, USA
| | - Craig Luccarini
- Centre for Cancer Genetic Epidemiology, Department of Oncology University of Cambridge, Cambridge, UK
| | - Arto Mannermaa
- Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH Johanniter Krankenhaus, Bonn, Germany
- Translational Cancer Research Area University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine University of Eastern Finland, Kuopio, Finland
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Medical Oncology and Hematology Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Sara Margolin
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
- Department of Clinical Science and Education, Södersjukhuset Karolinska Institutet, Stockholm, Sweden
| | - John W M Martens
- Department of Medical Oncology, Family Cancer Clinic Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Noura Mebirouk
- Genetic Epidemiology of Cancer team, Inserm, U900, Paris, France
- Institut Curie Paris, Paris, France
- Mines ParisTech Fontainebleau, Paris, France
- PSL University Paris, Paris, France
| | - Alfons Meindl
- Department of Gynecology and Obstetrics University of Munich, Campus Grosshadern, Munich, Germany
| | - Austin Miller
- NRG Oncology, Statistics and Data Management Center Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Roger L Milne
- Cancer Epidemiology Division Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health Monash University, Clayton, VIC, Australia
| | - 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 Genetics and Fundamental Medicine Bashkir State Medical University, Ufa, Russia
| | - Finn C Nielsen
- Center for Genomic Medicine Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Katie M O'Brien
- Epidemiology Branch National Institute of Environmental Health Sciences, NIH Research Triangle Park, Durham, NC, USA
| | | | - Janet E Olson
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Håkan Olsson
- Department of Cancer Epidemiology, Clinical Sciences Lund University, Lund, 22242, Sweden
| | - Ana Osorio
- Human Cancer Genetics Programme Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Laura Ottini
- Department of Molecular Medicine University La Sapienza, Rome, Italy
| | | | - Michael T Parsons
- Department of Genetics and Computational Biology QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Inge Sokilde Pedersen
- Molecular Diagnostics Aalborg University Hospital, Aalborg, Denmark
- Clinical Cancer Research Center Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine Aalborg University, Aalborg, Denmark
| | - Beth Peshkin
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Paolo Peterlongo
- Genome Diagnostics Program IFOM - the FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology, Milan, Italy
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology London School of Hygiene and Tropical Medicine, London, UK
| | - 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
| | - Kelly-Anne Phillips
- Department of Genetics and Computational Biology QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology The University of Melbourne, Melbourne, VIC, Australia
| | - Eric C Polley
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Bruce Poppe
- Centre for Medical Genetics Ghent University, Gent, Belgium
| | - Nadege Presneau
- School of Life Sciences University of Westminster, London, UK
| | - Miquel Angel Pujana
- Translational Research Laboratory IDIBELL (Bellvitge Biomedical Research Institute), Catalan Institute of Oncology, CIBERONC, Barcelona, Spain
| | - Kevin Punie
- Leuven Multidisciplinary Breast Center, Department of Oncology Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Research Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | | | - Muhammad U Rashid
- Molecular Genetics of Breast Cancer German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Basic Sciences Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH & RC), Lahore, Pakistan
| | - Gad Rennert
- Clalit National Cancer Control Center Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - Hedy S Rennert
- Clalit National Cancer Control Center Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - Mark Robson
- Clinical Genetics Service, Department of Medicine Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Atocha Romero
- Medical Oncology Department Hospital Universitario Puerta de Hierro, Madrid, Spain
| | - Maria Rossing
- Center for Genomic Medicine Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Dale P Sandler
- Epidemiology Branch National Institute of Environmental Health Sciences, NIH Research Triangle Park, Durham, NC, USA
| | - Regina Santella
- Department of Epidemiology, Mailman School of Public Health Columbia University, New York, NY, USA
| | - Maren T Scheuner
- Cancer Genetics and Prevention Program University of California San Francisco, San Francisco, CA, USA
| | - Marjanka K Schmidt
- Womenís Cancer Program at the Samuel Oschin Comprehensive Cancer Institute Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Psychosocial Research and Epidemiology The Netherlands Cancer Institute - Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Gunnar Schmidt
- Institute of Human Genetics Hannover Medical School, Hannover, Germany
| | - Christopher Scott
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Priyanka Sharma
- Department of Internal Medicine, Division of Medical Oncology University of Kansas Medical Center, Westwood, KS, USA
| | - Penny Soucy
- Genomics Center, Centre Hospitalier Universitaire de Québec - Université Laval Research Center, Québec City, QC, Canada
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health Monash University, Clayton, VIC, Australia
- Department of Clinical Pathology The University of Melbourne, Melbourne, VIC, Australia
| | - John J Spinelli
- Population Oncology BC Cancer, Vancouver, BC, Canada
- School of Population and Public Health University of British Columbia, Vancouver, BC, Canada
| | - Zoe Steinsnyder
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Jennifer Stone
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
- The Curtin UWA Centre for Genetic Origins of Health and Disease Curtin University and University of Western Australia, Perth, Western Australia, Australia
| | - Dominique Stoppa-Lyonnet
- Service de Génétique Institut Curie, Paris, France
- Department of Tumour Biology INSERM U830, Paris, France
- Université Paris Descartes, Paris, France
| | - Anthony Swerdlow
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Division of Breast Cancer Research Institute of Cancer Research, London, UK
| | - Rulla M Tamimi
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Epidemiology Harvard TH Chan School of Public Health, Boston, MA, USA
- Program in Genetic Epidemiology and Statistical Genetics Harvard TH Chan School of Public Health Boston, Boston, MA, USA
| | | | - Jack A Taylor
- Epidemiology Branch National Institute of Environmental Health Sciences, NIH Research Triangle Park, Durham, NC, USA
- Epigenetic and Stem Cell Biology Laboratory National Institute of Environmental Health Sciences, NIH Research Triangle Park, Triangle Park, NC, USA
| | - Mary Beth Terry
- Department of Epidemiology, Mailman School of Public Health Columbia University, New York, NY, USA
| | - Alex Teulé
- Hereditary Cancer Program ONCOBELL-IDIBELL-IDIBGI-IGTP, Catalan Institute of Oncology, CIBERONC, Barcelona, Spain
| | - 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 Center, University of Cambridge, Cambridge, UK
| | - Amanda E Toland
- Department of Cancer Biology and Genetics The Ohio State University, Columbus, OH, USA
| | - Diana Torres
- Molecular Genetics of Breast Cancer German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Human Genetics Pontificia Universidad Javeriana, Bogota, Colombia
| | - Alison H Trainer
- Parkville Familial Cancer Centre Peter MacCallum Cancer Center, Melbourne, VIC, Australia
- Department of medicine University Of Melbourne, Melbourne, VIC, Australia
| | - Thérèse Truong
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP) INSERM, University Paris-Sud, University Paris-Saclay, Villejuif, France
| | - Nadine Tung
- Department of Medical Oncology Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Celine M Vachon
- Department of Health Science Research, Division of Epidemiology Mayo Clinic, Rochester, MN, USA
| | - Ana Vega
- Fundación Pública Galega Medicina Xenómica-SERGAS, Instituto de Investigación Sanitaria Santiago de Compostela (IDIS); CIBERER, Santiago de Compostela, Spain
| | - Joseph Vijai
- Clinical Genetics Service, Department of Medicine Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Barbara Wappenschmidt
- Center for Hereditary 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
| | - Clarice R Weinberg
- Biostatistics and Computational Biology Branch National Institute of Environmental Health Sciences, NIH Research Triangle Park, Triangle Park, NC, USA
| | | | - Camilla Wendt
- Department of Clinical Science and Education, Södersjukhuset Karolinska Institutet, Stockholm, Sweden
| | - Alicja Wolk
- Institute of Environmental Medicine Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences Uppsala University, Uppsala, Sweden
| | | | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, INRASTES National Centre for Scientific Research íDemokritosí, Athens, Greece
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Argyrios Ziogas
- Department of Epidemiology, Genetic Epidemiology Research Institute University of California Irvine, Irvine, CA, USA
| | - Kristin K Zorn
- Magee-Womens Hospital, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - 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
| | - Mads Thomassen
- Department of Clinical Genetics Odense University Hospital, Odence C, Denmark
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Rita K Schmutzler
- Center for Hereditary 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
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology Mayo Clinic, Rochester, MN, USA
| | - Jacques Simard
- Department of Epidemiology, Genetic Epidemiology Research Institute University of California Irvine, Irvine, CA, USA
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - 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
| | - Nadine Andrieu
- Genetic Epidemiology of Cancer team, Inserm, U900, Paris, France.
- Institut Curie Paris, Paris, France.
- Mines ParisTech Fontainebleau, Paris, France.
- PSL University Paris, Paris, France.
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
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Hu J, Li T, Wang S, Zhang H. Supervariants identification for breast cancer. Genet Epidemiol 2020; 44:934-947. [PMID: 32808324 PMCID: PMC7924970 DOI: 10.1002/gepi.22350] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/24/2020] [Accepted: 08/05/2020] [Indexed: 01/02/2023]
Abstract
In genome-wide association studies, signals associated with rare variants and interactions between genes are hard to detect even when the sample size is in tens of thousands. To overcome these problems, we examine the concept of supervariant. Like the classic concept of the gene, a supervariant is a combination of alleles in multiple loci, but the contributing loci can be anywhere in the genome. We hypothesize that supervariants are easy to detect and the aggregated signals are more stable in their associations with the disease than that from a single nucleoid polymorphism. Using the UK Biobank databases, we develop a ranking and aggregation method for identifying supervariants. Specifically, we examine 9,377 breast cancer cases with 46,861 controls matched by sex and age. In our simulations, the use of supervariants outperforms single-nucleotide polymorphism-based association method in detecting rare variants and signals with interactive structure. In real data analysis, we identify supervariants on Chromosomes 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 16, and 22 which cover previously reported loci that have associations with breast or other cancers, and several novel loci on Chromosomes 2, 5, 9, and 12. These findings demonstrate the validity of supervariants and its potential of discovering replicable and novel results for complex disease.
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Affiliation(s)
- Jianchang Hu
- Department of Biostatistics, Yale University School of Public Health, New Haven, Connecticut
| | - Ting Li
- Department of Biostatistics, Yale University School of Public Health, New Haven, Connecticut
| | - Shiying Wang
- Department of Biostatistics, Yale University School of Public Health, New Haven, Connecticut
| | - Heping Zhang
- Department of Biostatistics, Yale University School of Public Health, New Haven, Connecticut
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9
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Vsevolozhskaya OA, Shi M, Hu F, Zaykin DV. DOT: Gene-set analysis by combining decorrelated association statistics. PLoS Comput Biol 2020; 16:e1007819. [PMID: 32287273 PMCID: PMC7182280 DOI: 10.1371/journal.pcbi.1007819] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 04/24/2020] [Accepted: 03/23/2020] [Indexed: 12/12/2022] Open
Abstract
Historically, the majority of statistical association methods have been designed assuming availability of SNP-level information. However, modern genetic and sequencing data present new challenges to access and sharing of genotype-phenotype datasets, including cost of management, difficulties in consolidation of records across research groups, etc. These issues make methods based on SNP-level summary statistics particularly appealing. The most common form of combining statistics is a sum of SNP-level squared scores, possibly weighted, as in burden tests for rare variants. The overall significance of the resulting statistic is evaluated using its distribution under the null hypothesis. Here, we demonstrate that this basic approach can be substantially improved by decorrelating scores prior to their addition, resulting in remarkable power gains in situations that are most commonly encountered in practice; namely, under heterogeneity of effect sizes and diversity between pairwise LD. In these situations, the power of the traditional test, based on the added squared scores, quickly reaches a ceiling, as the number of variants increases. Thus, the traditional approach does not benefit from information potentially contained in any additional SNPs, while our decorrelation by orthogonal transformation (DOT) method yields steady gain in power. We present theoretical and computational analyses of both approaches, and reveal causes behind sometimes dramatic difference in their respective powers. We showcase DOT by analyzing breast cancer and cleft lip data, in which our method strengthened levels of previously reported associations and implied the possibility of multiple new alleles that jointly confer disease risk.
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Affiliation(s)
- Olga A. Vsevolozhskaya
- Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, Kentucky, United States of America
| | - Min Shi
- Biostatistics and Computational Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - Fengjiao Hu
- Biostatistics and Computational Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - Dmitri V. Zaykin
- Biostatistics and Computational Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
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10
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Association of the functional genetic variants of TOX3 gene with breast cancer in Iran: A case-control study. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2019.100511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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11
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Kumaran M, Ghosh S, Joy AA, Mackey JR, Cass CE, Zheng W, Yasui Y, Damaraju S. Fine-mapping of a novel premenopausal breast cancer susceptibility locus at Chr4q31.22 in Caucasian women and validation in African and Chinese women. Int J Cancer 2020; 146:1219-1229. [PMID: 31087647 PMCID: PMC7004017 DOI: 10.1002/ijc.32407] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 05/08/2019] [Indexed: 12/12/2022]
Abstract
We previously identified a novel breast cancer susceptibility variant on chromosome 4q31.22 locus (rs1429142) conferring risk among women of European ancestry. Here, we report replication of findings, validation of the variant in diverse populations and fine-mapping of the associated locus in Caucasian population. The SNP rs1429142 (C/T, minor allele frequency 18%) showed association for the overall breast cancer risk in Stages 1-4 (n = 4,331 cases/4271 controls; p = 4.35 × 10-8 ; odds ratio, ORC-allele ,1.25), and an elevated risk among premenopausal women (n = 1,503 cases/4271 controls; p = 5.81 × 10-10 ; ORC-allele 1.40) in European populations. SNP rs1429142 was associated with premenopausal breast cancer risk in women of African (T/C; p-value 1.45 × 10-02 ; ORC-allele 1.2) but not from Chinese ancestry. Fine-mapping of the locus revealed several potential causal variants which are present within a single association signal, revealed from the conditional regression analysis. Functional annotation of the potential causal variants revealed three putative SNPs rs1366691, rs1429139 and rs7667633 with active enhancer functions inferred based on histone marks, DNase hypersensitive sites in breast cell line data. These putative variants were bound by transcription factors (C-FOS, STAT1/3 and POL2/3) with known roles in inflammatory pathways. Furthermore, Hi-C data revealed several short-range interactions in the fine-mapped locus harboring the putative variants. The fine mapped locus was predicted to be within a single topologically associated domain, potentially facilitating enhancer-promoter interactions possibly leading to the regulation of nearby genes.
