1
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Dalal PJ, Giro P, Rasmussen-Torvik LJ, Yancy CW, Shah SJ, Reiner AP, Haring B, Martin LW, Wells GL, Manson JE, Kooperberg C, Eaton CB, Patel RB. Heart Failure Risk Among African-American Women With an ICAM1 Missense Variant. JACC. HEART FAILURE 2024:S2213-1779(24)00145-8. [PMID: 38530700 DOI: 10.1016/j.jchf.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 03/28/2024]
Abstract
BACKGROUND A common genetic variant of ICAM1 among African-American individuals (rs5491; p.K56M) is associated with heart failure (HF) hospitalization, but whether this risk is specific to heart failure with preserved ejection fraction (HFpEF) remains unclear. Older women are at high risk for HFpEF, and the relationship between rs5491 and HFpEF across the age spectrum is unknown. OBJECTIVES This study assessed risk of HF and its subtypes conferred by ICAM1 p.K56M (rs5491). METHODS Associations of rs5491 with risk of HF and its subtypes were estimated among African American individuals in WHI (Women's Health Initiative). The study evaluated whether the association between rs5491 and HF hospitalizations was modified by baseline age. Subsequently, African-American women in WHI and MESA (Multi-Ethnic Study of Atherosclerosis) were pooled and analyses were repeated. RESULTS Among 8,401 women in WHI, the minor allele frequency of rs5491 was 20.7%, and 731 HF hospitalizations occurred over 19.2 years. The rs5491 variant was not associated with HF or its subtypes across WHI. Interaction analyses suggested that age as a continuous variable modified the association of rs5491 with HFpEF hospitalization (interaction P = 0.04). Upon categorizing women into age decades, rs5491 conferred increased risk of HFpEF among women ≥70 years (HR per additional rs5491 allele: 1.82 [95% CI: 1.25-2.65]; P = 0.002) but was not associated with HFpEF risk among women <70 years. Pooling African-American women in WHI (n = 8,401) and MESA (n = 856) demonstrated that the effect modification by age on the association of rs5491 with HFpEF became more significant (interaction P = 0.009), with consistent HFpEF risk effect estimates among women ≥70 years. CONCLUSIONS ICAM1 p.K56M (rs5491) is associated with HFpEF among African-American women ≥70 years.
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Affiliation(s)
- Prarthana J Dalal
- Division of Hematology and Oncology, University of Michigan School of Medicine, Ann Arbor, Michigan, USA
| | - Pedro Giro
- Division of Cardiology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Laura J Rasmussen-Torvik
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Clyde W Yancy
- Division of Cardiology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Sanjiv J Shah
- Division of Cardiology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Alex P Reiner
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Bernhard Haring
- Department of Medicine III, Saarland University Hospital, Homburg, Saarland, Germany; Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Lisa Warsinger Martin
- Division of Cardiology, George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA
| | - Gretchen L Wells
- Division of Cardiology, University of Alabama Birmingham Heersink School of Medicine, Birmingham, Alabama, USA
| | - JoAnn E Manson
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Charles B Eaton
- Center for Primary Care and Prevention, Department of Family Medicine, Department of Epidemiology, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA; Department of Epidemiology, Brown University School of Public Health, Providence, Rhode Island, USA
| | - Ravi B Patel
- Division of Cardiology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA; Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
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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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3
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Haring B, Hunt RP, Shadyab AH, Eaton C, Kaplan R, Martin LW, Panjrath G, Kuller LH, Assimes T, Kooperberg C, Wassertheil-Smoller S. Cardiovascular Disease and Mortality in Black Women Carrying the Amyloidogenic V122I Transthyretin Gene Variant. JACC. HEART FAILURE 2023; 11:1189-1199. [PMID: 36930136 PMCID: PMC10508305 DOI: 10.1016/j.jchf.2023.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/08/2023] [Accepted: 02/15/2023] [Indexed: 03/07/2023]
Abstract
BACKGROUND Long-term data on cardiovascular disease (CVD) and mortality in female carriers of the transthyretin (TTR) V122I (pV142I) variant, one of the most common variants of hereditary transthyretin cardiac amyloidosis, are sparse and the effects of blood pressure, heart rate, body mass index, and physical activity on CVD outcomes remain largely unknown. OBJECTIVES The aim was to first examine the relationship of TTR V122I (pV142I) carrier status with CVD and mortality and second to investigate the effects of blood pressure, heart rate, body mass index, and physical activity in a large cohort of postmenopausal women. METHODS The study population consisted of 9,862 non-Hispanic Black/African American women, 9,529 noncarriers and 333 TTR V122I carriers, enrolled in the Women's Health Initiative at 40 centers in the United States. Women were generally healthy and postmenopausal at the time of enrollment (1993-1998). CVD was defined as a composite endpoint consisting of coronary heart disease, stroke, acute heart failure or CVD death, and all-cause mortality. CVD cases were based on self-reported annual mailed health updates. All information was centrally adjudicated by trained physicians. HRs and 95% CIs were obtained from adjusted Cox proportional hazards models. RESULTS Among 9,862 Black female participants (mean age: 62 years [IQR: 56-67 years]), the population frequency of the TTR V122I variant was 3.4% (333 variant carriers and 9,529 noncarriers). During a mean follow-up of 16.1 years (IQR: 9.7-22.2 years), incident CVD occurred in 2,229 noncarriers and 96 carriers, whereas 2,689 noncarriers and 108 carriers died. In adjusted models including demographic, lifestyle, and medical history covariates, TTR V122I carriers were at higher risk of the composite endpoint CVD (HR: 1.52; 95% CI: 1.22-1.88), acute heart failure (HR: 2.21; 95% CI: 1.53-3.18), coronary heart disease (HR: 1.80; 95% CI: 1.30-2.47), CVD death (HR: 1.70; 95% CI: 1.26-2.30), and all-cause mortality (HR: 1.28; 95% CI: 1.04-1.56). The authors found a significant interaction by age but not by blood pressure, heart rate, body mass index, or physical activity. CONCLUSIONS Black female TTR V122I (pV142I) carriers have a higher CVD and all-cause mortality risk compared to noncarriers. In case of clinical suspicion of amyloidosis, they should be screened for TTR V122I (pV142I) carrier status to ensure early treatment onset.
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Affiliation(s)
- Bernhard Haring
- Department of Medicine III, Saarland University Hospital, Homburg, Saarland, Germany; Department of Medicine I, University of Würzburg, Würzburg, Bavaria, Germany; Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA.
| | - Rebecca P Hunt
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Aladdin H Shadyab
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California-San Diego, La Jolla, California, USA
| | - Charles Eaton
- Center for Primary Care and Prevention, Department of Family Medicine, Department of Epidemiology, Warren Alpert Medical Scholl of Brown University, Brown University School of Public Health, Providence, Rhode Island, USA
| | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Lisa Warsinger Martin
- Division of Cardiology, George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA
| | - Gurusher Panjrath
- Division of Cardiology, George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA
| | - Lewis H Kuller
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Themistocles Assimes
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA; VA Palo Alto Health Care System, Palo Alto, California, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Sylvia Wassertheil-Smoller
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, USA
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4
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2q35-rs13387042 variant and the risk of breast cancer: a case-control study. Mol Biol Rep 2022; 49:3549-3557. [PMID: 35445312 DOI: 10.1007/s11033-022-07195-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 01/25/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Breast Cancer is the most frequent neoplasm diagnosed among women worldwide. Genetic background and lifestyle/environment play a significant role in the disease etiology. According to Genome-wide association studies, some single-nucleotide polymorphisms such as 2q35-rs13387042-(G/A) have been introduced to be associated with breast cancer risk and features. In this study, we aimed to evaluate the association between this variant and the risk of breast cancer in a cohort of Iranian women. METHODS Demographics and clinical information were collected by interview and using patients' medical records, respectively. DNA was extracted from 506 blood samples, including 184 patients and 322 controls, and genotyping was performed using allele specific-PCR. SPSS v16 was used for statistical analysis. RESULT Statistically significant association was observed between AA genotype and disease risk in all patients [padj = 0.048; ORadj = 2.13, 95% CI (1.01-4.50)] and also ER-positive breast cancers [padj = 0.015; ORadj = 2.12, 95% CI (1.16-3.88)]. There was no association between rs13387042 and histopathological characteristics of the disease. Furthermore, overall survival was not statistically associated with genotype and allelic models even after adjustment for stage and receptor status (p > 0.05). CONCLUSION There is a statistically significant association between 2q35-rs13387042 and breast cancer risk. rs13387042-AA genotype might be a risk-conferring factor for breast cancer development in the Iranian population. However, further consideration is suggested to confirm its role in risk assessment and probable association with other genetic markers.