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Affiliation(s)
- Mahalakshmi Kumaran
- Department of Laboratory Medicine & PathologyUniversity of AlbertaEdmontonABCanada
| | - Sunita Ghosh
- Department of OncologyUniversity of AlbertaEdmontonABCanada
| | - Anil A. Joy
- Department of OncologyUniversity of AlbertaEdmontonABCanada
| | - John R. Mackey
- Department of OncologyUniversity of AlbertaEdmontonABCanada
| | - Carol E. Cass
- Department of OncologyUniversity of AlbertaEdmontonABCanada
| | - Wei Zheng
- Department of MedicineVanderbilt UniversityNashvilleTN
| | - Yutaka Yasui
- Department of Epidemiology & Cancer ControlSt. Jude Children's Research HospitalMemphisTN
| | - Sambasivarao Damaraju
- Department of Laboratory Medicine & PathologyUniversity of AlbertaEdmontonABCanada
- Cross Cancer InstituteAlberta Health ServicesEdmontonABCanada
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12
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Özgöz A, Mutlu İçduygu F, Yükseltürk A, ŞamlI H, Hekİmler Öztürk K, Başkan Z. Low-penetrance susceptibility variants and postmenopausal oestrogen receptor positive breast cancer. J Genet 2020. [DOI: 10.1007/s12041-019-1174-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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13
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Kapoor PM, Lindström S, Behrens S, Wang X, Michailidou K, Bolla MK, Wang Q, Dennis J, Dunning AM, Pharoah PDP, Schmidt MK, Kraft P, García-Closas M, Easton DF, Milne RL, Chang-Claude J. Assessment of interactions between 205 breast cancer susceptibility loci and 13 established risk factors in relation to breast cancer risk, in the Breast Cancer Association Consortium. Int J Epidemiol 2020; 49:216-232. [PMID: 31605532 PMCID: PMC7426027 DOI: 10.1093/ije/dyz193] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Previous gene-environment interaction studies of breast cancer risk have provided sparse evidence of interactions. Using the largest available dataset to date, we performed a comprehensive assessment of potential effect modification of 205 common susceptibility variants by 13 established breast cancer risk factors, including replication of previously reported interactions. METHODS Analyses were performed using 28 176 cases and 32 209 controls genotyped with iCOGS array and 44 109 cases and 48 145 controls genotyped using OncoArray from the Breast Cancer Association Consortium (BCAC). Gene-environment interactions were assessed using unconditional logistic regression and likelihood ratio tests for breast cancer risk overall and by estrogen-receptor (ER) status. Bayesian false discovery probability was used to assess the noteworthiness of the meta-analysed array-specific interactions. RESULTS Noteworthy evidence of interaction at ≤1% prior probability was observed for three single nucleotide polymorphism (SNP)-risk factor pairs. SNP rs4442975 was associated with a greater reduction of risk of ER-positive breast cancer [odds ratio (OR)int = 0.85 (0.78-0.93), Pint = 2.8 x 10-4] and overall breast cancer [ORint = 0.85 (0.78-0.92), Pint = 7.4 x 10-5) in current users of estrogen-progesterone therapy compared with non-users. This finding was supported by replication using OncoArray data of the previously reported interaction between rs13387042 (r2 = 0.93 with rs4442975) and current estrogen-progesterone therapy for overall disease (Pint = 0.004). The two other interactions suggested stronger associations between SNP rs6596100 and ER-negative breast cancer with increasing parity and younger age at first birth. CONCLUSIONS Overall, our study does not suggest strong effect modification of common breast cancer susceptibility variants by established risk factors.
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Affiliation(s)
- Pooja Middha Kapoor
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine, University of Heidelberg, Heidelberg, Germany
| | - Sara Lindström
- Department of Epidemiology, University of Washington School of Public Health, Seattle, WA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sabine Behrens
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Xiaoliang Wang
- Department of Epidemiology, University of Washington School of Public Health, Seattle, WA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Department of Electron Microscopy/Molecular Pathology and Cyprus School of Molecular Medicine, Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Qin Wang
- 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
| | - 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
| | - Marjanka K Schmidt
- 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
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Boston, MA, USA
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, 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
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
- Precision Medicine, Monash University, Clayton, VIC, Australia
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), Hamburg, Germany
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14
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Zuo X, Wang H, Mi Y, Zhang Y, Wang X, Yang Y, Zhai S. The association of CASC16 variants with breast Cancer risk in a northwest Chinese female population. Mol Med 2020; 26:11. [PMID: 31996122 PMCID: PMC6988193 DOI: 10.1186/s10020-020-0137-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 01/15/2020] [Indexed: 12/29/2022] Open
Abstract
Purpose Genetic variants play a critical role in the development of breast cancer. This investigation aimed to explore the association between CASC16 polymorphisms and breast cancer susceptibility. Methods We conducted a case-control study of 681 patients and 680 healthy individuals to investigate the correlation of five SNPs with breast cancer in a Northwest Chinese female population. Odds ratios (OR) and 95% confidence intervals (CIs) were used to assess the association. Results Our study found that rs4784227 and rs12922061 were significantly related to an increased susceptibility to breast cancer (OR 1.22, p = 0.022; OR 1.21, p = 0.026). While rs3803662 was a protective role in breast cancer risk (OR 0.69, p = 0.042). Stratified analyses indicated that rs4784227 and rs12922061 would increase breast cancer susceptibility at age > 50 years. Rs3803662 was a reduced factor of breast cancer risk by age ≤ 50 years. Rs4784227 was significantly increased risk of breast cancer in stage III/IV. The rs45544231 and rs3112612 had a protective effect on breast cancer with tumor size > 2 cm. Rs4784227 and rs12922061 could enhance breast cancer risk in lymph node metastasis positive individuals. CASC16 rs12922061 and rs4784227 polymorphisms correlated with an increased risk of breast cancer in BMI > 24 kg/m2. Haplotype analyses revealed that Grs45544231 Trs12922061 Ars3112612 and Grs45544231 Crs12922061 Ars3112612 haplotypes decreased breast cancer risk. Conclusion Our study revealed that CASC16 genetic variants were significantly related to breast cancer susceptibility, which might give scientific evidence for exploring the molecular mechanism of breast cancer.
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Affiliation(s)
- Xiaoxiao Zuo
- Department of Radiation Oncology, First Affiliated Hospital of Zhengzhou University, #2 East Jianshe Road, Zhengzhou, 450000, Henan, China.
| | - Huanhuan Wang
- Department of Radiation Oncology, First Affiliated Hospital of Zhengzhou University, #2 East Jianshe Road, Zhengzhou, 450000, Henan, China
| | - Yin Mi
- Department of Radiation Oncology, First Affiliated Hospital of Zhengzhou University, #2 East Jianshe Road, Zhengzhou, 450000, Henan, China
| | - Yue Zhang
- Department of Radiation Oncology, First Affiliated Hospital of Zhengzhou University, #2 East Jianshe Road, Zhengzhou, 450000, Henan, China
| | - Xiaofei Wang
- Department of Radiation Oncology, First Affiliated Hospital of Zhengzhou University, #2 East Jianshe Road, Zhengzhou, 450000, Henan, China
| | - Ya Yang
- Department of Radiation Oncology, First Affiliated Hospital of Zhengzhou University, #2 East Jianshe Road, Zhengzhou, 450000, Henan, China
| | - Suna Zhai
- Department of Radiation Oncology, First Affiliated Hospital of Zhengzhou University, #2 East Jianshe Road, Zhengzhou, 450000, Henan, China
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15
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Akhtar M, Jamal T, Din JU, Hayat C, Rauf M, Ul Haq SM, Sher Khan R, Shah AA, Jamal M, Jalil F. An in silico approach to characterize nonsynonymous SNPs and regulatory SNPs in human TOX3 gene. J Genet 2019; 98:104. [PMID: 31819019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cancer is one of the deadliest complex diseases having multigene nature where the role of single-nucleotide polymorphism (SNP) has been well explored in multiple genes. TOX high mobility group box family member 3 (TOX3) is one such gene, in which SNPs have been found to be associated with breast cancer. In this study, we have examined the potentially damaging nonsynonymous SNPs(nsSNPs) in TOX3 gene using in silico tools, namely PolyPhen2, SNP&GO, PhD-SNP and PROVEAN, which were further confirmed by I-Mutant, MutPred1.2 and ConSurf for their stability, functional and structural effects. nsSNPs rs368713418 (A266D), rs751141352 (P273S, P273T), rs200878352 (A275T) have been found to be the most deleterious that may have a vital role in breast cancer. Premature stop codon producing SNPs (Q527STOP), rs1259790811 (G495STOP), rs1294465822 (S395STOP) and rs1335372738 (G8STOP) were also found having prime importance in truncated and malfunctional protein formation. We also characterized regulatory SNPs for its potential effect on TOX3 gene regulation and found nine SNPs that may affect the gene regulation. Further, we have also designed 3D models using I-TASSER for the wild type and four mutant TOX3 proteins. Our study concludes that these SNPs can be of prime importance while studying breast cancer and other associated diseases as well. They are required to be studied in model organisms and cell cultures, and may have potential importance in personalized medicines and gene therapy.
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Affiliation(s)
- Mehran Akhtar
- Department of Biotechnology, Abdul Wali Khan University, Mardan 23200, Pakistan.
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16
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An in silico approach to characterize nonsynonymous SNPs and regulatory SNPs in human TOX3 gene. J Genet 2019. [DOI: 10.1007/s12041-019-1153-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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17
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Tajbakhsh A, Farjami Z, Darroudi S, Ayati SH, Vakili F, Asghari M, Alimardani M, Abedini S, Kushyar MM, Pasdar A. Association of rs4784227-CASC16 (LOC643714 locus) and rs4782447-ACSF3 polymorphisms and their association with breast cancer risk among Iranian population. EXCLI JOURNAL 2019; 18:429-438. [PMID: 31338012 PMCID: PMC6635718 DOI: 10.17179/excli2019-1374] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 06/11/2019] [Indexed: 12/22/2022]
Abstract
TOX3 and FOXA1 proteins are believed to be involved in the susceptibility of breast cancer. rs4784227-CASC16 and rs4782447-ACSF3, as single nucleotide polymorphisms (SNPs), located at the 16q may affect the FOXA1 DNA binding sequence change and therefore may enhance the FOXA1-binding affinity to the promoter of TOX3 gene. This study aimed to investigate the association of these SNPs/haplotypes with breast cancer susceptibility in an Iranian population. We conducted a case-control study of 1072 blood samples (505 breast cancer patients and 567 controls). Genotyping of rs4784227-CASC16 and rs4782447-ACSF3 SNPs was carried out by ARMS-PCR. Moreover, statistical analysis was done using SPSS version 20.0 (IBM Inc., Chicago, IL, USA), PHASE v 2.1 and SNP analyser 2.0. There was a strongly significant statistical association between alleles and genotypes of rs4784227-CASC16 with breast cancer risk in our study population (p<0.05). Moreover, a significant association was demonstrated between TA haplotype and breast cancer risk (OR=0.78; 95% CI (0.62-0.96); P-value=0.025). In this respect, although we did not observe a statistically significant association between rs4782447-ACSF3 with breast cancer susceptibility, the combination of the effects of rs4784227-CASC16 and rs4782447-ACSF3 SNPs may also affect the risk. This is in line with other studies suggesting these SNPs as risk-associated polymorphisms which may lead to a change in the affinity of FOXA1, as a distal enhancer, to TOX3 and thus change in TOX3 expression, which can eventually affect the risk of breast cancer.
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Affiliation(s)
- Amir Tajbakhsh
- Department of Modern Sciences & Technologies, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Young Researchers and Elite Club, Yasooj Branch, Islamic Azad University, Yasooj, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Farjami
- Department of Modern Sciences & Technologies, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Susan Darroudi
- Department of Modern Sciences & Technologies, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Hasan Ayati
- Immunology Research Center, Department of Immunology, Medical School, Mashhad University of Medical Sciences. Mashhad, Iran
| | - Fatemeh Vakili
- Midwifery department, Faculty of Nursing and Midwifery, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahla Asghari
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Maliheh Alimardani
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Soheila Abedini
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Mahdi Kushyar
- Department of Haematology-Oncology, Imam Reza Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alireza Pasdar
- Department of Modern Sciences & Technologies, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Division of Applied Medicine, Faculty of Medicine, University of Aberdeen, Foresterhill, Aberdeen, UK
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18
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Mohamad Shah NS, Sulong S, Wan Sulaiman WA, Halim AS. Two novel genes TOX3 and COL21A1 in large extended Malay families with nonsyndromic cleft lip and/or palate. Mol Genet Genomic Med 2019; 7:e635. [PMID: 30924295 PMCID: PMC6503016 DOI: 10.1002/mgg3.635] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 01/09/2019] [Accepted: 02/11/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Nonsyndromic cleft lip and/or palate is one of the most common human birth defects worldwide that affects the lip and/or palate. The incidence of clefts varies among populations through ethnic, race, or geographical differences. The focus on Malay nonsyndromic cleft lip and/or palate (NSCL/P) is because of a scarce report on genetic study in relation to this deformity in Malaysia. We are interested to discuss about the genes that are susceptible to cause orofacial cleft formation in the family. METHODS Genome-wide linkage analysis was carried out on eight large extended families of NSCL/P with the total of 91 individuals among Malay population using microarray platform. Based on linkage analyses findings, copy number variation (CNV) of LPHN2, SATB2, PVRL3, COL21A1, and TOX3 were identified in four large extended families that showed linkage evidence using quantitative polymerase chain reaction (qPCR) as for a validation purpose. Copy number calculated (CNC) for each genes were determined with Applied Biosystems CopyCallerTM Software v2.0. Normal CNC of the target sequence expected was set at two. RESULTS Genome-wide linkage analysis had discovered several genes including TOX3 and COL21A1 in four different loci 4p15.2-p16.1, 6p11.2-p12.3, 14q13-q21, and 16q12.1. There was significant decreased, p < 0.05 of SATB2, COL21A1, and TOX3 copy number in extended families compared to the normal controls. CONCLUSION Novel linkage evidence and significant low copy number of COL21A1 and TOX3 in NSCLP family was confirmed. These genes increased the risks toward NSCLP formation in that family traits.
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Affiliation(s)
- Nurul Syazana Mohamad Shah
- Reconstructive Science Unit, School of Medical SciencesUniversiti Sains MalaysiaKubang KerianKelantanMalaysia
| | - Sarina Sulong
- Human Genome Centre, School of Medical SciencesUniversiti Sains MalaysiaKubang KerianKelantanMalaysia
| | - Wan Azman Wan Sulaiman
- Reconstructive Science Unit, School of Medical SciencesUniversiti Sains MalaysiaKubang KerianKelantanMalaysia
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19
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Torres D, Lorenzo Bermejo J, Garcia Mesa K, Gilbert M, Briceño I, Pohl-Zeidler S, González Silos R, Boekstegers F, Plass C, Hamann U. Interaction between genetic ancestry and common breast cancer susceptibility variants in Colombian women. Int J Cancer 2019; 144:2181-2191. [PMID: 30485434 DOI: 10.1002/ijc.32023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 11/05/2018] [Indexed: 01/31/2023]
Abstract
Latino women show lower incidences of breast cancer (BC) than non-Hispanic whites. Large-scale genetic association studies have identified variants robustly associated with BC risk in European women. We examine here the relevance of these variants to Colombian BC and possible interactions with genetic ancestry. Native American, European and African proportions were estimated for 1022 Colombian BC cases and 1023 controls. Logistic regression was applied to assess the association between 78 variants and BC risk and interactions between the variants and ancestry proportions. We constructed a multifactorial risk score combining established BC risk factors, associated risk variants and individual ancestry proportions. Each 1% increase in the Native American proportion translated into a 2.2% lower BC risk (95% CI: 1.4-2.9). Thirteen variants were associated with BC in Colombian women, with allele frequencies and risk effects partially different from European women. Ancestry proportions moderated the risk effects of two variants. The ability of Native American proportions to separate Colombian cases and controls (area-under-the-curve (AUC) = 0.61) was similar to the discriminative ability of family history of BC in first-degree female relatives (AUC = 0.58) or the combined effect of all 13 associated risk variants (AUC = 0.57). Our findings demonstrate ample potential for individualized BC prevention in Hispanic women taking advantage of individual Native American proportions, information on established susceptibility factors and recently identified common risk variants.
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Affiliation(s)
- Diana Torres
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota, Colombia
| | - Justo Lorenzo Bermejo
- Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
| | - Karen Garcia Mesa
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
| | - Michael Gilbert
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ignacio Briceño
- Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota, Colombia.,Universidad de la Sabana, Bogota, Colombia
| | - Svenja Pohl-Zeidler
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rosa González Silos
- Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
| | - Felix Boekstegers
- Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
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20
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Significant association of TOX3/LOC643714 locus-rs3803662 and breast cancer risk in a cohort of Iranian population. Mol Biol Rep 2018; 46:805-811. [PMID: 30515698 DOI: 10.1007/s11033-018-4535-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 11/28/2018] [Indexed: 12/11/2022]
Abstract
Genome-wide association studies normally focus on low penetrance and moderate to high-frequency single nucleotide polymorphisms (SNPs), which lead to genetic susceptibility to breast cancer. In this regard, the T allele of rs3803662 has been associated with breast cancer risk and with lower expression level of TOX3. We aimed to assess the risk of breast cancer associated with this polymorphism in an Iranian population. Using Tetra Primer ARMS PCR, rs3803662 was analyzed in a total of 943 individuals (430 cases and 513 healthy controls form North East of Iran). Allele frequencies and genotype distribution were analyzed in case and control samples to find out any association using the Chi-squared test and Logistic regression. All cases were pathologically confirmed; all controls were mainly healthy individuals. Genotype frequencies were found to be in agreement with HWE in controls and cases. TOX3-rs3803662 SNP was associated with breast cancer risk in our study (T vs. C allele contrast model: OR 1.36, 95% CI 1.12-1.64, Pvalue = 0.002; TT vs. CT + TT dominant model: OR 0.67, 95% CI 0.51-0.87, Pvalue = 0.003; TT vs. CT + CC recessive model: OR 1.54, 95% CI 1.02-2.30, Pvlue = 0.036). Moreover, after adjusting for age, BMI, history of previous cancer and also family history of cancer, all results, except for the recessive model, were remained significant. TOX3-rs3803662, may confer some degrees of risk of breast cancer in Iranian population. This finding is in line with similar results in other populations. It highlights the importance of TOX3 pathway in tumorigenesis.
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21
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Genetic Variants in pre-miR-146a, pre-miR-499, pre-miR-125a, pre-miR-605, and pri-miR-182 Are Associated with Breast Cancer Susceptibility in a South American Population. Genes (Basel) 2018; 9:genes9090427. [PMID: 30135399 PMCID: PMC6162394 DOI: 10.3390/genes9090427] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 08/13/2018] [Accepted: 08/17/2018] [Indexed: 12/17/2022] Open
Abstract
Breast cancer (BC) is one of the most frequent tumors affecting women worldwide. microRNAs (miRNAs) single-nucleotide polymorphisms (SNPs) likely contribute to BC susceptibility. We evaluated the association of five SNPs with BC risk in non-carriers of the BRCA1/2-mutation from a South American population. The SNPs were genotyped in 440 Chilean BRCA1/2-negative BC cases and 1048 controls. Our data do not support an association between rs2910164:G>C or rs3746444:A>G and BC risk. The rs12975333:G>T is monomorphic in the Chilean population. The pre-miR-605 rs2043556-C allele was associated with a decreased risk of BC, both in patients with a strong family history of BC and in early-onset non-familial BC (Odds ratio (OR) = 0.5 [95% confidence interval (CI) 0.4⁻0.9] p = 0.006 and OR = 0.6 [95% CI 0.5⁻0.9] p = 0.02, respectively). The rs4541843-T allele is associated with increased risk of familial BC. This is the first association study on rs4541843 and BC risk. Previously, we showed that the TOX3-rs3803662:C>T was significantly associated with increased risk of familial BC. Given that TOX3 mRNA is a target of miR-182, and that both the TOX3 rs3803662-T and pri-miR-182 rs4541843-T alleles are associated with increased BC risk, we evaluated their combined effect. Risk of familial BC increased in a dose-dependent manner with the number of risk alleles (p-trend = 0.0005), indicating an additive effect.
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22
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Rivandi M, Martens JWM, Hollestelle A. Elucidating the Underlying Functional Mechanisms of Breast Cancer Susceptibility Through Post-GWAS Analyses. Front Genet 2018; 9:280. [PMID: 30116257 PMCID: PMC6082943 DOI: 10.3389/fgene.2018.00280] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/09/2018] [Indexed: 12/12/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified more than 170 single nucleotide polymorphisms (SNPs) associated with the susceptibility to breast cancer. Together, these SNPs explain 18% of the familial relative risk, which is estimated to be nearly half of the total familial breast cancer risk that is collectively explained by low-risk susceptibility alleles. An important aspect of this success has been the access to large sample sizes through collaborative efforts within the Breast Cancer Association Consortium (BCAC), but also collaborations between cancer association consortia. Despite these achievements, however, understanding of each variant's underlying mechanism and how these SNPs predispose women to breast cancer remains limited and represents a major challenge in the field, particularly since the vast majority of the GWAS-identified SNPs are located in non-coding regions of the genome and are merely tags for the causal variants. In recent years, fine-scale mapping studies followed by functional evaluation of putative causal variants have begun to elucidate the biological function of several GWAS-identified variants. In this review, we discuss the findings and lessons learned from these post-GWAS analyses of 22 risk loci. Identifying the true causal variants underlying breast cancer susceptibility and their function not only provides better estimates of the explained familial relative risk thereby improving polygenetic risk scores (PRSs), it also increases our understanding of the biological mechanisms responsible for causing susceptibility to breast cancer. This will facilitate the identification of further breast cancer risk alleles and the development of preventive medicine for those women at increased risk for developing the disease.
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Affiliation(s)
- Mahdi Rivandi
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, Netherlands.,Department of Modern Sciences and Technologies, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, Netherlands.,Cancer Genomics Centre, Utrecht, Netherlands
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23
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Lilyquist J, Ruddy KJ, Vachon CM, Couch FJ. Common Genetic Variation and Breast Cancer Risk-Past, Present, and Future. Cancer Epidemiol Biomarkers Prev 2018; 27:380-394. [PMID: 29382703 PMCID: PMC5884707 DOI: 10.1158/1055-9965.epi-17-1144] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/05/2018] [Accepted: 01/11/2018] [Indexed: 11/16/2022] Open
Abstract
Breast cancer is the most common cancer among women in the United States, with up to 30% of those diagnosed displaying a family history of breast cancer. To date, 18% of the familial risk of breast cancer can be explained by SNPs. This review summarizes the discovery of risk-associated SNPs using candidate gene and genome-wide association studies (GWAS), including discovery and replication in large collaborative efforts such as The Collaborative Oncologic Gene-environment Study and OncoArray. We discuss the evolution of GWAS studies, efforts to discover additional SNPs, and methods for identifying causal variants. We summarize findings associated with overall breast cancer, pathologic subtypes, and mutation carriers (BRCA1, BRCA2, and CHEK2). In addition, we summarize the development of polygenic risk scores (PRS) using the risk-associated SNPs and show how PRS can contribute to estimation of individual risks for developing breast cancer. Cancer Epidemiol Biomarkers Prev; 27(4); 380-94. ©2018 AACRSee all articles in this CEBP Focus section, "Genome-Wide Association Studies in Cancer."
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Affiliation(s)
- Jenna Lilyquist
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Celine M Vachon
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Fergus J Couch
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota.
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
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24
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Abstract
Genome-wide association studies (GWAS) have identified approximately 100 breast cancer risk loci. Translating these findings into a greater understanding of the mechanisms that influence disease risk requires identification of the genes or non-coding RNAs that mediate these associations. Here, we use Capture Hi-C (CHi-C) to annotate 63 loci; we identify 110 putative target genes at 33 loci. To assess the support for these target genes in other data sources we test for associations between levels of expression and SNP genotype (eQTLs), disease-specific survival (DSS), and compare them with somatically mutated cancer genes. 22 putative target genes are eQTLs, 32 are associated with DSS and 14 are somatically mutated in breast, or other, cancers. Identifying the target genes at GWAS risk loci will lead to a greater understanding of the mechanisms that influence breast cancer risk and prognosis.
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25
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Jiang C, Yu S, Qian P, Guo R, Zhang R, Ao Z, Li Q, Wu G, Chen Y, Li J, Wang C, Yao W, Xu J, Qian G, Ji F. The breast cancer susceptibility-related polymorphisms at the TOX3/LOC643714 locus associated with lung cancer risk in a Han Chinese population. Oncotarget 2018; 7:59742-59753. [PMID: 27486757 PMCID: PMC5312345 DOI: 10.18632/oncotarget.10874] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 07/09/2016] [Indexed: 11/25/2022] Open
Abstract
It has been well established that besides environmental factors, genetic factors are also associated with lung cancer risk. However, to date, the prior identified genetic variants and loci only explain a small fraction of the familial risk of lung cancer. Hence it is vital to investigate the remaining missing heritability to understand the development and process of lung cancer. In the study, to test our hypothesis that the previously identified breast cancer risk-associated genetic polymorphisms at the TOX3/LOC643714 locus might contribute to lung cancer risk, 16 SNPs at the TOX3/LOC643714 locus were evaluated in a Han Chinese population based on a case-control study. Pearson's chi-square test or Fisher's exact test revealed that rs9933638, rs12443621, and rs3104746 were significantly associated with lung cancer risk (P < 0.001, P < 0.001, and P = 0.005, respectively). Logistic regression analyses displayed that lung cancer risk of individuals with rs9933638(GG+GA) were 1.89 times higher than that of rs9933638AA carriers (OR = 1.893, 95% CI = 1.308-2.741, P = 0.001). Similar findings were manifested for rs12443621 (OR = 1.824, 95% CI = 1.272-2.616, P = 0.001, rs12443621(GG+GA) carriers vs. rs12443621AA carriers) and rs3104746 (OR = 1.665, 95% CI = 1.243-2.230, P = 0.001, rs3104746TT carriers vs. rs3104746(TA+AA) carriers). The study discovered for the first time that three SNPs (rs9933638, rs12443621, and rs3104746) at the TOX3/LOC643714 locus contributed to lung cancer risk, providing new evidences that lung cancer and breast cancer are linked at the molecular and genetic level to a certain extent.