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5
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Crowder SL, Hoogland AI, Welniak TL, LaFranchise EA, Carpenter KM, Li D, Rotroff DM, Mariam A, Pierce CM, Extermann M, Kim RD, Tometich DB, Figueiredo JC, Muzaffar J, Bari S, Turner K, Weinstock GM, Jim HS. Metagenomics and chemotherapy-induced nausea: A roadmap for future research. Cancer 2022; 128:461-470. [PMID: 34643945 PMCID: PMC8776572 DOI: 10.1002/cncr.33892] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 07/06/2021] [Accepted: 08/13/2021] [Indexed: 02/03/2023]
Abstract
Uncontrolled chemotherapy-induced nausea and vomiting can reduce patients' quality of life and may result in premature discontinuation of chemotherapy. Although nausea and vomiting are commonly grouped together, research has shown that antiemetics are clinically effective against chemotherapy-induced vomiting (CIV) but less so against chemotherapy-induced nausea (CIN). Nausea remains a problem for up to 68% of patients who are prescribed guideline-consistent antiemetics. Despite the high prevalence of CIN, relatively little is known regarding its etiology independent of CIV. This review summarizes a metagenomics approach to the study and treatment of CIN with the goal of encouraging future research. Metagenomics focuses on genetic risk factors and encompasses both human (ie, host) and gut microbial genetic variation. Little work to date has focused on metagenomics as a putative biological mechanism of CIN. Metagenomics has the potential to be a powerful tool in advancing scientific understanding of CIN by identifying new biological pathways and intervention targets. The investigation of metagenomics in the context of well-established demographic, clinical, and patient-reported risk factors may help to identify patients at risk and facilitate the prevention and management of CIN.
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Affiliation(s)
| | | | | | | | | | - Daneng Li
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center
| | - Daniel M. Rotroff
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Arshiya Mariam
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | | | | | - Richard D. Kim
- Department of Hematology Oncology, Moffitt Cancer Center
| | | | | | - Jameel Muzaffar
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer Center
| | - Shahla Bari
- Department of Hematology Oncology, Moffitt Cancer Center
| | - Kea Turner
- Department of Health Outcomes and Behavior, Moffitt Cancer Center
| | | | - Heather S.L. Jim
- Department of Health Outcomes and Behavior, Moffitt Cancer Center
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6
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Gu X, Tadesse MG, Foulkes AS, Ma Y, Balasubramanian R. Bayesian variable selection for high dimensional predictors and self-reported outcomes. BMC Med Inform Decis Mak 2020; 20:212. [PMID: 32894123 PMCID: PMC7487595 DOI: 10.1186/s12911-020-01223-w] [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: 02/26/2020] [Accepted: 08/16/2020] [Indexed: 11/28/2022] Open
Abstract
Background The onset of silent diseases such as type 2 diabetes is often registered through self-report in large prospective cohorts. Self-reported outcomes are cost-effective; however, they are subject to error. Diagnosis of silent events may also occur through the use of imperfect laboratory-based diagnostic tests. In this paper, we describe an approach for variable selection in high dimensional datasets for settings in which the outcome is observed with error. Methods We adapt the spike and slab Bayesian Variable Selection approach in the context of error-prone, self-reported outcomes. The performance of the proposed approach is studied through simulation studies. An illustrative application is included using data from the Women’s Health Initiative SNP Health Association Resource, which includes extensive genotypic (>900,000 SNPs) and phenotypic data on 9,873 African American and Hispanic American women. Results Simulation studies show improved sensitivity of our proposed method when compared to a naive approach that ignores error in the self-reported outcomes. Application of the proposed method resulted in discovery of several single nucleotide polymorphisms (SNPs) that are associated with risk of type 2 diabetes in a dataset of 9,873 African American and Hispanic participants in the Women’s Health Initiative. There was little overlap among the top ranking SNPs associated with type 2 diabetes risk between the racial groups, adding support to previous observations in the literature of disease associated genetic loci that are often not generalizable across race/ethnicity populations. The adapted Bayesian variable selection algorithm is implemented in R. The source code for the simulations are available in the Supplement. Conclusions Variable selection accuracy is reduced when the outcome is ascertained by error-prone self-reports. For this setting, our proposed algorithm has improved variable selection performance when compared to approaches that neglect to account for the error-prone nature of self-reports.
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Affiliation(s)
- Xiangdong Gu
- Department of Biostatistics and Epidemiology, University of Massachusetts, Amherst, MA, USA
| | - Mahlet G Tadesse
- Department of Mathematics and Statistics, Georgetown University, Washington, DC, USA
| | - Andrea S Foulkes
- Biostatistics Center, Division of Clinical Research, Massachusetts General Hospital Research Institute, Boston, MA, USA
| | - Yunsheng Ma
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Raji Balasubramanian
- Department of Biostatistics and Epidemiology, University of Massachusetts, Amherst, MA, USA.
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7
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Manichaikul A, Peres LC, Wang XQ, Barnard ME, Chyn D, Sheng X, Du Z, Tyrer J, Dennis J, Schwartz AG, Cote ML, Peters E, Moorman PG, Bondy M, Barnholtz-Sloan JS, Terry P, Alberg AJ, Bandera EV, Funkhouser E, Wu AH, Pearce CL, Pike M, Setiawan VW, Haiman CA, Palmer JR, LeMarchand L, Wilkens LR, Berchuck A, Doherty JA, Modugno F, Ness R, Moysich K, Karlan BY, Whittemore AS, McGuire V, Sieh W, Lawrenson K, Gayther S, Sellers TA, Pharoah P, Schildkraut JM. Identification of novel epithelial ovarian cancer loci in women of African ancestry. Int J Cancer 2020; 146:2987-2998. [PMID: 31469419 PMCID: PMC7523187 DOI: 10.1002/ijc.32653] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/29/2019] [Accepted: 08/12/2019] [Indexed: 12/11/2022]
Abstract
Women of African ancestry have lower incidence of epithelial ovarian cancer (EOC) yet worse survival compared to women of European ancestry. We conducted a genome-wide association study in African ancestry women with 755 EOC cases, including 537 high-grade serous ovarian carcinomas (HGSOC) and 1,235 controls. We identified four novel loci with suggestive evidence of association with EOC (p < 1 × 10-6 ), including rs4525119 (intronic to AKR1C3), rs7643459 (intronic to LOC101927394), rs4286604 (12 kb 3' of UGT2A2) and rs142091544 (5 kb 5' of WWC1). For HGSOC, we identified six loci with suggestive evidence of association including rs37792 (132 kb 5' of follistatin [FST]), rs57403204 (81 kb 3' of MAGEC1), rs79079890 (LOC105376360 intronic), rs66459581 (5 kb 5' of PRPSAP1), rs116046250 (GABRG3 intronic) and rs192876988 (32 kb 3' of GK2). Among the identified variants, two are near genes known to regulate hormones and diseases of the ovary (AKR1C3 and FST), and two are linked to cancer (AKR1C3 and MAGEC1). In follow-up studies of the 10 identified variants, the GK2 region SNP, rs192876988, showed an inverse association with EOC in European ancestry women (p = 0.002), increased risk of ER positive breast cancer in African ancestry women (p = 0.027) and decreased expression of GK2 in HGSOC tissue from African ancestry women (p = 0.004). A European ancestry-derived polygenic risk score showed positive associations with EOC and HGSOC in women of African ancestry suggesting shared genetic architecture. Our investigation presents evidence of variants for EOC shared among European and African ancestry women and identifies novel EOC risk loci in women of African ancestry.
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Affiliation(s)
- Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA
| | - Lauren C. Peres
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Xin-Qun Wang
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA
| | - Mollie E. Barnard
- Huntsman Cancer Institute, Department of Population Health Sciences, University of Utah, Salt Lake City, UT
| | - Deanna Chyn
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA
| | - Xin Sheng
- Department of Preventive Medicine, Keck School of Medicine of USC, Los Angeles, CA
| | - Zhaohui Du
- Department of Preventive Medicine, Keck School of Medicine of USC, Los Angeles, CA
| | - Jonathan Tyrer
- Strangeways Research Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Joseph Dennis
- Strangeways Research Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Ann G. Schwartz
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI
| | - Michele L. Cote
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI
| | - Edward Peters
- Epidemiology Program, Louisiana State University Health Sciences Center School of Public Health, New Orleans, LA
| | - Patricia G. Moorman
- Department of Community and Family Medicine, Duke University Medical Center, Durham, NC
| | - Melissa Bondy
- Cancer Prevention and Population Sciences Program, Baylor College of Medicine, Houston, TX
| | - Jill S. Barnholtz-Sloan
- Department of Population and Quantitative Health Sciences and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH
| | - Paul Terry
- Department of Medicine, University of Tennessee Medical Center – Knoxville, Knoxville, TN
| | - Anthony J. Alberg
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC
| | - Elisa V. Bandera
- Department of Population Science, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ
| | - Ellen Funkhouser
- Division of Preventive Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Anna H. Wu
- Department of Preventive Medicine, Keck School of Medicine of USC, Los Angeles, CA
| | - Celeste Leigh Pearce
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Malcom Pike
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | | | | | - Andrew Berchuck
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC
| | - Jennifer A. Doherty
- Huntsman Cancer Institute, Department of Population Health Sciences, University of Utah, Salt Lake City, UT
| | - Francesmary Modugno
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA
- Ovarian Cancer Center of Excellence, Womens Cancer Research Program, Magee-Womens Research Institute and University of Pittsburgh Cancer Institute, Pittsburgh, PA
| | - Roberta Ness
- The University of Texas School of Public Health, Houston, TX
| | - Kirsten Moysich
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY
| | - Beth Y. Karlan
- Department of Obstetrics and Gynecology, Ronald Regan UCLA Medical Center, Los Angeles, CA
| | - Alice S. Whittemore
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, CA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA
| | - Valerie McGuire
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA
| | - Weiva Sieh
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, NY, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, NY, New York
| | - Kate Lawrenson
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Simon Gayther
- Center for Bioinformatics and Functional Genomics and the Cedars-Sinai Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Thomas A. Sellers
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL
| | - Paul Pharoah
- Strangeways Research Laboratory, University of Cambridge, Cambridge, United Kingdom
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8
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Dutil J, Chen Z, Monteiro AN, Teer JK, Eschrich SA. An Interactive Resource to Probe Genetic Diversity and Estimated Ancestry in Cancer Cell Lines. Cancer Res 2019; 79:1263-1273. [PMID: 30894373 DOI: 10.1158/0008-5472.can-18-2747] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/08/2018] [Accepted: 12/26/2018] [Indexed: 12/21/2022]
Abstract
Recent work points to a lack of diversity in genomics studies from genome-wide association studies to somatic (tumor) genome analyses. Yet, population-specific genetic variation has been shown to contribute to health disparities in cancer risk and outcomes. Immortalized cancer cell lines are widely used in cancer research, from mechanistic studies to drug screening. Larger collections of cancer cell lines better represent the genomic heterogeneity found in primary tumors. Yet, the genetic ancestral origin of cancer cell lines is rarely acknowledged and often unknown. Using genome-wide genotyping data from 1,393 cancer cell lines from the Catalogue of Somatic Mutations in Cancer (COSMIC) and Cancer Cell Line Encyclopedia (CCLE), we estimated the genetic ancestral origin for each cell line. Our data indicate that cancer cell line collections are not representative of the diverse ancestry and admixture characterizing human populations. We discuss the implications of genetic ancestry and diversity of cellular models for cancer research and present an interactive tool, Estimated Cell Line Ancestry (ECLA), where ancestry can be visualized with reference populations of the 1000 Genomes Project. Cancer researchers can use this resource to identify cell line models for their studies by taking ancestral origins into consideration.
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Affiliation(s)
- Julie Dutil
- Cancer Biology Division, Ponce Research Institute, Ponce Health Sciences University, Ponce, Puerto Rico.
| | - Zhihua Chen
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Alvaro N Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jamie K Teer
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Steven A Eschrich
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.
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9
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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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10
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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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11
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Goto A, Chen BH, Chan KHK, Lee C, Nelson SC, Crenshaw A, Bookman E, Margolis KL, Sale MM, Ng MCY, Reiner AP, Liu S. Genetic variants in sex hormone pathways and the risk of type 2 diabetes among African American, Hispanic American, and European American postmenopausal women in the US. J Diabetes 2018; 10:524-533. [PMID: 29417738 PMCID: PMC5980699 DOI: 10.1111/1753-0407.12648] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 01/10/2018] [Accepted: 01/30/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Sex hormones are implicated in the development of diabetes. However, whether genetic variations in sex hormone pathways (SHPs) contribute to the risk of type 2 diabetes mellitus (T2DM) remains to be determined. This study investigated associations between genetic variations in all candidate genes in SHPs and T2DM risk among a cohort of women participating in the Women's Health Initiative (WHI). METHODS Single nucleotide polymorphisms (SNPs) located within 30 kb upstream and downstream of SHP genes were comprehensively examined in 8180 African American, 3498 Hispanic American, and 3147 European American women in the WHI. In addition, whether significant SNPs would be replicated in independent populations was examined. RESULTS After adjusting for age, region, and ancestry estimates and correcting for multiple testing, seven SNPs were significantly associated with the risk of T2DM among Hispanic American women were identified in the progesterone receptor (PGR) gene, with rs948516 showing the greatest significance (odds ratio 0.67; 95% confidence interval 0.57-0.78; P = 8.8 × 10-7 ; false discovery rate, Q = 7.8 × 10-4 ). These findings were not replicated in other ethnic groups in the WHI or in sex-combined analyses in replication studies. CONCLUSION Significant signals were identified implicating the PGR gene in T2DM development in Hispanic American women in the WHI, which are consistent with genome-wide association studies findings linking PGR to glucose homeostasis. Nevertheless, the PGR SNPs-T2DM association was not statistically significant in other ethnic populations. Further studies, especially sex-specific analyses, are needed to confirm the findings and clarify the role of SHPs in T2DM.
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Affiliation(s)
- Atsushi Goto
- Metabolic Epidemiology Section, Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Brian H Chen
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kei-Hang K Chan
- Department of Epidemiology, Brown University, Providence, Rhode Island, USA
| | - Cathy Lee
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Sarah C Nelson
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Andrew Crenshaw
- Genetic Analysis Platform, Broad Institute, Cambridge, Massachusetts, USA
| | - Ebony Bookman
- Office of Population Genomics, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Michèle M Sale
- Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
| | - Maggie C Y Ng
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, Winston-Salem, North Carolina, USA
| | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Simin Liu
- Department of Epidemiology, Brown University, Providence, Rhode Island, USA
- Department of Epidemiology and Center for Global Cardiometabolic Health, Brown University, Providence, Rhode Island, USA
- Division of Endocrinology, Department of Medicine, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
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12
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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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13
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Shi M, O'Brien KM, Sandler DP, Taylor JA, Zaykin DV, Weinberg CR. Previous GWAS hits in relation to young-onset breast cancer. Breast Cancer Res Treat 2017; 161:333-344. [PMID: 27848153 PMCID: PMC5226879 DOI: 10.1007/s10549-016-4053-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 11/09/2016] [Indexed: 12/17/2022]
Abstract
PURPOSE Genome-wide association studies (GWAS) have identified dozens of single-nucleotide polymorphisms (SNPs) associated with breast cancer. Few studies focused on young-onset breast cancer, which exhibits etiologic and tumor-type differences from older-onset disease. Possible confounding by prenatal effects of the maternal genome has also not been considered. METHODS Using a family-based design for breast cancer before age 50, we assessed the relationship between breast cancer and 77 GWAS-identified breast cancer risk SNPs. We estimated relative risks (RR) for inherited and maternally mediated genetic effects. We also used published RR estimates to calculate genetic risk scores and model joint effects. RESULTS Seventeen of the candidate SNPs were nominally associated with young-onset breast cancer in our 1296 non-Hispanic white affected families (uncorrected p value <0.05). Top-ranked SNPs included rs3803662-A (TOX3, RR = 1.39; p = 7.0 × 10-6), rs12662670-G (ESR1, RR = 1.56; p = 5.7 × 10-4), rs2981579-A (FGFR2, RR = 1.24; p = 0.002), and rs999737-G (RAD51B, RR = 1.37; p = 0.003). No maternally mediated effects were found. A risk score based on all 77 SNPs indicated that their overall relationship to young-onset breast cancer risk was more than additive (additive-fit p = 2.2 × 10-7) and consistent with a multiplicative joint effect (multiplicative-fit p = 0.27). With the multiplicative formulation, the case sister's genetic risk score exceeded that of her unaffected sister in 59% of families. CONCLUSIONS The results of this family-based study indicate that no effects of previously identified risk SNPs were explained by prenatal effects of maternal variants. Many of the known breast cancer risk variants were associated with young-onset breast cancer, with evidence that TOX3, ESR1, FGFR2, and RAD51B are important for young-onset disease.
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Affiliation(s)
- Min Shi
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, 111 TW Alexander Dr, Research Triangle Park, Durham, NC, 27709, USA
| | - Katie M O'Brien
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, 111 TW Alexander Dr, Research Triangle Park, Durham, NC, 27709, USA
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, 111 TW Alexander Fr, Research Triangle Park, Durham, NC, 27709, USA
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, 111 TW Alexander Fr, Research Triangle Park, Durham, NC, 27709, USA
| | - Dmitri V Zaykin
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, 111 TW Alexander Dr, Research Triangle Park, Durham, NC, 27709, USA
| | - Clarice R Weinberg
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, 111 TW Alexander Dr, Research Triangle Park, Durham, NC, 27709, USA.