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Affiliation(s)
- Chaowen Jiang
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Shilong Yu
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Pin Qian
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Ruiling Guo
- Department of Respiratory Diseases, 324th Hospital of People's Liberation Army (No.324 Hospital of PLA), Chongqing 400020, China
| | - Ruijie Zhang
- Department of Respiratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Zhi Ao
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Qi Li
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Guoming Wu
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Yan Chen
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Jin Li
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Changzheng Wang
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Wei Yao
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Jiancheng Xu
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Guisheng Qian
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Fuyun Ji
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
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26
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Sadik CD, Bischof J, van Beek N, Dieterich A, Benoit S, Sárdy M, Worm M, Meller S, Gläser R, Zillikens D, Homey B, Setterfield J, Minassian D, Schmidt E, Dart J, Ibrahim SM. Genomewide association study identifies GALC
as susceptibility gene for mucous membrane pemphigoid. Exp Dermatol 2017; 26:1214-1220. [DOI: 10.1111/exd.13464] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Christian D. Sadik
- Department of Dermatology, Allergy, and Venereology; University of Lübeck; Lübeck Germany
| | - Julia Bischof
- Lübeck Institute of Experimental Dermatology; University of Lübeck; Lübeck Germany
| | - Nina van Beek
- Department of Dermatology, Allergy, and Venereology; University of Lübeck; Lübeck Germany
| | - Anabelle Dieterich
- Department of Dermatology, Allergy, and Venereology; University of Lübeck; Lübeck Germany
| | - Sandrine Benoit
- Department of Dermatology, Venereology and Allergology; University Hospital Würzburg; Würzburg Germany
| | - Miklós Sárdy
- Department of Dermatology and Allergy; Ludwig Maximilian University; Munich Germany
| | - Margitta Worm
- Department of Dermatology, Allergy, and Venereology; Charité; Berlin Germany
| | - Stephan Meller
- Department of Dermatology; Heinrich Heine University; Düsseldorf Germany
| | - Regine Gläser
- Department of Dermatology, Venereology, and Allergy; Christian Albrechts University zu Kiel; Kiel Germany
| | - Detlef Zillikens
- Department of Dermatology, Allergy, and Venereology; University of Lübeck; Lübeck Germany
| | - Bernhard Homey
- Department of Dermatology; Heinrich Heine University; Düsseldorf Germany
| | - Jane Setterfield
- Guy's and St Thomas's NHS Foundation Trust and King's College London; London UK
| | | | - Enno Schmidt
- Lübeck Institute of Experimental Dermatology; University of Lübeck; Lübeck Germany
| | - John Dart
- Moorfields Eye Hospital NHS Foundation Trust and the UCL Institute of Ophthalmology; London UK
| | - Saleh M. Ibrahim
- Lübeck Institute of Experimental Dermatology; University of Lübeck; Lübeck Germany
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27
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Xu Y, Yuan Q, Zhou J, Chang X, Wang K, Han J. Association of TOX3 polymorphisms with breast cancer: A meta-analysis. Meta Gene 2017. [DOI: 10.1016/j.mgene.2017.05.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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28
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Moazzeni H, Najafi A, Khani M. Identification of direct target genes of miR-7, miR-9, miR-96, and miR-182 in the human breast cancer cell lines MCF-7 and MDA-MB-231. Mol Cell Probes 2017; 34:45-52. [PMID: 28546132 DOI: 10.1016/j.mcp.2017.05.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 05/05/2017] [Accepted: 05/16/2017] [Indexed: 12/24/2022]
Abstract
Some microRNAs have carcinogenic or tumor suppressive effects in breast cancer, which is the most common cancer in women worldwide. MiR-7 and miR-9 are tumor suppressor microRNAs, which induce apoptosis and inhibit proliferation in breast cancer cells. Moreover, miR-96 and miR-182 are onco-microRNAs that increase proliferation, migration, and tumorigenesis in breast cancer cells. This study aimed to identify the direct target genes of these four microRNAs in the human breast cancer cell lines MCF-7 and MDA-MB-231. Initially, bioinformatics tools were used to identify the target genes that have binding sites for miR-7, MiR-9, MiR-96, and miR-182 and are also associated with breast cancer. Subsequently, the findings of the bioinformatics analysis relating to the effects of these four microRNAs on the 3'-UTR activity of the potential target genes were confirmed using the dual luciferase assay in MCF-7 and MDA-MB-231 cells co-transfected with the vectors containing 3'-UTR segments of the target genes downstream of a luciferase coding gene and each of the microRNAs. Finally, the effects of microRNAs on the endogenous expression of potential target genes were assessed by the overexpression of each of the four microRNAs in MCF-7 and MDA-MB-231 cells. Respectively, three, three, three, and seven genes were found to have binding sites for miR-7, miR-9, miR-96, and miR-182 and were associated with breast cancer. The results of empirical studies including dual luciferase assays and real-time PCR confirmed that miR-7 regulates the expression of BRCA1 and LASP1; MiR-9 regulates the expression of AR; miR-96 regulates the expression of ABCA1; and miR-182 regulates the expression of NBN, TOX3, and LASP1. Taken together, our results suggest that the tumor suppressive effects of miR-7 may be mediated partly by regulating the expression of BRCA1 as a tumor suppressor gene in breast cancer. In addition, this microRNA and miR-182 may have effects on the nodal-positivity and tumor size of breast carcinoma through the regulation of LASP1. The tumor suppressive functions of miR-9 may be mediated partly by suppressing the expression of AR-an oncogene in breast cancer. Moreover, miR-96 may play an oncogenic role in breast cancer by suppressing the apoptosis through the regulation of ABCA1.
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Affiliation(s)
- Hamidreza Moazzeni
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran; Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ali Najafi
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.
| | - Marzieh Khani
- School of Biology, College of Science, University of Tehran, Tehran, Iran
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29
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Liu CT, Raghavan S, Maruthur N, Kabagambe EK, Hong J, Ng MCY, Hivert MF, Lu Y, An P, Bentley AR, Drolet AM, Gaulton KJ, Guo X, Armstrong LL, Irvin MR, Li M, Lipovich L, Rybin DV, Taylor KD, Agyemang C, Palmer ND, Cade BE, Chen WM, Dauriz M, Delaney JAC, Edwards TL, Evans DS, Evans MK, Lange LA, Leong A, Liu J, Liu Y, Nayak U, Patel SR, Porneala BC, Rasmussen-Torvik LJ, Snijder MB, Stallings SC, Tanaka T, Yanek LR, Zhao W, Becker DM, Bielak LF, Biggs ML, Bottinger EP, Bowden DW, Chen G, Correa A, Couper DJ, Crawford DC, Cushman M, Eicher JD, Fornage M, Franceschini N, Fu YP, Goodarzi MO, Gottesman O, Hara K, Harris TB, Jensen RA, Johnson AD, Jhun MA, Karter AJ, Keller MF, Kho AN, Kizer JR, Krauss RM, Langefeld CD, Li X, Liang J, Liu S, Lowe WL, Mosley TH, North KE, Pacheco JA, Peyser PA, Patrick AL, Rice KM, Selvin E, Sims M, Smith JA, Tajuddin SM, Vaidya D, Wren MP, Yao J, Zhu X, Ziegler JT, Zmuda JM, Zonderman AB, Zwinderman AH, Adeyemo A, Boerwinkle E, Ferrucci L, Hayes MG, Kardia SLR, Miljkovic I, Pankow JS, Rotimi CN, Sale MM, Wagenknecht LE, Arnett DK, Chen YDI, Nalls MA, Province MA, Kao WHL, Siscovick DS, Psaty BM, Wilson JG, Loos RJF, Dupuis J, Rich SS, Florez JC, Rotter JI, Morris AP, Meigs JB. Trans-ethnic Meta-analysis and Functional Annotation Illuminates the Genetic Architecture of Fasting Glucose and Insulin. Am J Hum Genet 2016; 99:56-75. [PMID: 27321945 PMCID: PMC5005440 DOI: 10.1016/j.ajhg.2016.05.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 05/02/2016] [Indexed: 12/11/2022] Open
Abstract
Knowledge of the genetic basis of the type 2 diabetes (T2D)-related quantitative traits fasting glucose (FG) and insulin (FI) in African ancestry (AA) individuals has been limited. In non-diabetic subjects of AA (n = 20,209) and European ancestry (EA; n = 57,292), we performed trans-ethnic (AA+EA) fine-mapping of 54 established EA FG or FI loci with detailed functional annotation, assessed their relevance in AA individuals, and sought previously undescribed loci through trans-ethnic (AA+EA) meta-analysis. We narrowed credible sets of variants driving association signals for 22/54 EA-associated loci; 18/22 credible sets overlapped with active islet-specific enhancers or transcription factor (TF) binding sites, and 21/22 contained at least one TF motif. Of the 54 EA-associated loci, 23 were shared between EA and AA. Replication with an additional 10,096 AA individuals identified two previously undescribed FI loci, chrX FAM133A (rs213676) and chr5 PELO (rs6450057). Trans-ethnic analyses with regulatory annotation illuminate the genetic architecture of glycemic traits and suggest gene regulation as a target to advance precision medicine for T2D. Our approach to utilize state-of-the-art functional annotation and implement trans-ethnic association analysis for discovery and fine-mapping offers a framework for further follow-up and characterization of GWAS signals of complex trait loci.
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Affiliation(s)
- Ching-Ti Liu
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA.
| | - Sridharan Raghavan
- Division of General Internal Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Department of Veterans Affairs Medical Center, Eastern Colorado Health Care System, Denver, CO 80220, USA; Division of General Internal Medicine, Department of Medicine, University of Colorado School of Medicine, Denver, CO 80220, USA
| | - Nisa Maruthur
- Division of General Internal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, MD 21287, USA; Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21287, USA
| | - Edmond Kato Kabagambe
- Division of Epidemiology, Department of Medicine, School of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Jaeyoung Hong
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Maggie C Y Ng
- Center for Genomics and Personalized Medicine Research, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA; Center for Diabetes Research, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Harvard Medical School, Boston, MA 02215, USA; Diabetes Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Medicine, Universite de Sherbrooke, Sherbrooke, QC J1G 0A2, Canada
| | - Yingchang Lu
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Genetics of Obesity and Related Metabolic Traits Program, The Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ping An
- Division of Statistical Genomics, Department of Genetics, School of Medicine, Washington University, St Louis, MO 63108, USA
| | - Amy R Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Anne M Drolet
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 48201, USA
| | - Kyle J Gaulton
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Loren L Armstrong
- Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Marguerite R Irvin
- Department of Epidemiology, School of Public Health, University of Alabama - Birmingham, Birmingham, AL 35294, USA
| | - Man Li
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21287, USA
| | - Leonard Lipovich
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 48201, USA; Department of Neurology, School of Medicine, Wayne State University, Detroit, MI 48201, USA
| | - Denis V Rybin
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Charles Agyemang
- Department of Public Health, Academic Medical Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands
| | - Nicholette D Palmer
- Center for Genomics and Personalized Medicine Research, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA; Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Brian E Cade
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Wei-Min Chen
- Center for Public Health Genomics, Department of Public Health Sciences, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Marco Dauriz
- Division of Endocrinology, Diabetes & Metabolism, Department of Medicine, University of Verona, 37126 Verona, Italy
| | - Joseph A C Delaney
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Todd L Edwards
- Division of Epidemiology, Department of Medicine, School of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Daniel S Evans
- California Pacific Medical Center Research Institute, San Francisco, CA 94107, USA
| | - Michele K Evans
- Health Disparities Research Section, Laboratory of Epidemiology and Population Sciences, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Leslie A Lange
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27607, USA
| | - Aaron Leong
- Division of General Internal Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jingmin Liu
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Yongmei Liu
- Center for Human Genetics, Division of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Uma Nayak
- Center for Public Health Genomics, Department of Public Health Sciences, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Sanjay R Patel
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Bianca C Porneala
- Division of General Internal Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Laura J Rasmussen-Torvik
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Marieke B Snijder
- Department of Public Health, Academic Medical Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands
| | - Sarah C Stallings
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute of Aging at Harbor Hospital, Baltimore, MD 21225, USA
| | - Lisa R Yanek
- GeneSTAR Research Program, Division of General Internal Medicine, Department of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Diane M Becker
- GeneSTAR Research Program, Division of General Internal Medicine, Department of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA; Department of Health Policy and Management, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21287, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mary L Biggs
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA; Cardiovascular Health Research Unit, Department of Medicine, School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Erwin P Bottinger
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Donald W Bowden
- Center for Genomics and Personalized Medicine Research, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA; Center for Diabetes Research, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA; Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - David J Couper
- Collaborative Studies Coordinating Center, Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Dana C Crawford
- Department of Epidemiology and Biostatistics, Institute for Computational Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Mary Cushman
- Department of Medicine and Pathology, University of Vermont, College of Medicine, Burlington, VT 05405, USA
| | - John D Eicher
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA 01702, USA; Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, NIH, Framingham, MA 01702, USA
| | - Myriam Fornage
- Institute of Molecular Medicine and Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Yi-Ping Fu
- Cardiovascular Epidemiology and Human Genomics Branch, National Heart, Lung, and Blood Institute, NIH, Framingham, MA 01702, USA
| | - Mark O Goodarzi
- Division of Endocrinology, Diabetes & Metabolism, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Omri Gottesman
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kazuo Hara
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; Department of Diabetes, Endocrinology, and Metabolism, Tokyo Medical University, Tokyo 163-0023, Japan
| | - Tamara B Harris
- Laboratory of Epidemiology and Population Sciences, NIH, Bethesda, MD 20892, USA
| | - Richard A Jensen
- Cardiovascular Health Research Unit, Department of Medicine, School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Andrew D Johnson
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, NIH, Framingham, MA 01702, USA
| | - Min A Jhun
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andrew J Karter
- Division of Research, Kaiser Permanente, Northern California Region, Oakland, CA 94612, USA
| | - Margaux F Keller
- Department of Genetics and Pharmacogenomics, Merck Research Laboratories, 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Abel N Kho
- Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jorge R Kizer
- Department of Medicine, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY 10461, USA; Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Ronald M Krauss
- Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA
| | - Carl D Langefeld
- Center for Public Health Genomics, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA; Department of Biostatistical Sciences, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Xiaohui Li
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Jingling Liang
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Simin Liu
- Department of Epidemiology, Brown University, Providence, RI 02912, USA; Department of Medicine, Brown University, Providence, RI 02903, USA
| | - William L Lowe
- Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Thomas H Mosley
- Division of Geriatrics/Gerontology, Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Jennifer A Pacheco
- Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alan L Patrick
- Tobago Health Studies Office, Scarborough, Tobago, Trinidad and Tobago
| | - Kenneth M Rice
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Elizabeth Selvin
- Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University, Baltimore, MD 21287, USA; Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21287, USA
| | - Mario Sims
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Salman M Tajuddin
- Health Disparities Research Section, Laboratory of Epidemiology and Population Sciences, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Dhananjay Vaidya
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21287, USA; GeneSTAR Research Program, Division of General Internal Medicine, Department of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Mary P Wren
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Jie Yao
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Xiaofeng Zhu
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Julie T Ziegler
- Center for Public Health Genomics, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA; Department of Biostatistical Sciences, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Joseph M Zmuda
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Alan B Zonderman
- Behavioral Epidemiology Section, Laboratory of Epidemiology & Population Science, Intramural Research Program, National Institute on Aging, NIH, Baltimore, MD 21224, US
| | - Aeilko H Zwinderman
- Department of Public Health, Academic Medical Center Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Eric Boerwinkle