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14
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Zhu Q, Shepherd L, Lunetta KL, Yao S, Liu Q, Hu Q, Haddad SA, Sucheston-Campbell L, Bensen JT, Bandera EV, Rosenberg L, Liu S, Haiman CA, Olshan AF, Palmer JR, Ambrosone CB. Trans-ethnic follow-up of breast cancer GWAS hits using the preferential linkage disequilibrium approach. Oncotarget 2016; 7:83160-83176. [PMID: 27825120 PMCID: PMC5341253 DOI: 10.18632/oncotarget.13075] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 10/12/2016] [Indexed: 12/22/2022] Open
Abstract
Leveraging population-distinct linkage equilibrium (LD) patterns, trans-ethnic follow-up of variants discovered from genome-wide association studies (GWAS) has proved to be useful in facilitating the identification of bona fide causal variants. We previously developed the preferential LD approach, a novel method that successfully identified causal variants driving the GWAS signals within European-descent populations even when the causal variants were only weakly linked with the GWAS-discovered variants. To evaluate the performance of our approach in a trans-ethnic setting, we applied it to follow up breast cancer GWAS hits identified mostly from populations of European ancestry in African Americans (AA). We evaluated 74 breast cancer GWAS variants in 8,315 AA women from the African American Breast Cancer Epidemiology and Risk (AMBER) consortium. Only 27% of them were associated with breast cancer risk at significance level α=0.05, suggesting race-specificity of the identified breast cancer risk loci. We followed up on those replicated GWAS hits in the AMBER consortium utilizing the preferential LD approach, to search for causal variants or better breast cancer markers from the 1000 Genomes variant catalog. Our approach identified stronger breast cancer markers for 80% of the GWAS hits with at least nominal breast cancer association, and in 81% of these cases, the marker identified was among the top 10 of all 1000 Genomes variants in the corresponding locus. The results support trans-ethnic application of the preferential LD approach in search for candidate causal variants, and may have implications for future genetic research of breast cancer in AA women.
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Affiliation(s)
- Qianqian Zhu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Lori Shepherd
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Kathryn L. Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Qian Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Qiang Hu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | | | - Lara Sucheston-Campbell
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Jeannette T. Bensen
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Elisa V. Bandera
- Cancer Prevention and Control, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Lynn Rosenberg
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Andrew F. Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Julie R. Palmer
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | - Christine B. Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, USA
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15
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Phenome-Wide Association Study for Alcohol and Nicotine Risk Alleles in 26394 Women. Neuropsychopharmacology 2016; 41:2688-96. [PMID: 27187070 PMCID: PMC5026736 DOI: 10.1038/npp.2016.72] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 05/09/2016] [Accepted: 05/10/2016] [Indexed: 02/07/2023]
Abstract
To identify novel traits associated with alleles known to predispose to alcohol and nicotine use, we conducted a phenome-wide association study (PheWAS) in a large multi-population cohort. We investigated 7688 African-Americans, 1133 Asian-Americans, 14 081 European-Americans, and 3492 Hispanic-Americans from the Women's Health Initiative, analyzing alleles at the CHRNA3-CHRNA5 locus, ADH1B, and ALDH2 with respect to phenotypic traits related to anthropometric characteristics, dietary habits, social status, psychological traits, reproductive history, health conditions, and nicotine/alcohol use. In ADH1B trans-population meta-analysis and population-specific analysis, we replicated prior associations with drinking behaviors and identified multiple novel phenome-wide significant and suggestive findings related to psychological traits, socioeconomic status, vascular/metabolic conditions, and reproductive health. We then applied Bayesian network learning algorithms to provide insight into the causative relationships of the novel ADH1B associations: ADH1B appears to affect phenotypic traits via both alcohol-mediated and alcohol-independent effects. In an independent sample of 2379 subjects, we also replicated the novel ADH1B associations related to socioeconomic status (household gross income and highest grade finished in school). For CHRNA3-CHRNA5 risk alleles, we replicated association with smoking behaviors, lung cancer, and asthma. There were also novel suggestive CHRNA3-CHRNA5 findings with respect to high-cholesterol-medication use and distrustful attitude. In conclusion, the genetics of alcohol and tobacco use potentially has broader implications on physical and mental health than is currently recognized. In particular, ADH1B may be a gene relevant for the human phenome via both alcohol metabolism-related mechanisms and other alcohol metabolism-independent mechanisms.
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16
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Xu M, Xu Y, Chen M, Li Y, Li W, Zhu J, Zhang M, Chen Z, Zhang X, Liu J, Zhang B. Association study confirms two susceptibility loci for breast cancer in Chinese Han women. Breast Cancer Res Treat 2016; 159:433-42. [PMID: 27572337 DOI: 10.1007/s10549-016-3952-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 08/18/2016] [Indexed: 12/17/2022]
Abstract
To date, many loci associated with breast cancer have been identified through genome-wide association studies; most of these studies were conducted using populations of European descent. Thus, it is not clear whether these susceptibility loci are also risk factors for Chinese populations. We selected and genotyped 32 single nucleotide polymorphisms (SNPs) using the Sequenom iPLEX platform in a female Chinese cohort of 3036 breast cancer cases and 3036 healthy controls. A total of 23 SNPs passed the quality control test. The associations of these SNPs with disease susceptibility were assessed using logistic regression, adjusting for age. The Bonferroni correction was used to conservatively account for multiple testing, and the threshold for statistical significance was P < 2.17 × 10(-3) (0.05/23). We confirmed ten risk-associated variants within three reported breast cancer susceptibility loci in a Chinese Han population: 5q11.2 (rs16886181, P = 5.29 × 10(-6), OR = 1.19; rs1017226, P = 5.24 × 10(-4), OR = 1.22; rs16886034, P = 2.00 × 10(-3), OR = 1.21; rs16886113, P = 1.24 × 10(-3), OR = 1.20; rs16886364, P = 9.20 × 10(-4), OR = 1.21; rs16886397, P = 1.17 × 10(-3), OR = 1.20; rs16886448, P = 1.62 × 10(-3,)OR = 1.20; and rs2229882, P = 5.14 × 10(-4), OR = 1.31), 5q14.3 (rs421379, P = 2.83 × 10(-13), OR = 1.83), and 10q26.1 (rs35054928, P = 7.73 × 10(-6), OR = 1.18). The 10q26.1 locus was found to be a susceptibility locus for breast cancer in Chinese Han women in our previous studies. 5q11.2 and 5q14.3 are confirmed here for the first time as susceptibility loci for breast cancer in Chinese Han women. This study reports three breast cancer susceptibility loci that were previously identified in European populations and are also risk factors for Chinese populations. This study may extend the genetic basis of breast cancer in Chinese Han women and highlight the contribution of multiple variants of modest effect.
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Affiliation(s)
- Minggui Xu
- Department of Oncology, No. 2 Hospital, Anhui Medical University, Hefei, Anhui, China.,School of Life Sciences, Anhui Medical University, Hefei, Anhui, China.,Institute of Dermatology and Department of Dermatology the First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
| | - Yihui Xu
- Department of Oncology, No. 2 Hospital, Anhui Medical University, Hefei, Anhui, China.,School of Life Sciences, Anhui Medical University, Hefei, Anhui, China
| | - Mengyun Chen
- Department of Oncology, No. 2 Hospital, Anhui Medical University, Hefei, Anhui, China.,School of Life Sciences, Anhui Medical University, Hefei, Anhui, China.,Institute of Dermatology and Department of Dermatology the First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
| | - Yang Li
- Institute of Dermatology and Department of Dermatology the First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
| | - Wei Li
- Department of Oncology, No. 2 Hospital, Anhui Medical University, Hefei, Anhui, China
| | - Jun Zhu
- Institute of Dermatology and Department of Dermatology the First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
| | - Mingjun Zhang
- Department of Oncology, No. 2 Hospital, Anhui Medical University, Hefei, Anhui, China
| | - Zhendong Chen
- Department of Oncology, No. 2 Hospital, Anhui Medical University, Hefei, Anhui, China
| | - Xuejun Zhang
- Institute of Dermatology and Department of Dermatology the First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China. .,State Key Laboratory Incubation Base of Dermatology, Ministry of National Science and Technology, Hefei, Anhui, China.
| | - Jianjun Liu
- School of Life Sciences, Anhui Medical University, Hefei, Anhui, China.
| | - Bo Zhang
- Department of Oncology, No. 2 Hospital, Anhui Medical University, Hefei, Anhui, China. .,School of Life Sciences, Anhui Medical University, Hefei, Anhui, China.
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17
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Haddad SA, Ruiz-Narváez EA, Haiman CA, Sucheston-Campbell LE, Bensen JT, Zhu Q, Liu S, Yao S, Bandera EV, Rosenberg L, Olshan AF, Ambrosone CB, Palmer JR, Lunetta KL. An exome-wide analysis of low frequency and rare variants in relation to risk of breast cancer in African American Women: the AMBER Consortium. Carcinogenesis 2016; 37:870-877. [PMID: 27267999 DOI: 10.1093/carcin/bgw067] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 05/30/2016] [Indexed: 01/14/2023] Open
Abstract
A large percentage of breast cancer heritability remains unaccounted for, and most of the known susceptibility loci have been established in European and Asian populations. Rare variants may contribute to the unexplained heritability of this disease, including in women of African ancestry (AA). We conducted an exome-wide analysis of rare variants in relation to risk of overall and subtype-specific breast cancer in the African American Breast Cancer Epidemiology and Risk (AMBER) Consortium, which includes data from four large studies of AA women. Genotyping on the Illumina Human Exome Beadchip yielded data for 170 812 SNPs and 8287 subjects: 3629 cases (1093 estrogen receptor negative (ER-), 1968 ER+, 568 ER unknown) and 4658 controls, the largest exome chip study to date for AA breast cancer. Pooled gene-based association analyses were performed using the unified optimal sequence kernel association test (SKAT-O) for variants with minor allele frequency (MAF) ≤ 5%. In addition, each variant with MAF >0.5% was tested for association using logistic regression. There were no significant associations with overall breast cancer. However, a novel gene, FBXL22 (P = 8.2×10(-6)), and a gene previously identified in GWAS of European ancestry populations, PDE4D (P = 1.2×10(-6)), were significantly associated with ER- breast cancer after correction for multiple testing. Cases with the associated rare variants were also negative for progesterone and human epidermal growth factor receptors-thus, triple-negative cancer. Replication is required to confirm these gene-level associations, which are based on very small counts at extremely rare SNPs.