- Institute of Molecular Medicine and Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute of Aging at Harbor Hospital, Baltimore, MD 21225, USA
| | - M Geoffrey Hayes
- Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Iva Miljkovic
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - James S Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Michele M Sale
- Center for Public Health Genomics, Department of Public Health Sciences, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Lynne E Wagenknecht
- Division of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Donna K Arnett
- University of Kentucky College of Public Health, Lexington, KY 40563, USA
| | - Yii-Der Ida Chen
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Michael A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD 20892, USA
| | - Michael A Province
- Division of Statistical Genomics, Department of Genetics, School of Medicine, Washington University, St Louis, MO 63108, USA
| | - W H Linda Kao
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21287, USA
| | - David S Siscovick
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA; Cardiovascular Health Research Unit, Department of Medicine, School of Medicine, University of Washington, Seattle, WA 98195, USA; The New York Academy of Medicine, New York, NY 10029, USA
| | - Bruce M Psaty
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA; Cardiovascular Health Research Unit, Department of Medicine, School of Medicine, University of Washington, Seattle, WA 98195, USA; Department of Health Services, University of Washington, Seattle, WA 98195, USA; Group Health Research Institute, Group Health Cooperative, Seattle, WA 98101, USA
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Genetics of Obesity and Related Metabolic Traits Program, The Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Mindich Child Health and Development Institute, The Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Josée Dupuis
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA; National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA 01702, USA
| | - Stephen S Rich
- Center for Public Health Genomics, Department of Public Health Sciences, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Jose C Florez
- Diabetes Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA; Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Andrew P Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Institute of Translational Medicine, Department of Biostatistics, University of Liverpool, Liverpool L69 3BX, UK
| | - James B Meigs
- Division of General Internal Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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30
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Association of single nucleotide polymorphism rs3803662 with the risk of breast cancer. Sci Rep 2016; 6:29008. [PMID: 27350156 PMCID: PMC4924094 DOI: 10.1038/srep29008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 06/09/2016] [Indexed: 02/02/2023] Open
Abstract
Large scale association studies have identified the single nucleotide polymorphism rs3803662 associated with breast cancer risk. However, the sample size of most studies is too small. Here, we performed this meta-analysis to make the result more convincing. Relevant articles published up to 2016 were identified by searching the PubMed database. 13 studies, involving a total of 29405 participants, were included in the meta-analysis. Odds Ratios (ORs) with 95% confidence intervals (CIs) was calculated with random or fixed effects model. All data analyses were analyzed by Review Manger 5.3 software. In Caucasian subgroup: Dominant model (TT + CT vs CC): OR = 1.17 (1.06, 1.29), Recessive model (TT vs CT + CC): OR = 1.25 (1.13, 1.39) and Allele frequency (T vs C): OR = 1.15 (1.08, 1.22). The present meta-analysis suggests that rs3803662 polymorphism is significantly associated with breast cancer risk in Caucasian women, and we did not find the association in Asian women.
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Zheng SC, Widschwendter M, Teschendorff AE. Epigenetic drift, epigenetic clocks and cancer risk. Epigenomics 2016; 8:705-19. [PMID: 27104983 DOI: 10.2217/epi-2015-0017] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
It is well-established that the DNA methylation landscape of normal cells undergoes a gradual modification with age, termed as 'epigenetic drift'. Here, we review the current state of knowledge of epigenetic drift and its potential role in cancer etiology. We propose a new terminology to help distinguish the different components of epigenetic drift, with the aim of clarifying the role of the epigenetic clock, mitotic clocks and active changes, which accumulate in response to environmental disease risk factors. We further highlight the growing evidence that epigenetic changes associated with cancer risk factors may play an important causal role in cancer development, and that monitoring these molecular changes in normal cells may offer novel risk prediction and disease prevention strategies.
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Affiliation(s)
- Shijie C Zheng
- CAS Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Martin Widschwendter
- Department of Women's Cancer, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Andrew E Teschendorff
- CAS Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Department of Women's Cancer, University College London, 74 Huntley Street, London, WC1E 6AU, UK.,Statistical Cancer Genomics, UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK
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O'Brien KM, Shi M, Sandler DP, Taylor JA, Zaykin DV, Keller J, Wise AS, Weinberg CR. A family-based, genome-wide association study of young-onset breast cancer: inherited variants and maternally mediated effects. Eur J Hum Genet 2016; 24:1316-23. [PMID: 26883092 DOI: 10.1038/ejhg.2016.11] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 01/11/2016] [Accepted: 01/15/2016] [Indexed: 12/26/2022] Open
Abstract
Young-onset breast cancer shows certain phenotypic and etiologic differences from older-onset breast cancer and may be influenced by some distinct genetic variants. Few genetic studies of breast cancer have targeted young women and no studies have examined whether maternal variants influence disease in their adult daughters through prenatal effects. We conducted a family-based, genome-wide association study of young-onset breast cancer (age at diagnosis <50 years). A total of 602 188 single-nucleotide polymorphisms (SNPs) were genotyped for 1279 non-Hispanic white cases and their parents or sisters. We used likelihood-based log-linear models to test for transmission asymmetry within families and for maternally mediated genetic effects. Three autosomal SNPs (rs28373882, P=2.8 × 10(-7); rs879162, P=9.2 × 10(-7); rs12606061, P=9.1 × 10(-7)) were associated with risk of young-onset breast cancer at a false-discovery rate below 0.20. None of these loci has been previously linked with young-onset or overall breast cancer risk, and their functional roles are unknown. There was no evidence of maternally mediated, X-linked, or mitochondrial genetic effects, and no notable findings within cancer subcategories defined by menopausal status, estrogen receptor status, or by tumor invasiveness. Further investigations are needed to explore other potential genetic, epigenetic, or epistatic mechanisms and to confirm the association between these three novel loci and young-onset breast cancer.
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Affiliation(s)
- Katie M O'Brien
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Min Shi
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Dmitri V Zaykin
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | | | - Alison S Wise
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Clarice R Weinberg
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
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33
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Yu X, Li Z. TOX gene: a novel target for human cancer gene therapy. Am J Cancer Res 2015; 5:3516-3524. [PMID: 26885442 PMCID: PMC4731627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 06/26/2015] [Indexed: 06/05/2023] Open
Abstract
Thymocyte selection-associated high mobility group box factor (TOX) is a member of an evolutionarily conserved DNA-binding protein family and is expressed in several immune-relevant cell subsets. TOX encodes a nuclear protein of the high-mobility group box superfamily. It contains a DNA-binding domain, which allows it to regulate transcription by modifying local chromatin structure and modulating the formation of multi-protein complexes. Previous studies have shown that TOX play important roles in immune system. More recently, several studies have described TOX expression is frequently upregulated in diverse types of human tumors and the overregulation often associates with tumor progression. Moreover, TOXis involved in the control of cell apoptosis, growth, metastasis, DNA repair and so on. In this review, we provide an overview of current knowledge concerning the role of TOX in tumor development and progression biology function. To our knowledge, this is the first review about the role of thisnew oncogene in tumor development and progression.
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Affiliation(s)
- Xin Yu
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100042, China
| | - Zheng Li
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China
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34
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Amin Al Olama A, Dadaev T, Hazelett DJ, Li Q, Leongamornlert D, Saunders EJ, Stephens S, Cieza-Borrella C, Whitmore I, Benlloch Garcia S, Giles GG, Southey MC, Fitzgerald L, Gronberg H, Wiklund F, Aly M, Henderson BE, Schumacher F, Haiman CA, Schleutker J, Wahlfors T, Tammela TL, Nordestgaard BG, Key TJ, Travis RC, Neal DE, Donovan JL, Hamdy FC, Pharoah P, Pashayan N, Khaw KT, Stanford JL, Thibodeau SN, Mcdonnell SK, Schaid DJ, Maier C, Vogel W, Luedeke M, Herkommer K, Kibel AS, Cybulski C, Wokołorczyk D, Kluzniak W, Cannon-Albright L, Brenner H, Butterbach K, Arndt V, Park JY, Sellers T, Lin HY, Slavov C, Kaneva R, Mitev V, Batra J, Clements JA, Spurdle A, Teixeira MR, Paulo P, Maia S, Pandha H, Michael A, Kierzek A, Govindasami K, Guy M, Lophatonanon A, Muir K, Viñuela A, Brown AA, Freedman M, Conti DV, Easton D, Coetzee GA, Eeles RA, Kote-Jarai Z. Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans. Hum Mol Genet 2015; 24:5589-602. [PMID: 26025378 PMCID: PMC4572072 DOI: 10.1093/hmg/ddv203] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 05/26/2015] [Accepted: 05/27/2015] [Indexed: 02/02/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same region.
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Affiliation(s)
- Ali Amin Al Olama
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Strangeways Research Laboratory
| | - Tokhir Dadaev
- Division of Genetics and Epidemiology, The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
| | - Dennis J Hazelett
- Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA, USA, Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA, USA
| | - Qiuyan Li
- Medical College, Xiamen University, Xiamen, China
| | - Daniel Leongamornlert
- Division of Genetics and Epidemiology, The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
| | - Edward J Saunders
- Division of Genetics and Epidemiology, The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
| | - Sarah Stephens
- Division of Genetics and Epidemiology, The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
| | - Clara Cieza-Borrella
- Division of Genetics and Epidemiology, The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
| | - Ian Whitmore
- Division of Genetics and Epidemiology, The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
| | - Sara Benlloch Garcia
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Strangeways Research Laboratory
| | - Graham G Giles
- Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, VIC, Australia, Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health
| | - Melissa C Southey
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, VIC, Australia
| | | | - Henrik Gronberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Markus Aly
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden, Department of Clinical Sciences, Danderyds Hospital, Stockholm, Sweden
| | - Brian E Henderson
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA, USA
| | - Fredrick Schumacher
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA, USA
| | - Johanna Schleutker
- Department of Medical Biochemistry and Genetics Institute of Biomedicine, University of Turku, Turku, Finland, BioMediTech, University of Tampere and FimLab Laboratories, Tampere, Finland
| | - Tiina Wahlfors
- BioMediTech, University of Tampere and FimLab Laboratories, Tampere, Finland
| | - Teuvo L Tammela
- Department of Urology, Tampere University Hospital and Medical School, University of Tampere, Tampere, Finland
| | - Børge G Nordestgaard
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tim J Key
- Cancer Epidemiology, Nuffield Department of Population Health
| | - Ruth C Travis
- Cancer Epidemiology, Nuffield Department of Population Health
| | - David E Neal
- Department of Oncology, Addenbrooke's Hospital, Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
| | - Jenny L Donovan
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Freddie C Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK, Faculty of Medical Science, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Paul Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, Strangeways Laboratory
| | - Nora Pashayan
- Centre for Cancer Genetic Epidemiology, Department of Oncology, Strangeways Laboratory, Department of Applied Health Research, University College London, London, UK
| | - Kay-Tee Khaw
- Clinical Gerontology Unit, University of Cambridge, Cambridge, UK
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA, Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
| | | | | | | | | | - Walther Vogel
- Institute of Human Genetics, University of Ulm, Ulm, Germany
| | - Manuel Luedeke
- Department of Urology, University Hospital Ulm, Ulm, Germany
| | - Kathleen Herkommer
- Department of Urology, Klinikum rechts der Isar der Technischen Universitaet Muenchen, Munich, Germany
| | - Adam S Kibel
- Division of Urologic Surgery, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Boston, USA
| | - Cezary Cybulski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Dominika Wokołorczyk
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Wojciech Kluzniak
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Lisa Cannon-Albright
- Division of Genetic Epidemiology, Department of Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA, George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, UT, USA
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany, German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Katja Butterbach
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany, German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jong Y Park
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Thomas Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Hui-Yi Lin
- Biostatistics Program, Moffitt Cancer Center, Tampa, FL, USA
| | - Chavdar Slavov
- Department of Urology and Alexandrovska University Hospital, Medical University, Sofia, Bulgaria
| | - Radka Kaneva
- Department of Medical Chemistry and Biochemistry, Molecular Medicine Center, Medical University, Sofia, Bulgaria
| | - Vanio Mitev
- Department of Medical Chemistry and Biochemistry, Molecular Medicine Center, Medical University, Sofia, Bulgaria
| | - Jyotsna Batra
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Science, Queensland University of Technology, Brisbane, Australia
| | - Judith A Clements
- Australian Prostate Cancer Research Centre-Qld, Institute of Health and Biomedical Innovation and School of Biomedical Science, Queensland University of Technology, Brisbane, Australia
| | - Amanda Spurdle
- Molecular Cancer Epidemiology Laboratory, Queensland Institute of Medical Research, Brisbane, Australia
| | - Manuel R Teixeira
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal, Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Paula Paulo
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Sofia Maia
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | | | | | | | - Koveela Govindasami
- Division of Genetics and Epidemiology, The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
| | - Michelle Guy
- Division of Genetics and Epidemiology, The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
| | - Artitaya Lophatonanon
- Institute of Population Health, University of Manchester, Manchester, UK, Warwick Medical School, University of Warwick, Coventry, UK
| | - Kenneth Muir
- Institute of Population Health, University of Manchester, Manchester, UK, Warwick Medical School, University of Warwick, Coventry, UK
| | - Ana Viñuela
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Andrew A Brown
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway, Department of Genetic Medicine and Development, University of Geneva, Switzerland and
| | | | - David V Conti
- Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA, USA, Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA, USA
| | - Douglas Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, Strangeways Research Laboratory
| | - Gerhard A Coetzee
- Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA, USA, Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, USC, Los Angeles, CA, USA
| | - Rosalind A Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK
| | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute of Cancer Research & Royal Marsden NHS Foundation Trust, London, UK,
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Association of three SNPs in TOX3 and breast cancer risk: Evidence from 97275 cases and 128686 controls. Sci Rep 2015; 5:12773. [PMID: 26239137 PMCID: PMC4523945 DOI: 10.1038/srep12773] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 07/09/2015] [Indexed: 11/21/2022] Open
Abstract
The associations of SNPs in TOX3 gene with breast cancer risk were investigated by some Genome-wide association studies and epidemiological studies, but the study results were contradictory. To derive a more precise estimate of the associations, we conducted a meta-analysis. ORs with 95% CI were used to assess the strength of association between TOX3 polymorphisms and breast cancer risk in fixed or random effect model. A total of 37 publications with 97275 cases and 128686 controls were identified. We observed that the rs3803662 C > T, rs12443621 A > G and rs8051542 C > T were all correlated with increased risk of breast cancer. In the stratified analyses by ethnicity, significantly elevated risk was detected for all genetic models of the three SNPs in Caucasians. In Asian populations, there were significant associations of rs3803662 and rs8051542 with breast cancer risk. Whereas there was no evidence for statistical significant association between the three SNPs and breast cancer risk in Africans. Additionally, we observed different associations of rs3803662 with breast cancer risk based on different ER subtype and BRCA1/BRCA2 mutation carriers. In conclusion, the meta-analysis suggested that three SNPs in TOX3 were significantly associated with breast cancer risk in different populations.