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Affiliation(s)
| | | | - Christopher A Haiman
- Department of Preventive Medicine , Keck School of Medicine , University of Southern California/Norris Comprehensive Cancer Center , Los Angeles, CA 90033 , USA
| | - Lara E Sucheston-Campbell
- Department of Cancer Prevention and Control , Roswell Park Cancer Institute , Buffalo, NY 14263 , USA
| | - Jeannette T Bensen
- Department of Epidemiology , Gillings School of Global Public Health , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
| | - Qianqian Zhu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute , Buffalo, NY 14263 , USA
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute , Buffalo, NY 14263 , USA
| | - Song Yao
- Department of Cancer Prevention and Control , Roswell Park Cancer Institute , Buffalo, NY 14263 , USA
| | - Elisa V Bandera
- Cancer Prevention and Control, Rutgers Cancer Institute of New Jersey , New Brunswick, NJ 08903 , USA and
| | | | - Andrew F Olshan
- Department of Epidemiology , Gillings School of Global Public Health , University of North Carolina at Chapel Hill , Chapel Hill , NC 27599 , USA
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control , Roswell Park Cancer Institute , Buffalo, NY 14263 , USA
| | | | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health , Boston, MA 02118 , USA
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Sun Y, Ye C, Guo X, Wen W, Long J, Gao YT, Shu XO, Zheng W, Cai Q. Evaluation of potential regulatory function of breast cancer risk locus at 6q25.1. Carcinogenesis 2015; 37:163-168. [PMID: 26645718 DOI: 10.1093/carcin/bgv170] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 11/29/2015] [Indexed: 01/10/2023] Open
Abstract
In a genome-wide association study conducted among Chinese women, we identified the single nucleotide polymorphism (SNP) rs2046210 at 6q25.1 for breast cancer risk. To explore a potential regulatory role for this risk locus, we measured expression levels of nine genes at the locus in breast cancer tissue and adjacent normal tissue samples obtained from 67 patients recruited in the Shanghai Breast Cancer Study. We found that rs2046210 had a statistically significant association with the expression levels of the AKAP12 and ESR1 genes in adjacent normal breast tissues. Women who carry the AA/AG risk genotypes had higher expressions of these two genes compared to those who carry G/G genotypes (P = 0.02 and 0.04 for the AKAP12 and ESR1, respectively). However, no significant differences of SNP rs2046210 with gene expression levels were found in tumor tissues. In The Cancer Genome Atlas samples, the AA/AG risk genotypes of SNP rs2046210 were associated with a significantly higher expression level of the AKAP12 gene and a lower level of the ESR1 gene in tumor tissue. Functional analysis using ENCODE data revealed that SNP rs7763637, which is in strong linkage disequilibrium with SNP rs2046210, is likely a potential functional variant, regulating the AKAP12 gene. Taken together, these results from our study suggest that the association between the 6q25.1 locus and breast cancer risk may be mediated through SNPs that regulate expressions of the AKAP12 gene.
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Affiliation(s)
- Yaqiong Sun
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, 37203, USA.,Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China and
| | - Chuanzhong Ye
- Division of Epidemiology , Department of Medicine , Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center , Vanderbilt University School of Medicine, Nashville , TN, 37203 , USA
| | - Xingyi Guo
- Division of Epidemiology , Department of Medicine , Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center , Vanderbilt University School of Medicine, Nashville , TN, 37203 , USA
| | - Wanqing Wen
- Division of Epidemiology , Department of Medicine , Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center , Vanderbilt University School of Medicine, Nashville , TN, 37203 , USA
| | - Jirong Long
- Division of Epidemiology , Department of Medicine , Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center , Vanderbilt University School of Medicine, Nashville , TN, 37203 , USA
| | - Yu-Tang Gao
- Department of Epidemiology , Shanghai Cancer Institute , Shanghai , China
| | - Xiao Ou Shu
- Division of Epidemiology , Department of Medicine , Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center , Vanderbilt University School of Medicine, Nashville , TN, 37203 , USA
| | - Wei Zheng
- Division of Epidemiology , Department of Medicine , Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center , Vanderbilt University School of Medicine, Nashville , TN, 37203 , USA
| | - Qiuyin Cai
- Division of Epidemiology , Department of Medicine , Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center , Vanderbilt University School of Medicine, Nashville , TN, 37203 , USA
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Dong Y, Chen J, Chen Z, Tian C, Lu H, Ruan J, Yang W. Evaluating the Association of Eight Polymorphisms with Cancer Susceptibility in a Han Chinese Population. PLoS One 2015; 10:e0132797. [PMID: 26176862 PMCID: PMC4503434 DOI: 10.1371/journal.pone.0132797] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 06/18/2015] [Indexed: 01/05/2023] Open
Abstract
Background The identification of susceptibility genes for specific types of cancer can provide necessary information for the complete characterization of cancer syndromes. Eight single nucleotide polymorphisms (SNPs), rs465498, rs17728461, rs4488809, rs753955, rs13361707, rs9841504, rs2274223, and rs13042395, were reported by genome wide association studies (GWASs) to be closely related to the susceptibility of lung cancer (LC), gastric cancer (GC) or esophageal cancer (EC) in Han population from northern or southern China. However, Chinese Han people from different geographic areas may have different genetic backgrounds. This study aims to assess the genetic associations of the eight SNPs mentioned above with three cancers risk in a Han population from northwest China. Methods A total of 186 cancer-free controls and 436 cases with non-small cell lung cancer (NSCLC) (159 cases), non-cardia GC (167 cases) or EC (110 cases) were enrolled in this study. Chi-square test and polytomous logistic regression analyses were used to estimate the association between eight cancer-related SNPs and three cancers in a Han Chinese population from northwest China. The logistic regression results were adjusted for confounding factors and Benjamini and Hochberg False Discovery Rate (FDR) method was used to adjust the multiple hypothesis tests. Association analyses by cigarette smoking or alcohol drinking status were analyzed by crossover analyses. Results One of the eight SNPs, rs17728461 was associated with NSCLC susceptibility (in a heterozygous model, OR = 0.44, 95% CI = 0.27–0.72, p = 0.001). Two SNPs, rs753955 and rs13042395, were associated with the risk of non-cardia GC in different genetic models (p < 0.05). No SNPs were associated with EC. The crossover analyses showed that the rs13042395 CT genotype, combined with cigarette smoking or alcohol drinking, could further increase the risk for non-cardia GC (p < 0.05). Conclusions These results indicated that rs17728461 may be specifically associated with the risk of NSCLC. rs753955 and rs13042395 were specifically associated with susceptibility to non-cardia GC in Ningxia Han Chinese. Susceptibility-associated polymorphisms in the northwestern Han Chinese were not very consistent with those in the northern Han Chinese or southern Han Chinese. The validation of these findings with a functional evaluation and a larger population is still required.