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Fachal L, Dunning AM. From candidate gene studies to GWAS and post-GWAS analyses in breast cancer. Curr Opin Genet Dev 2015; 30:32-41. [PMID: 25727315 DOI: 10.1016/j.gde.2015.01.004] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 12/16/2014] [Accepted: 01/21/2015] [Indexed: 12/31/2022]
Abstract
There are now more than 90 established breast cancer risk loci, with 57 new ones, revealed through genome-wide-association studies (GWAS) during the last two years. Established high, moderate and low penetrance genetic variants currently explain ∼49% of familial breast cancer risk. GWAS-discovered variants account for 14%, and it is estimated that another 1000 yet-to-be-discovered loci could contribute an additional ∼14% of familial risk. Polygenic risk scores can already be used to stratify breast cancer risk in the female population and could improve the targeting of mammographic screening programmes, which are at present largely based on age-specific risks. Fine-scale mapping and functional analyses are revealing candidate causal variants and the molecular mechanisms by which GWAS-hits may act. Better-powered GWAS and genome-wide sequencing projects are likely to continue identifying new breast cancer causal variants.
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Affiliation(s)
- Laura Fachal
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK; Genomic Medicine Group, CIBERER, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | - Alison M Dunning
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK.
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Ahsan H, Halpern J, Kibriya MG, Pierce BL, Tong L, Gamazon E, McGuire V, Felberg A, Shi J, Jasmine F, Roy S, Brutus R, Argos M, Melkonian S, Chang-Claude J, Andrulis I, Hopper JL, John EM, Malone K, Ursin G, Gammon MD, Thomas DC, Seminara D, Casey G, Knight JA, Southey MC, Giles GG, Santella RM, Lee E, Conti D, Duggan D, Gallinger S, Haile R, Jenkins M, Lindor NM, Newcomb P, Michailidou K, Apicella C, Park DJ, Peto J, Fletcher O, Silva IDS, Lathrop M, Hunter DJ, Chanock SJ, Meindl A, Schmutzler RK, Müller-Myhsok B, Lochmann M, Beckmann L, Hein R, Makalic E, Schmidt DF, Bui QM, Stone J, Flesch-Janys D, Dahmen N, Nevanlinna H, Aittomäki K, Blomqvist C, Hall P, Czene K, Irwanto A, Liu J, Rahman N, Turnbull C, Dunning AM, Pharoah P, Waisfisz Q, Meijers-Heijboer H, Uitterlinden AG, Rivadeneira F, Nicolae D, Easton DF, Cox NJ, Whittemore AS. A genome-wide association study of early-onset breast cancer identifies PFKM as a novel breast cancer gene and supports a common genetic spectrum for breast cancer at any age. Cancer Epidemiol Biomarkers Prev 2014; 23:658-69. [PMID: 24493630 PMCID: PMC3990360 DOI: 10.1158/1055-9965.epi-13-0340] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Early-onset breast cancer (EOBC) causes substantial loss of life and productivity, creating a major burden among women worldwide. We analyzed 1,265,548 Hapmap3 single-nucleotide polymorphisms (SNP) among a discovery set of 3,523 EOBC incident cases and 2,702 population control women ages ≤ 51 years. The SNPs with smallest P values were examined in a replication set of 3,470 EOBC cases and 5,475 control women. We also tested EOBC association with 19,684 genes by annotating each gene with putative functional SNPs, and then combining their P values to obtain a gene-based P value. We examined the gene with smallest P value for replication in 1,145 breast cancer cases and 1,142 control women. The combined discovery and replication sets identified 72 new SNPs associated with EOBC (P < 4 × 10(-8)) located in six genomic regions previously reported to contain SNPs associated largely with later-onset breast cancer (LOBC). SNP rs2229882 and 10 other SNPs on chromosome 5q11.2 remained associated (P < 6 × 10(-4)) after adjustment for the strongest published SNPs in the region. Thirty-two of the 82 currently known LOBC SNPs were associated with EOBC (P < 0.05). Low power is likely responsible for the remaining 50 unassociated known LOBC SNPs. The gene-based analysis identified an association between breast cancer and the phosphofructokinase-muscle (PFKM) gene on chromosome 12q13.11 that met the genome-wide gene-based threshold of 2.5 × 10(-6). In conclusion, EOBC and LOBC seem to have similar genetic etiologies; the 5q11.2 region may contain multiple distinct breast cancer loci; and the PFKM gene region is worthy of further investigation. These findings should enhance our understanding of the etiology of breast cancer.
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Affiliation(s)
- Habibul Ahsan
- Center for Cancer Epidemiology and Prevention, Departments of Health Studies, University of Chicago, IL
- Department of Medicine, University of Chicago, IL
- Department of Human Genetics, University of Chicago, IL
- Comprehensive Cancer Center, University of Chicago, IL
| | - Jerry Halpern
- Department of Health Research and Policy, Stanford University School of Medicine, CA
| | - Muhammad G Kibriya
- Center for Cancer Epidemiology and Prevention, Departments of Health Studies, University of Chicago, IL
| | - Brandon L Pierce
- Center for Cancer Epidemiology and Prevention, Departments of Health Studies, University of Chicago, IL
- Comprehensive Cancer Center, University of Chicago, IL
| | - Lin Tong
- Center for Cancer Epidemiology and Prevention, Departments of Health Studies, University of Chicago, IL
| | - Eric Gamazon
- Department of Medicine, University of Chicago, IL
| | - Valerie McGuire
- Department of Health Research and Policy, Stanford University School of Medicine, CA
| | - Anna Felberg
- Department of Health Research and Policy, Stanford University School of Medicine, CA
| | - Jianxin Shi
- Epidemiology and Genetics Research Program, National Cancer Institute, MD
| | - Farzana Jasmine
- Center for Cancer Epidemiology and Prevention, Departments of Health Studies, University of Chicago, IL
| | - Shantanu Roy
- Center for Cancer Epidemiology and Prevention, Departments of Health Studies, University of Chicago, IL
| | - Rachelle Brutus
- Center for Cancer Epidemiology and Prevention, Departments of Health Studies, University of Chicago, IL
| | - Maria Argos
- Center for Cancer Epidemiology and Prevention, Departments of Health Studies, University of Chicago, IL
| | - Stephanie Melkonian
- Center for Cancer Epidemiology and Prevention, Departments of Health Studies, University of Chicago, IL
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Irene Andrulis
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto Ontario
| | - John L Hopper
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, Melbourne School of Population Health, The University of Melbourne, Australia
| | - Esther M. John
- Cancer Prevention Institute of California, Fremont, CA and Department of Health Research and Policy, Stanford University School of Medicine and Stanford Cancer Institute, Stanford, CA
| | - Kathi Malone
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - Marilie D Gammon
- Department of Epidemiology, University of North Carolina at Chapel Hill, NC
| | - Duncan C Thomas
- Department of Preventive Medicine, University of Southern California, CA
| | - Daniela Seminara
- Epidemiology and Genetics Research Program, National Cancer Institute, MD
| | - Graham Casey
- Department of Preventive Medicine, University of Southern California, CA
| | - Julia A Knight
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto Ontario
| | - Melissa C Southey
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, Melbourne School of Population Health, The University of Melbourne, Australia
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Australia
| | - Graham G Giles
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, Melbourne School of Population Health, The University of Melbourne, Australia
- Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Regina M Santella
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health
| | - Eunjung Lee
- Department of Preventive Medicine, University of Southern California, CA
| | - David Conti
- Department of Preventive Medicine, University of Southern California, CA
| | - David Duggan
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, AZ
| | - Steve Gallinger
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Robert Haile
- Department of Preventive Medicine, University of Southern California, CA
| | - Mark Jenkins
- Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Noralane M Lindor
- Department of Health Science Research, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Polly Newcomb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Carmel Apicella
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, Melbourne School of Population Health, The University of Melbourne, Australia
| | - Daniel J Park
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Australia
| | - Julian Peto
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Olivia Fletcher
- Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK
| | - Isabel dos Santos Silva
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Mark Lathrop
- Centre National de Genotypage, Evry, France
- Fondation Jean Dausset – CEPH, Paris, France
| | - David J Hunter
- Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Alfons Meindl
- Clinic of Gynaecology and Obstetrics, Division for Gynaecological Tumor-Genetics, Technische Universität München, München, Germany
| | - Rita K Schmutzler
- Department of Obstetrics and Gynaecology, Division of Molecular Gynaeco-Oncology, University of Cologne, Germany
| | | | - Magdalena Lochmann
- Clinic of Gynaecology and Obstetrics, Division for Gynaecological Tumor-Genetics, Technische Universität München, München, Germany
| | - Lars Beckmann
- Foundation for Quality and Efficiency in Health Care IQWIG, Cologne, Germany
| | - Rebecca Hein
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
- PMV Research Group at the Department of Child and Adolescent Psychiatry and Psychotherapy, University of Cologne, Cologne, Germany
| | - Enes Makalic
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, Melbourne School of Population Health, The University of Melbourne, Australia
| | - Daniel F Schmidt
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, Melbourne School of Population Health, The University of Melbourne, Australia
| | - Quang Minh Bui
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, Melbourne School of Population Health, The University of Melbourne, Australia
| | - Jennifer Stone
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, Melbourne School of Population Health, The University of Melbourne, Australia
| | - Dieter Flesch-Janys
- Department of Cancer Epidemiology/Clinical Cancer Registry, University Clinic Hamburg-Eppendorf, Hamburg, Germany
- Institute for Medical Biometrics and Epidemiology, University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | - Norbert Dahmen
- Department of Psychiatry, University of Mainz, Mainz, Germany
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Kristiina Aittomäki
- Department of Clinical Genetics, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Carl Blomqvist
- Department of Oncology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Per Hall
- Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Kamila Czene
- Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Astrid Irwanto
- Human Genetics Division, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Jianjun Liu
- Human Genetics Division, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Nazneen Rahman
- Section of Cancer Genetics, Institute of Cancer Research, Sutton, UK
| | - Clare Turnbull
- Section of Cancer Genetics, Institute of Cancer Research, Sutton, UK
| | - Alison M. Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Paul 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
| | - Quinten Waisfisz
- Department of Clinical Genetics, VU University Medical Center, section Oncogenetics, Amsterdam, The Netherlands
| | - Hanne Meijers-Heijboer
- Department of Clinical Genetics, VU University Medical Center, section Oncogenetics, Amsterdam, The Netherlands
| | - Andre G. Uitterlinden
- Department of Internal Medicine and Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Fernando Rivadeneira
- Department of Internal Medicine and Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Dan Nicolae
- Department of Medicine, University of Chicago, IL
| | - 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
| | - Nancy J Cox
- Department of Medicine, University of Chicago, IL
- Department of Human Genetics, University of Chicago, IL
- Comprehensive Cancer Center, University of Chicago, IL
| | - Alice S Whittemore
- Department of Health Research and Policy, Stanford University School of Medicine, CA
- Stanford Cancer Institute, Palo Alto, CA
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Association of genetic variants at TOX3, 2q35 and 8q24 with the risk of familial and early-onset breast cancer in a South-American population. Mol Biol Rep 2014; 41:3715-22. [PMID: 24532140 DOI: 10.1007/s11033-014-3236-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 02/06/2014] [Indexed: 10/25/2022]
Abstract
Recent Genome-Wide Association Studies have identified several single nucleotide polymorphisms (SNPs) associated with breast cancer (BC) among women of Asian, European, and African-American ancestry. Nevertheless, the contribution of these variants in the South American population is unknown. Furthermore, there is little information about the effect of these risk alleles in women with early BC diagnosis. In the present study, we evaluated the association between rs3803662 (TOX3, also known as TNRC9), rs13387042 (2q35), and rs13281615 (8q24) with BC risk in 344 Chilean BRCA1/2-negative BC cases and in 801 controls. Two SNPs, rs3803662 and rs13387042, were significantly associated with increased BC risk in familial BC and in non-familial early-onset BC. The risk of BC increased in a dose-dependent manner with the number of risk alleles (P-trend < 0.0001 and 0.0091, respectively). The odds ratios for BC in familial BC and in early-onset non-familial BC were 3.76 (95%CI 1.02-13.84, P = 0.046) and 8.0 (95%CI 2.20-29.04, P = 0.002), respectively, for the maximum versus minimum number of risk alleles. These results indicate an additive effect of the TOX3 rs3803662 and 2q35 rs13387042 alleles for BC risk. We also evaluated the interaction between rs3803662 and rs13387042 SNPs. We observed an additive interaction only in non-familial early-onset BC cases (AP = 0.72 (0.28-1.16), P = 0.001). No significant association was observed for rs13281615 (8q24) with BC risk in women from the Chilean population. The strongly increased risk associated with the combination of low-penetrance risk alleles supports the polygenic inheritance model of BC.
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O'Brien KM, Cole SR, Poole C, Bensen JT, Herring AH, Engel LS, Millikan RC. Replication of breast cancer susceptibility loci in whites and African Americans using a Bayesian approach. Am J Epidemiol 2014; 179:382-94. [PMID: 24218030 DOI: 10.1093/aje/kwt258] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Genome-wide association studies (GWAS) and candidate gene analyses have led to the discovery of several dozen genetic polymorphisms associated with breast cancer susceptibility, many of which are considered well-established risk factors for the disease. Despite attempts to replicate these same variant-disease associations in African Americans, the evaluable populations are often too small to produce precise or consistent results. We estimated the associations between 83 previously identified single nucleotide polymorphisms (SNPs) and breast cancer among Carolina Breast Cancer Study (1993-2001) participants using maximum likelihood, Bayesian, and hierarchical methods. The selected SNPs were previous GWAS hits (n = 22), near-hits (n = 19), otherwise well-established risk loci (n = 5), or located in the same genes as selected variants (n = 37). We successfully replicated 18 GWAS-identified SNPs in whites (n = 2,352) and 10 in African Americans (n = 1,447). SNPs in the fibroblast growth factor receptor 2 gene (FGFR2) and the TOC high mobility group box family member 3 gene (TOX3) were strongly associated with breast cancer in both races. SNPs in the mitochondrial ribosomal protein S30 gene (MRPS30), mitogen-activated protein kinase kinase kinase 1 gene (MAP3K1), zinc finger, MIZ-type containing 1 gene (ZMIZ1), and H19, imprinted maternally expressed transcript gene (H19) were associated with breast cancer in whites, and SNPs in the estrogen receptor 1 gene (ESR1) and H19 gene were associated with breast cancer in African Americans. We provide precise and well-informed race-stratified odds ratios for key breast cancer-related SNPs. Our results demonstrate the utility of Bayesian methods in genetic epidemiology and provide support for their application in small, etiologically driven investigations.
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40
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Risk-association of five SNPs in TOX3/LOC643714 with breast cancer in southern China. Int J Mol Sci 2014; 15:2130-41. [PMID: 24481062 PMCID: PMC3958841 DOI: 10.3390/ijms15022130] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Revised: 01/16/2014] [Accepted: 01/21/2014] [Indexed: 11/17/2022] Open
Abstract
The specific mechanism by which low-risk genetic variants confer breast cancer risk is currently unclear, with contradictory evidence on the role of single nucleotide polymorphisms (SNPs) in TOX3/LOC643714 as a breast cancer susceptibility locus. Investigations of this locus using a Chinese population may indicate whether the findings initially identified in a European population are generalizable to other populations, and may provide new insight into the role of genetic variants in the etiology of breast cancer. In this case-control study, 623 Chinese female breast cancer patients and 620 cancer-free controls were recruited to investigate the role of five SNPs in TOX3/LOC643714 (rs8051542, rs12443621, rs3803662, rs4784227, and rs3112612); Linkage disequilibrium (LD) pattern analysis was performed. Additionally, we evaluated how these common SNPs influence the risk of specific types of breast cancer, as defined by estrogen receptor (ER) status, progesterone receptor (PR) status and human epidermal growth factor receptor 2 (HER2) status. Significant associations with breast cancer risk were observed for rs4784227 and rs8051542 with odds ratios (OR) of 1.31 ((95% confidence intervals (CI), 1.10-1.57)) and 1.26 (95% CI, 1.02-1.56), respectively, per T allele. The T-rs8051542 allele was significantly associated with ER-positive and HER2-negative carriers. No significant association existed between rs12443621, rs3803662, and rs3112612 polymorphisms and risk of breast cancer. Our results support the hypothesis that the applicability of a common susceptibility locus must be confirmed among genetically different populations, which may together explain an appreciable fraction of the genetic etiology of breast cancer.
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41
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Spencer AV, Cox A, Walters K. Comparing the efficacy of SNP filtering methods for identifying a single causal SNP in a known association region. Ann Hum Genet 2013; 78:50-61. [PMID: 24205929 PMCID: PMC4282378 DOI: 10.1111/ahg.12043] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 09/05/2013] [Indexed: 01/20/2023]
Abstract
Genome-wide association studies have successfully identified associations between common diseases and a large number of single nucleotide polymorphisms (SNPs) across the genome. We investigate the effectiveness of several statistics, including p-values, likelihoods, genetic map distance and linkage disequilibrium between SNPs, in filtering SNPs in several disease-associated regions. We use simulated data to compare the efficacy of filters with different sample sizes and for causal SNPs with different minor allele frequencies (MAFs) and effect sizes, focusing on the small effect sizes and MAFs likely to represent the majority of unidentified causal SNPs. In our analyses, of all the methods investigated, filtering on the ranked likelihoods consistently retains the true causal SNP with the highest probability for a given false positive rate. This was the case for all the local linkage disequilibrium patterns investigated. Our results indicate that when using this method to retain only the top 5% of SNPs, even a causal SNP with an odds ratio of 1.1 and MAF of 0.08 can be retained with a probability exceeding 0.9 using an overall sample size of 50,000.
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Affiliation(s)
- Amy Victoria Spencer
- School of Mathematics and Statistics, University of Sheffield, Sheffield, S3 7RH, UK
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42
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Edwards SL, Beesley J, French JD, Dunning AM. Beyond GWASs: illuminating the dark road from association to function. Am J Hum Genet 2013; 93:779-97. [PMID: 24210251 PMCID: PMC3824120 DOI: 10.1016/j.ajhg.2013.10.012] [Citation(s) in RCA: 544] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Indexed: 12/15/2022] Open
Abstract
Genome-wide association studies (GWASs) have enabled the discovery of common genetic variation contributing to normal and pathological traits and clinical drug responses, but recognizing the precise targets of these associations is now the major challenge. Here, we review recent approaches to the functional follow-up of GWAS loci, including fine mapping of GWAS signal(s), prioritization of putative functional SNPs by the integration of genetic epidemiological and bioinformatic methods, and in vitro and in vivo experimental verification of predicted molecular mechanisms for identifying the targeted genes. The majority of GWAS-identified variants fall in noncoding regions of the genome. Therefore, this review focuses on strategies for assessing likely mechanisms affected by noncoding variants; such mechanisms include transcriptional regulation, noncoding RNA function, and epigenetic regulation. These approaches have already accelerated progress from genetic studies to biological knowledge and might ultimately guide the development of prognostic, preventive, and therapeutic measures.
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Affiliation(s)
- Stacey L Edwards
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia; School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia.
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Ghoussaini M, Pharoah PDP, Easton DF. Inherited genetic susceptibility to breast cancer: the beginning of the end or the end of the beginning? THE AMERICAN JOURNAL OF PATHOLOGY 2013; 183:1038-1051. [PMID: 23973388 DOI: 10.1016/j.ajpath.2013.07.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Revised: 06/24/2013] [Accepted: 07/22/2013] [Indexed: 02/06/2023]
Abstract
Genome-wide association studies have identified 72 loci associated with breast cancer susceptibility. Seventeen of these are known to predispose to other cancers. High-penetrance susceptibility loci for breast cancer usually result from coding alterations, principally in genes involved in DNA repair, whereas almost all of the associations identified through genome-wide association studies are found in noncoding regions of the genome and are likely to involve regulation of genes in multiple pathways. However, the genes underlying most associations are not yet known. In this review, we summarize the findings from genome-wide association studies in breast cancer and describe the genes and mechanisms that are likely to be involved in the tumorigenesis process. We also discuss approaches to fine-scale mapping of susceptibility regions used to identify the likely causal variant(s) underlying the associations, a major challenge in genetic epidemiology. Finally, we discuss the potential impact of such findings on personalized medicine and future avenues for screening, prediction, and prevention programs.
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Affiliation(s)
- Maya Ghoussaini
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom.
| | - Paul D P Pharoah
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom; Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Douglas F Easton
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
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Jones JO, Chin SF, Wong-Taylor LA, Leaford D, Ponder BAJ, Caldas C, Maia AT. TOX3 mutations in breast cancer. PLoS One 2013; 8:e74102. [PMID: 24069272 PMCID: PMC3777980 DOI: 10.1371/journal.pone.0074102] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 07/29/2013] [Indexed: 11/19/2022] Open
Abstract
TOX3 maps to 16q12, a region commonly lost in breast cancers and recently implicated in the risk of developing breast cancer. However, not much is known of the role of TOX3 itself in breast cancer biology. This is the first study to determine the importance of TOX3 mutations in breast cancers. We screened TOX3 for mutations in 133 breast tumours and identified four mutations (three missense, one in-frame deletion of 30 base pairs) in six primary tumours, corresponding to an overall mutation frequency of 4.5%. One potentially deleterious missense mutation in exon 3 (Leu129Phe) was identified in one tumour (genomic DNA and cDNA). Whilst copy number changes of 16q12 are common in breast cancer, our data show that mutations of TOX3 are present at low frequency in tumours. Our results support that TOX3 should be further investigated to elucidate its role in breast cancer biology.
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Affiliation(s)
- James Owain Jones
- Cambridge Research Institute, Cancer Research UK, Cambridge, United Kingdom
| | - Suet-Feung Chin
- Cambridge Research Institute, Cancer Research UK, Cambridge, United Kingdom
- Department of Oncology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Li-An Wong-Taylor
- Cambridge Research Institute, Cancer Research UK, Cambridge, United Kingdom
| | - Donna Leaford
- Cambridge Research Institute, Cancer Research UK, Cambridge, United Kingdom
| | - Bruce A. J. Ponder
- Cambridge Research Institute, Cancer Research UK, Cambridge, United Kingdom
- Department of Oncology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Carlos Caldas
- Cambridge Research Institute, Cancer Research UK, Cambridge, United Kingdom
- Department of Oncology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
- Cambridge Experimental Cancer Medicine Centre, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Ana-Teresa Maia
- Cambridge Research Institute, Cancer Research UK, Cambridge, United Kingdom
- Department of Oncology, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
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Abstract
Many SNPs associated with human disease are located in non-coding regions of the genome. A new study shows that SNPs associated with breast cancer risk are located in enhancer regions and alter binding affinity for the pioneer factor FOXA1.
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Zheng Y, Ogundiran TO, Falusi AG, Nathanson KL, John EM, Hennis AJM, Ambs S, Domchek SM, Rebbeck TR, Simon MS, Nemesure B, Wu SY, Leske MC, Odetunde A, Niu Q, Zhang J, Afolabi C, Gamazon ER, Cox NJ, Olopade CO, Olopade OI, Huo D. Fine mapping of breast cancer genome-wide association studies loci in women of African ancestry identifies novel susceptibility markers. Carcinogenesis 2013; 34:1520-8. [PMID: 23475944 DOI: 10.1093/carcin/bgt090] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Numerous single nucleotide polymorphisms (SNPs) associated with breast cancer susceptibility have been identified by genome-wide association studies (GWAS). However, these SNPs were primarily discovered and validated in women of European and Asian ancestry. Because linkage disequilibrium is ancestry-dependent and heterogeneous among racial/ethnic populations, we evaluated common genetic variants at 22 GWAS-identified breast cancer susceptibility loci in a pooled sample of 1502 breast cancer cases and 1378 controls of African ancestry. None of the 22 GWAS index SNPs could be validated, challenging the direct generalizability of breast cancer risk variants identified in Caucasians or Asians to other populations. Novel breast cancer risk variants for women of African ancestry were identified in regions including 5p12 (odds ratio [OR] = 1.40, 95% confidence interval [CI] = 1.11-1.76; P = 0.004), 5q11.2 (OR = 1.22, 95% CI = 1.09-1.36; P = 0.00053) and 10p15.1 (OR = 1.22, 95% CI = 1.08-1.38; P = 0.0015). We also found positive association signals in three regions (6q25.1, 10q26.13 and 16q12.1-q12.2) previously confirmed by fine mapping in women of African ancestry. In addition, polygenic model indicated that eight best markers in this study, compared with 22 GWAS-identified SNPs, could better predict breast cancer risk in women of African ancestry (per-allele OR = 1.21, 95% CI = 1.16-1.27; P = 9.7 × 10(-16)). Our results demonstrate that fine mapping is a powerful approach to better characterize the breast cancer risk alleles in diverse populations. Future studies and new GWAS in women of African ancestry hold promise to discover additional variants for breast cancer susceptibility with clinical implications throughout the African diaspora.