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Affiliation(s)
- Ying Dong
- Medical Oncology Department of General Hospital, Ningxia Medical University, Yinchuan, Ningxia, China
- Key Laboratory of Ningxia Reproduction and Heredity, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Jing Chen
- Key Laboratory of Ningxia Reproduction and Heredity, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Zhiqiang Chen
- Radiology Department of General Hospital, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Chaoyong Tian
- Key Laboratory of Ningxia Reproduction and Heredity, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Huaisheng Lu
- Pathology Department of Ningxia People’s Hospital, Yinchuan, Ningxia, China
| | - Jigang Ruan
- Digestive Department of General Hospital, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Wenjun Yang
- Medical Oncology Department of General Hospital, Ningxia Medical University, Yinchuan, Ningxia, China
- Key Laboratory of Ningxia Reproduction and Heredity, Ningxia Medical University, Yinchuan, Ningxia, China
- * E-mail:
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Siegert S, Wolf A, Cooper DN, Krawczak M, Nothnagel M. Mutations Causing Complex Disease May under Certain Circumstances Be Protective in an Epidemiological Sense. PLoS One 2015; 10:e0132150. [PMID: 26161957 PMCID: PMC4498598 DOI: 10.1371/journal.pone.0132150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 06/10/2015] [Indexed: 01/19/2023] Open
Abstract
Guided by the practice of classical epidemiology, research into the genetic basis of complex disease has usually taken for granted the dictum that causative mutations are invariably over-represented among clinically affected as compared to unaffected individuals. However, we show that this supposition is not true and that a mutation contributing to the etiology of a complex disease can, under certain circumstances, be depleted among patients. Populations with defined disease prevalence were repeatedly simulated under a Wright-Fisher model, assuming various types of population history and genotype-phenotype relationship. For each simulation, the resulting mutation-specific population frequencies and odds ratios (ORs) were evaluated. In addition, the relationship between mutation frequency and OR was studied using real data from the NIH GWAS catalogue of reported phenotype associations of single-nucleotide polymorphisms (SNPs). While rare diseases (prevalence <1%) were found to be consistently caused by rare mutations with ORs>1, up to 20% of mutations causing a pandemic disease (prevalence 10-20%) had ORs<1, and their population frequency ranged from 0% to 100%. Moreover, simulation-based ORs exhibited a wide distribution, irrespective of mutation frequency. In conclusion, a substantial proportion of mutations causing common complex diseases may appear 'protective' in genetic epidemiological studies and hence would normally tend to be excluded, albeit erroneously, from further study. This apparently paradoxical result is explicable in terms of mutual confounding of the respective genotype-phenotype relationships due to a negative correlation between causal mutations induced by their common gene genealogy. As would be predicted by our findings, a significant negative correlation became apparent in published genome-wide association studies between the OR of genetic variants associated with a particular disease and the prevalence of that disease.
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Affiliation(s)
- Sabine Siegert
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Institute of Epidemiology, Christian-Albrechts University, Kiel, Germany
| | - Andreas Wolf
- Institute of Medical Informatics and Statistics, Christian-Albrechts University, Kiel, Germany
| | - David N. Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian-Albrechts University, Kiel, Germany
| | - Michael Nothnagel
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Institute of Medical Informatics and Statistics, Christian-Albrechts University, Kiel, Germany
- * E-mail:
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21
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Keller BM, McCarthy AM, Chen J, Armstrong K, Conant EF, Domchek SM, Kontos D. Associations between breast density and a panel of single nucleotide polymorphisms linked to breast cancer risk: a cohort study with digital mammography. BMC Cancer 2015; 15:143. [PMID: 25881232 PMCID: PMC4365961 DOI: 10.1186/s12885-015-1159-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 03/04/2015] [Indexed: 12/16/2022] Open
Abstract
Background Breast density and single-nucleotide polymorphisms (SNPs) have both been associated with breast cancer risk. To determine the extent to which these two breast cancer risk factors are associated, we investigate the association between a panel of validated SNPs related to breast cancer and quantitative measures of mammographic density in a cohort of Caucasian and African-American women. Methods In this IRB-approved, HIPAA-compliant study, we analyzed a screening population of 639 women (250 African American and 389 Caucasian) who were tested with a validated panel assay of 12 SNPs previously associated to breast cancer risk. Each woman underwent digital mammography as part of routine screening and all were interpreted as negative. Both absolute and percent estimates of area and volumetric density were quantified on a per-woman basis using validated software. Associations between the number of risk alleles in each SNP and the density measures were assessed through a race-stratified linear regression analysis, adjusted for age, BMI, and Gail lifetime risk. Results The majority of SNPs were not found to be associated with any measure of breast density. SNP rs3817198 (in LSP1) was significantly associated with both absolute area (p = 0.004) and volumetric (p = 0.019) breast density in Caucasian women. In African-American women, SNPs rs3803662 (in TNRC9/TOX3) and rs4973768 (in NEK10) were significantly associated with absolute (p = 0.042) and percent (p = 0.028) volume density respectively. Conclusions The majority of SNPs investigated in our study were not found to be significantly associated with breast density, even when accounting for age, BMI, and Gail risk, suggesting that these two different risk factors contain potentially independent information regarding a woman’s risk to develop breast cancer. Additionally, the few statistically significant associations between breast density and SNPs were different for Caucasian versus African American women. Larger prospective studies are warranted to validate our findings and determine potential implications for breast cancer risk assessment. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1159-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Brad M Keller
- Department of Radiology, University of Pennsylvania Perelman School of Medicine, 3600 Market St. Ste 360, Philadelphia, PA, 19104, USA.
| | - Anne Marie McCarthy
- Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.
| | - Jinbo Chen
- Department of Biostatistics and Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
| | - Katrina Armstrong
- Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.
| | - Emily F Conant
- Department of Radiology, University of Pennsylvania Perelman School of Medicine, 3600 Market St. Ste 360, Philadelphia, PA, 19104, USA.
| | - Susan M Domchek
- Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
| | - Despina Kontos
- Department of Radiology, University of Pennsylvania Perelman School of Medicine, 3600 Market St. Ste 360, Philadelphia, PA, 19104, USA.
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McCarthy AM, Keller B, Kontos D, Boghossian L, McGuire E, Bristol M, Chen J, Domchek S, Armstrong K. The use of the Gail model, body mass index and SNPs to predict breast cancer among women with abnormal (BI-RADS 4) mammograms. Breast Cancer Res 2015; 17:1. [PMID: 25567532 PMCID: PMC4311477 DOI: 10.1186/s13058-014-0509-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 12/18/2014] [Indexed: 11/10/2022] Open
Abstract
Introduction Mammography screening results in a significant number of false-positives. The use of pretest breast cancer risk factors to guide follow-up of abnormal mammograms could improve the positive predictive value of screening. We evaluated the use of the Gail model, body mass index (BMI), and genetic markers to predict cancer diagnosis among women with abnormal mammograms. We also examined the extent to which pretest risk factors could reclassify women without cancer below the biopsy threshold. Methods We recruited a prospective cohort of women referred for biopsy with abnormal (BI-RADS 4) mammograms according to the American College of Radiology’s Breast Imaging-Reporting and Data System (BI-RADS). Breast cancer risk factors were assessed prior to biopsy. A validated panel of 12 single-nucleotide polymorphisms (SNPs) associated with breast cancer were measured. Logistic regression was used to assess the association of Gail risk factors, BMI and SNPs with cancer diagnosis (invasive or ductal carcinoma in situ). Model discrimination was assessed using the area under the receiver operating characteristic curve, and calibration was assessed using the Hosmer-Lemeshow goodness-of-fit test. The distribution of predicted probabilities of a cancer diagnosis were compared for women with or without breast cancer. Results In the multivariate model, age (odds ratio (OR) = 1.05; 95% confidence interval (CI), 1.03 to 1.08; P < 0.001), SNP panel relative risk (OR = 2.30; 95% CI, 1.06 to 4.99, P = 0.035) and BMI (≥30 kg/m2 versus <25 kg/m2; OR = 2.20; 95% CI, 1.05 to 4.58; P = 0.036) were significantly associated with breast cancer diagnosis. Older women were more likely than younger women to be diagnosed with breast cancer. The SNP panel relative risk remained strongly associated with breast cancer diagnosis after multivariable adjustment. Higher BMI was also strongly associated with increased odds of a breast cancer diagnosis. Obese women (OR = 2.20; 95% CI, 1.05 to 4.58; P = 0.036) had more than twice the odds of cancer diagnosis compared to women with a BMI <25 kg/m2. The SNP panel appeared to have predictive ability among both white and black women. Conclusions Breast cancer risk factors, including BMI and genetic markers, are predictive of cancer diagnosis among women with BI-RADS 4 mammograms. Using pretest risk factors to guide follow-up of abnormal mammograms could reduce the burden of false-positive mammograms. Electronic supplementary material The online version of this article (doi:10.1186/s13058-014-0509-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anne Marie McCarthy
- Department of Medicine, Massachusetts General Hospital, 50 Staniford Street, 940F, Boston, MA, 02114, USA.
| | - Brad Keller
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA.
| | - Despina Kontos
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA.
| | - Leigh Boghossian
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA.
| | - Erin McGuire
- Department of General Internal Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Mirar Bristol
- Department of Medicine, Massachusetts General Hospital, 50 Staniford Street, 940F, Boston, MA, 02114, USA.
| | - Jinbo Chen
- Department of Clinical Epidemiology and Biostatistics, University of Pennsylvania, Philadelphia, PA, USA.
| | - Susan Domchek
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA.
| | - Katrina Armstrong
- Department of Medicine, Massachusetts General Hospital, 50 Staniford Street, 940F, Boston, MA, 02114, USA.
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Figlioli G, Köhler A, Chen B, Elisei R, Romei C, Cipollini M, Cristaudo A, Bambi F, Paolicchi E, Hoffmann P, Herms S, Kalemba M, Kula D, Pastor S, Marcos R, Velázquez A, Jarząb B, Landi S, Hemminki K, Försti A, Gemignani F. Novel genome-wide association study-based candidate loci for differentiated thyroid cancer risk. J Clin Endocrinol Metab 2014; 99:E2084-92. [PMID: 25029422 DOI: 10.1210/jc.2014-1734] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT Genome-wide association studies (GWASs) on differentiated thyroid cancer (DTC) have identified robust associations with single nucleotide polymorphisms (SNPs) at 9q22.33 (FOXE1), 14q13.3 (NKX2-1), and 2q35 (DIRC3). Our recently published GWAS suggested additional susceptibility loci specific for the high-incidence Italian population. OBJECTIVE The purpose of this study was to identify novel Italian-specific DTC risk variants based on our GWAS and to test them further in low-incidence populations. DESIGN We investigated 45 SNPs selected from our GWAS first in an Italian population. SNPs that showed suggestive evidence of association were investigated in the Polish and Spanish cohorts. RESULTS The combined analysis of the GWAS and the Italian replication study (2260 case patients and 2218 control subjects) provided strong evidence of association with rs10136427 near BATF (odds ratio [OR] =1.40, P = 4.35 × 10(-7)) and rs7267944 near DHX35 (OR = 1.39, P = 2.13 × 10(-8)). A possible role in DTC susceptibility in the Italian populations was also found for rs13184587 (ARSB) (P = 8.54 × 10(-6)) and rs1220597 (SPATA13) (P = 3.25 × 10(-6)). Only the associations between rs10136427 and rs7267944 and DTC risk were replicated in the Polish and the Spanish populations with little evidence of population heterogeneity (GWAS and all replications combined, OR = 1.30, P = 9.30 × 10(-7) and OR = 1.32, P = 1.34 × 10(-8), respectively). In silico analyses provided new insights into the possible functional consequences of the SNPs that showed the strongest association with DTC. CONCLUSIONS Our findings provide evidence for novel DTC susceptibility variants. Further studies are warranted to identify the specific genetic variants responsible for the observed associations and to functionally validate our in silico predictions.
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Affiliation(s)
- Gisella Figlioli
- Department of Biology (G.F., M.C., E.P., S.L., F.G.), University of Pisa, 56123 Pisa, Italy; Molecular Genetic Epidemiology (A.K., B.C., K.H., A.F.), German Cancer Research Center, 69120 Heidelberg, Germany; Department of Endocrinology and Metabolism (R.E., C.R., A.C.), University of Pisa, 56124 Pisa, Italy; Blood Centre (F.B.), Azienda Ospedaliero Universitaria A. Meyer, 50139 Firenze, Italy; Department of Genomics (P.H., S.H.), Life and Brain Center and Institute of Human Genetics (P.H., S.H.), University of Bonn, D-53127 Bonn, Germany; Division of Medical Genetics (P.H., S.H.), University Hospital Basel and Department of Biomedicine, University of Basel, CH-4058 Basel, Switzerland; Department of Nuclear Medicine and Endocrine Oncology (M.K., D.K., B.J.), Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, 44-101 Gliwice, Poland; Grup de Mutagènesi (S.P., R.M., A.V.), Departament de Genètica i de Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Barcelona, Spain; Centro de Investigación Biomédica en Red y Epidemiologia y Salud Pública (S.P., R.M., A.V.), Instituto de Salud Carlos III, 28029 Madrid, Spain; and Center for Primary Health Care Research (K.H., A.F.), Clinical Research Center, Lund University, 205 02 Malmö, Sweden
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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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Quan L, Hong CC, Zirpoli G, Roberts MR, Khoury T, Sucheston-Campbell LE, Bovbjerg DH, Jandorf L, Pawlish K, Ciupak G, Davis W, Bandera EV, Ambrosone CB, Yao S. Variants of estrogen-related genes and breast cancer risk in European and African American women. Endocr Relat Cancer 2014; 21:853-64. [PMID: 25228414 PMCID: PMC4214251 DOI: 10.1530/erc-14-0250] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
It has been observed previously that compared with women of European ancestry (EA), those of African ancestry (AA) are more likely to develop estrogen receptor (ER)-negative breast cancer, although the mechanisms have not been elucidated. We tested the associations between breast cancer risk and a targeted set of 20 genes known to be involved in estrogen synthesis, metabolism, and response and potential gene-environment interactions using data and samples from 1307 EA (658 cases) and 1365 AA (621 cases) participants from the Women's Circle of Health Study (WCHS). Multivariable logistic regression found evidence of associations with single-nucleotide polymorphisms (SNPs) in the ESR1 gene in EA women (rs1801132, odds ratio (OR)=1.47, 95% CI=1.20-1.80, P=0.0002; rs2046210, OR=1.24, 95% CI=1.04-1.47, P=0.02; and rs3020314, OR=1.43, 95% CI=1.19-1.70, P=0.00009), but not in AA women. The only other gene associated with breast cancer risk was CYP1A2 in AA women (rs2470893, OR=1.42, 95% CI=1.00-2.02, P=0.05), but not in EA women. When stratified by ER status, ESR1 rs1801132, rs2046210, and rs3020314 showed stronger associations in ER-positive than in ER-negative breast cancer in only EA women. Associations with the ESR1 SNPs in EA women also appeared to be stronger with longer endogenous estrogen exposure or hormonal replacement therapy use. Our results indicate that there may be differential genetic influences on breast cancer risk in EA compared with AA women and that these differences may be modified by tumor subtype and estrogen exposures. Future studies with a larger sample size may determine the full contribution of estrogen-related genes to racial/ethnic differences in breast cancer.
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Affiliation(s)
- Lei Quan
- Roswell Park Cancer InstituteElm and Carlton Streets, Buffalo, New York 14263, USAUniversity of Pittsburgh Cancer InstitutePittsburgh, Pennsylvania, USAIcahn School of Medicine at Mount SinaiNew York, New York, USANew Jersey Department of HealthTrenton, New Jersey, USARutgers Cancer Institute of New JerseyNew Brunswick, New Jersey, USA Roswell Park Cancer InstituteElm and Carlton Streets, Buffalo, New York 14263, USAUniversity of Pittsburgh Cancer InstitutePittsburgh, Pennsylvania, USAIcahn School of Medicine at Mount SinaiNew York, New York, USANew Jersey Department of HealthTrenton, New Jersey, USARutgers Cancer Institute of New JerseyNew Brunswick, New Jersey, USA
| | - Chi-Chen Hong
- Roswell Park Cancer InstituteElm and Carlton Streets, Buffalo, New York 14263, USAUniversity of Pittsburgh Cancer InstitutePittsburgh, Pennsylvania, USAIcahn School of Medicine at Mount SinaiNew York, New York, USANew Jersey Department of HealthTrenton, New Jersey, USARutgers Cancer Institute of New JerseyNew Brunswick, New Jersey, USA
| | - Gary Zirpoli
- Roswell Park Cancer InstituteElm and Carlton Streets, Buffalo, New York 14263, USAUniversity of Pittsburgh Cancer InstitutePittsburgh, Pennsylvania, USAIcahn School of Medicine at Mount SinaiNew York, New York, USANew Jersey Department of HealthTrenton, New Jersey, USARutgers Cancer Institute of New JerseyNew Brunswick, New Jersey, USA
| | - Michelle R Roberts
- Roswell Park Cancer InstituteElm and Carlton Streets, Buffalo, New York 14263, USAUniversity of Pittsburgh Cancer InstitutePittsburgh, Pennsylvania, USAIcahn School of Medicine at Mount SinaiNew York, New York, USANew Jersey Department of HealthTrenton, New Jersey, USARutgers Cancer Institute of New JerseyNew Brunswick, New Jersey, USA
| | - Thaer Khoury
- Roswell Park Cancer InstituteElm and Carlton Streets, Buffalo, New York 14263, USAUniversity of Pittsburgh Cancer InstitutePittsburgh, Pennsylvania, USAIcahn School of Medicine at Mount SinaiNew York, New York, USANew Jersey Department of HealthTrenton, New Jersey, USARutgers Cancer Institute of New JerseyNew Brunswick, New Jersey, USA
| | - Lara E Sucheston-Campbell
- Roswell Park Cancer InstituteElm and Carlton Streets, Buffalo, New York 14263, USAUniversity of Pittsburgh Cancer InstitutePittsburgh, Pennsylvania, USAIcahn School of Medicine at Mount SinaiNew York, New York, USANew Jersey Department of HealthTrenton, New Jersey, USARutgers Cancer Institute of New JerseyNew Brunswick, New Jersey, USA
| | - Dana H Bovbjerg
- Roswell Park Cancer InstituteElm and Carlton Streets, Buffalo, New York 14263, USAUniversity of Pittsburgh Cancer InstitutePittsburgh, Pennsylvania, USAIcahn School of Medicine at Mount SinaiNew York, New York, USANew Jersey Department of HealthTrenton, New Jersey, USARutgers Cancer Institute of New JerseyNew Brunswick, New Jersey, USA
| | - Lina Jandorf
- Roswell Park Cancer InstituteElm and Carlton Streets, Buffalo, New York 14263, USAUniversity of Pittsburgh Cancer InstitutePittsburgh, Pennsylvania, USAIcahn School of Medicine at Mount SinaiNew York, New York, USANew Jersey Department of HealthTrenton, New Jersey, USARutgers Cancer Institute of New JerseyNew Brunswick, New Jersey, USA
| | - Karen Pawlish