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MESH Headings
- Adult
- Alleles
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Black People/genetics
- Breast Neoplasms/genetics
- Case-Control Studies
- Chromosome Mapping/methods
- Chromosomes, Human, Pair 16/genetics
- Chromosomes, Human, Pair 16/metabolism
- Chromosomes, Human, Pair 6/genetics
- Chromosomes, Human, Pair 6/metabolism
- Confidence Intervals
- Female
- Genetic Loci
- Genetic Predisposition to Disease
- Genome-Wide Association Study/methods
- Humans
- Middle Aged
- Odds Ratio
- Polymorphism, Single Nucleotide
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Affiliation(s)
- Yonglan Zheng
- Department of Medicine, Center for Clinical Cancer Genetics and Global Health, The University of Chicago, Chicago, IL 60637, USA
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Gudmundsdottir ET, Barkardottir RB, Arason A, Gunnarsson H, Amundadottir LT, Agnarsson BA, Johannsson OT, Reynisdottir I. The risk allele of SNP rs3803662 and the mRNA level of its closest genes TOX3 and LOC643714 predict adverse outcome for breast cancer patients. BMC Cancer 2012; 12:621. [PMID: 23270421 PMCID: PMC3553017 DOI: 10.1186/1471-2407-12-621] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 12/21/2012] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The minor allele of SNP rs3803662 has been shown to correlate with increased breast cancer risk and with lower expression of TOX3. The SNP is closely located to TOX3 residing within an uncharacterised gene LOC643714. The aim of the study was to examine the association of the risk allele with expression of TOX3 and LOC643714, and of mRNA levels and genotype with clinical and pathological characteristics. METHODS The SNP was genotyped in DNA isolated from blood and normal tissue from 160 breast cancer patients and mRNA levels were measured by microarrays and quantitative real-time (qRT)-PCR in breast tumours. Association with clinical and pathological characteristics was analysed by parametric tests. RESULTS An association of the risk allele of rs3803662 with lower TOX3 expression was confirmed in oestrogen receptor (ER) positive tumours. It was more often observed in lobular tumours (p = 0.04), and carriers of the risk allele who had been diagnosed with luminal A tumours had shorter overall survival (OS) than carriers of the non-risk allele (p = 0.01). Positive correlation between the mRNA levels of TOX3 and LOC643714 was observed (r = 0.44 and p < 0.001). Association analysis with tumour pathology showed that low TOX3 and LOC643714 expression correlated with high Ki67 levels (p = 0.026 and p = 0.002) and the basal subtype (p < 0.001 and p < 0.001), whereas high expression correlated with ER (p = 0.004 and p < 0.001) and progesterone receptor (PgR) (p = 0.005 and p < 0.001) expression. Furthermore, high TOX3 and LOC643714 correlated with positive lymph nodes (p < 0.001 and p = 0.01). Patients with ER positive tumours and high levels of TOX3 mRNA had shorter overall- and distant metastasis free-survival (p = 0.017 and p = 0.021), an effect mostly attributable to patients with luminal B tumours. CONCLUSIONS The results suggest that the effect of the risk allele of rs3803662 is strongest in luminal A tumours and that the expression levels of TOX3 and/or LOC643714 affect the progression of breast cancer. The effect may vary depending on the subtype and developmental stage of the tumour.
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Affiliation(s)
- Eydis Th Gudmundsdottir
- Department of Pathology, Landspitali-University Hospital, Hringbraut, 101, Reykjavik, Iceland
| | - Rosa B Barkardottir
- Department of Pathology, Landspitali-University Hospital, Hringbraut, 101, Reykjavik, Iceland
- BMC, Faculty of Medicine, University of Iceland, Vatnsmyrarvegi 16, 101, Reykjavik, Iceland
| | - Adalgeir Arason
- Department of Pathology, Landspitali-University Hospital, Hringbraut, 101, Reykjavik, Iceland
- BMC, Faculty of Medicine, University of Iceland, Vatnsmyrarvegi 16, 101, Reykjavik, Iceland
| | - Haukur Gunnarsson
- Department of Pathology, Landspitali-University Hospital, Hringbraut, 101, Reykjavik, Iceland
- Present address: Actavis, Hafnarfjordur, Iceland
| | - Laufey Th Amundadottir
- Department of Health and Human Services, Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Bjarni A Agnarsson
- Department of Pathology, Landspitali-University Hospital, Hringbraut, 101, Reykjavik, Iceland
- BMC, Faculty of Medicine, University of Iceland, Vatnsmyrarvegi 16, 101, Reykjavik, Iceland
| | - Oskar Th Johannsson
- BMC, Faculty of Medicine, University of Iceland, Vatnsmyrarvegi 16, 101, Reykjavik, Iceland
- Department of Oncology, 20A, Landspitali-University Hospital, Hringbraut, 101, Reykjavik, Iceland
| | - Inga Reynisdottir
- Department of Pathology, Landspitali-University Hospital, Hringbraut, 101, Reykjavik, Iceland
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Cowper-Sal lari R, Zhang X, Wright JB, Bailey SD, Cole MD, Eeckhoute J, Moore JH, Lupien M. Breast cancer risk-associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression. Nat Genet 2012; 44:1191-8. [PMID: 23001124 PMCID: PMC3483423 DOI: 10.1038/ng.2416] [Citation(s) in RCA: 294] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 08/29/2012] [Indexed: 12/12/2022]
Abstract
Genome-wide association studies (GWAS) have identified thousands of SNPs that are associated with human traits and diseases. But, because the vast majority of these SNPs are located in non-coding regions of the genome, the mechanisms by which they promote disease risk have remained elusive. Employing a new methodology that combines cistromics, epigenomics and genotype imputation, we annotate the non-coding regions of the genome in breast cancer cells and systematically identify the functional nature of SNPs associated with breast cancer risk. Our results show that breast cancer risk-associated SNPs are enriched in the cistromes of FOXA1 and ESR1 and the epigenome of histone H3 lysine 4 monomethylation (H3K4me1) in a cancer- and cell type-specific manner. Furthermore, the majority of the risk-associated SNPs modulate the affinity of chromatin for FOXA1 at distal regulatory elements, thereby resulting in allele-specific gene expression, which is exemplified by the effect of the rs4784227 SNP on the TOX3 gene within the 16q12.1 risk locus.
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Affiliation(s)
- Richard Cowper-Sal lari
- Department of Genetics, Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, New Hampshire, USA
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Shan J, Mahfoudh W, Dsouza SP, Hassen E, Bouaouina N, Abdelhak S, Benhadjayed A, Memmi H, Mathew RA, Aigha II, Gabbouj S, Remadi Y, Chouchane L. Genome-Wide Association Studies (GWAS) breast cancer susceptibility loci in Arabs: susceptibility and prognostic implications in Tunisians. Breast Cancer Res Treat 2012; 135:715-24. [PMID: 22910930 PMCID: PMC3439608 DOI: 10.1007/s10549-012-2202-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 08/07/2012] [Indexed: 11/24/2022]
Abstract
Genome-wide Association Studies (GWAS) revealed novel genetic markers for breast cancer susceptibility. But little is known about the risk factors and molecular events associated with breast cancer in Arab Population. Therefore, we designed a broad study to investigate the susceptibility and prognostic implications of the GWAS breast cancer loci in the Tunisian population. In a cohort of 640 unrelated patients with breast cancer and 371 healthy control subjects, we characterized the variation of 9 single nucleotide polymorphisms (SNPs), namely rs1219648, rs2981582; rs8051542, rs12443621, and rs3803662; rs889312; rs3817198; rs13387042 and rs13281615. Only 5 out of 9 GWAS breast cancer loci were found to be significantly associated with breast cancer in Tunisians: The rs1219648 (G vs. A allele: OR = 1.36, P = 1 × 10−3) and rs2981582 (A vs. G allele: OR = 1.55, P = 3 × 10−6) of FGFR2 gene; the rs8051542 of the TNRC9 gene (T vs. C allele: OR = 1.40, P = 4 × 10−4); the rs889312 of the MAP3K1 gene (C vs. A allele: OR = 1.33, P = 3 × 10−3) and the rs13281615 located on 8q24 (G vs. A allele: OR = 1.21, P = 0.03). Homozygous variant genotypes of rs2981582 were strongly related to lymph node negative breast cancer (OR = 3.33, P = 6 × 10−7) and the minor allele of rs2981582 was associated with increased risk of ER+ tumors (OR = 1.57, P = 0.02; OR = 2.15, P = 0.001, for heterozygous and homozygous variant genotypes, respectively) and increased risk of distant metastasis development (OR = 2.30, P = 4 × 10−3; OR = 3.57, P = 6 × 10−5, for heterozygous and homozygous variant genotypes, respectively) in a dose dependent manner. The association for rs8051542 was stronger for high-grade SBR tumors (OR = 2.54, P = 2 × 10−4). GG genotype of rs13387042 on 2q35 showed a significant association with the risk of developing distant metastasis (OR = 1.94, P = 0.02). The G allele of rs1219648 in FGFR2 and the A allele of rs13387042 on 2q35 indicated a better prognosis by showing a significantly higher overall survival rates (P = 0.013 and P = 0.005, respectively). In conclusion, GWAS breast cancer FGFR2, TNRC9, MAP3K1, and 8q24 loci are associated with an increased risk of breast cancer and genetic variation in FGFR2 gene may predict the aggressiveness of breast cancer in Tunisians.
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Affiliation(s)
- Jingxuan Shan
- Genetic Medicine and Immunology Laboratory, Weill Cornell Medical College in Qatar, Qatar Foundation, Education City, P.O. Box 24144, Doha, Qatar
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50
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Fasching PA, Pharoah PDP, Cox A, Nevanlinna H, Bojesen SE, Karn T, Broeks A, van Leeuwen FE, van't Veer LJ, Udo R, Dunning AM, Greco D, Aittomäki K, Blomqvist C, Shah M, Nordestgaard BG, Flyger H, Hopper JL, Southey MC, Apicella C, Garcia-Closas M, Sherman M, Lissowska J, Seynaeve C, Huijts PEA, Tollenaar RAEM, Ziogas A, Ekici AB, Rauh C, Mannermaa A, Kataja V, Kosma VM, Hartikainen JM, Andrulis IL, Ozcelik H, Mulligan AM, Glendon G, Hall P, Czene K, Liu J, Chang-Claude J, Wang-Gohrke S, Eilber U, Nickels S, Dörk T, Schiekel M, Bremer M, Park-Simon TW, Giles GG, Severi G, Baglietto L, Hooning MJ, Martens JWM, Jager A, Kriege M, Lindblom A, Margolin S, Couch FJ, Stevens KN, Olson JE, Kosel M, Cross SS, Balasubramanian SP, Reed MWR, Miron A, John EM, Winqvist R, Pylkäs K, Jukkola-Vuorinen A, Kauppila S, Burwinkel B, Marme F, Schneeweiss A, Sohn C, Chenevix-Trench G, Lambrechts D, Dieudonne AS, Hatse S, van Limbergen E, Benitez J, Milne RL, Zamora MP, Pérez JIA, Bonanni B, Peissel B, Loris B, Peterlongo P, Rajaraman P, Schonfeld SJ, Anton-Culver H, Devilee P, Beckmann MW, Slamon DJ, Phillips KA, Figueroa JD, Humphreys MK, Easton DF, Schmidt MK. The role of genetic breast cancer susceptibility variants as prognostic factors. Hum Mol Genet 2012; 21:3926-39. [PMID: 22532573 DOI: 10.1093/hmg/dds159] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Recent genome-wide association studies identified 11 single nucleotide polymorphisms (SNPs) associated with breast cancer (BC) risk. We investigated these and 62 other SNPs for their prognostic relevance. Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2), rs13281615 (8q24), rs3817198 (LSP1), rs889312 (MAP3K1), rs3803662 (TOX3), rs13387042 (2q35), rs4973768 (SLC4A7), rs6504950 (COX11) and rs10941679 (5p12) were genotyped for 25 853 BC patients with the available follow-up; 62 other SNPs, which have been suggested as BC risk SNPs by a GWAS or as candidate SNPs from individual studies, were genotyped for replication purposes in subsets of these patients. Cox proportional hazard models were used to test the association of these SNPs with overall survival (OS) and BC-specific survival (BCS). For the confirmed loci, we performed an accessory analysis of publicly available gene expression data and the prognosis in a different patient group. One of the 11 SNPs, rs3803662 (TOX3) and none of the 62 candidate/GWAS SNPs were associated with OS and/or BCS at P<0.01. The genotypic-specific survival for rs3803662 suggested a recessive mode of action [hazard ratio (HR) of rare homozygous carriers=1.21; 95% CI: 1.09-1.35, P=0.0002 and HR=1.29; 95% CI: 1.12-1.47, P=0.0003 for OS and BCS, respectively]. This association was seen similarly in all analyzed tumor subgroups defined by nodal status, tumor size, grade and estrogen receptor. Breast tumor expression of these genes was not associated with prognosis. With the exception of rs3803662 (TOX3), there was no evidence that any of the SNPs associated with BC susceptibility were associated with the BC survival. Survival may be influenced by a distinct set of germline variants from those influencing susceptibility.
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Affiliation(s)
- Peter A Fasching
- University Breast Center, Department of Gynecology and Obstetrics, University Hospital Erlangen, Comprehensive Cancer Center Erlangen Nuremberg, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany.
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