- Roswell Park Cancer InstituteElm and Carlton Streets, Buffalo, New York 14263, USAUniversity of Pittsburgh Cancer InstitutePittsburgh, Pennsylvania, USAIcahn School of Medicine at Mount SinaiNew York, New York, USANew Jersey Department of HealthTrenton, New Jersey, USARutgers Cancer Institute of New JerseyNew Brunswick, New Jersey, USA
| | - Gregory Ciupak
- Roswell Park Cancer InstituteElm and Carlton Streets, Buffalo, New York 14263, USAUniversity of Pittsburgh Cancer InstitutePittsburgh, Pennsylvania, USAIcahn School of Medicine at Mount SinaiNew York, New York, USANew Jersey Department of HealthTrenton, New Jersey, USARutgers Cancer Institute of New JerseyNew Brunswick, New Jersey, USA
| | - Warren Davis
- Roswell Park Cancer InstituteElm and Carlton Streets, Buffalo, New York 14263, USAUniversity of Pittsburgh Cancer InstitutePittsburgh, Pennsylvania, USAIcahn School of Medicine at Mount SinaiNew York, New York, USANew Jersey Department of HealthTrenton, New Jersey, USARutgers Cancer Institute of New JerseyNew Brunswick, New Jersey, USA
| | - Elisa V Bandera
- Roswell Park Cancer InstituteElm and Carlton Streets, Buffalo, New York 14263, USAUniversity of Pittsburgh Cancer InstitutePittsburgh, Pennsylvania, USAIcahn School of Medicine at Mount SinaiNew York, New York, USANew Jersey Department of HealthTrenton, New Jersey, USARutgers Cancer Institute of New JerseyNew Brunswick, New Jersey, USA
| | - Christine B Ambrosone
- Roswell Park Cancer InstituteElm and Carlton Streets, Buffalo, New York 14263, USAUniversity of Pittsburgh Cancer InstitutePittsburgh, Pennsylvania, USAIcahn School of Medicine at Mount SinaiNew York, New York, USANew Jersey Department of HealthTrenton, New Jersey, USARutgers Cancer Institute of New JerseyNew Brunswick, New Jersey, USA
| | - Song Yao
- Roswell Park Cancer InstituteElm and Carlton Streets, Buffalo, New York 14263, USAUniversity of Pittsburgh Cancer InstitutePittsburgh, Pennsylvania, USAIcahn School of Medicine at Mount SinaiNew York, New York, USANew Jersey Department of HealthTrenton, New Jersey, USARutgers Cancer Institute of New JerseyNew Brunswick, New Jersey, USA
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Maxwell KN, Nathanson KL. Common breast cancer risk variants in the post-COGS era: a comprehensive review. Breast Cancer Res 2013; 15:212. [PMID: 24359602 PMCID: PMC3978855 DOI: 10.1186/bcr3591] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Breast cancer has a strong heritable component, with approximately 15% of cases exhibiting a family history of the disease. Mutations in genes such as BRCA1, BRCA2 and TP53 lead to autosomal dominant inherited cancer susceptibility and confer a high lifetime risk of breast cancers. Identification of mutations in these genes through clinical genetic testing enables patients to undergo screening and prevention strategies, some of which provide overall survival benefit. In addition, a number of mutant alleles have been identified in genes such as CHEK2, PALB2, ATM and BRIP1, which often display incomplete penetrance and confer moderate lifetime risks of breast cancer. Studies are underway to determine how to use the identification of mutations in these genes to guide clinical practice. Altogether, however, mutations in high and moderate penetrance genes probably account for approximately 25% of familial breast cancer risk; the remainder may be due to mutations in as yet unidentified genes or lower penetrance variants. Common low penetrance alleles, which have been mainly identified through genome-wide association studies (GWAS), are generally present at 10 to 50% population frequencies and confer less than 1.5-fold increases in breast cancer risk. A number of single nucleotide polymorphisms (SNPs) have been identified and risk associations extensively replicated in populations of European ancestry, the number of which has substantially increased as a result of GWAS performed by the Collaborative Oncological Gene–environment Study consortium. It is now estimated that 28% of familial breast cancer risk is explained by common breast cancer susceptibility loci. In some cases, SNP associations may be specific to different subsets of women with breast cancer, as defined by ethnicity or estrogen receptor status. Although not yet clinically established, it is hoped that identification of common risk variants may eventually allow identification of women at higher risk of breast cancer and enable implementation of breast cancer screening, prevention or treatment strategies that provide clinical benefit.
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A collaborative study of the etiology of breast cancer subtypes in African American women: the AMBER consortium. Cancer Causes Control 2013; 25:309-19. [PMID: 24343304 DOI: 10.1007/s10552-013-0332-8] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 12/06/2013] [Indexed: 12/16/2022]
Abstract
PURPOSE Breast cancer is a heterogeneous disease, with at least five intrinsic subtypes defined by molecular characteristics. Tumors that express the estrogen receptor (ER+) have better outcomes than ER- tumors, due in part to the success of hormonal therapies that target ER+ tumors. The incidence of ER- breast cancer, and the subset of ER- cancers that are basal-like, is about twice as high among African American (AA) women as among US women of European descent (EA). This disparity appears to explain, in part, the disproportionately high mortality from breast cancer that occurs in AA women. Epidemiologic research on breast cancer in AA women lags behind research in EA women. Here, we review differences in the etiology of breast cancer subtypes among AA women and describe a new consortium of ongoing studies of breast cancer in AA women. METHODS We combined samples and data from four large epidemiologic studies of breast cancer in AA women, two cohort and two case-control, creating the African American Breast Cancer Epidemiology and Risk consortium. Tumor tissue is obtained and stored in tissue microarrays, with assays of molecular markers carried out at a pathology core. Genotyping, carried out centrally, includes a whole exome SNP array and over 180,000 custom SNPs for fine-mapping of genome-wide association studies loci and candidate pathways. RESULTS To date, questionnaire data from 5,739 breast cancer cases and 14,273 controls have been harmonized. Genotyping of the first 3,200 cases and 3,700 controls is underway, with a total of 6,000 each expected by the end of the study period. CONCLUSIONS The new consortium will likely have sufficient statistical power to assess potential risk factors, both genetic and non-genetic, in relation to specific subtypes of breast cancer in AA women.
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Huang T, Hong J, Lin W, Yang Q, Ni K, Wu Q, Sun J. Assessing interactions between common genetic variant on 2q35 and hormone receptor status with breast cancer risk: evidence based on 26 studies. PLoS One 2013; 8:e69056. [PMID: 23976942 PMCID: PMC3745398 DOI: 10.1371/journal.pone.0069056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Accepted: 06/04/2013] [Indexed: 01/17/2023] Open
Abstract
Genome-wide association studies have identified 2q35-rs13387042 as a new breast cancer (BC) susceptibility locus in populations of European descent. Since then, the relationship between 2q35-rs13387042 and breast cancer has been reported in various ethnic groups; however, these studies have yielded inconsistent results. To investigate this inconsistency, we performed a meta-analysis of 26 studies involving a total of 101,529 cases and 167,363 controls for 2q35-rs13387042 polymorphism to evaluate its effect on genetic susceptibility for breast cancer. An overall random effects odds ratio of 1.14 (95% CI: 1.11-1.16, P<10⁻⁵) was found for rs13387042-A variant. Significant results were also observed using dominant (OR = 1.14, 95% CI: 1.12-1.17, P<10⁻⁵), recessive (OR = 1.17, 95% CI: 1.13-1.21, P<10⁻⁵) and co-dominant genetic model (heterozygous: OR = 1.15, 95% CI: 1.12-1.19, P<10⁻⁵; homozygous: OR = 1.20, 95% CI: 1.15-1.24, P<10⁻⁵). There was strong evidence of heterogeneity, which largely disappeared after stratification by ethnicity. Significant associations were found in East Asians, and White populations when stratified by ethnicity; while no significant associations were observed in Africans and other ethnic populations. An association was observed for both ER-positive (OR = 1.17, 95% 1.15-1.19; P<10⁻⁵) and ER-negative disease (OR = 1.08, 95% CI: 1.04-1.13; P<10⁻⁴) and both progesterone receptor (PR)-positive (OR = 1.18, 95% CI: 1.15-1.21; P<10⁻⁵) and PR-negative disease (OR = 1.10, 95% CI: 1.05-1.15; P<10⁻⁴). In conclusion, this meta-analysis demonstrated that the A allele of 2q35-rs13387042 is a risk factor associated with increased breast cancer susceptibility.
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Affiliation(s)
- Tao Huang
- Department of General Surgery, Shanghai Eighth People's Hospital, Shanghai, People's Republic of China
| | - Jun Hong
- Department of General Surgery, Shanghai Putuo District Center Hospital, Shanghai, People's Republic of China
| | - Wanlong Lin
- Department of Oncology, Shanghai Zhabei District Shibei Hospital, Shanghai, People's Republic of China
| | - Qungqing Yang
- Department of General Surgery, Shanghai Zhabei District Shibei Hospital, Shanghai, People's Republic of China
| | - Keliang Ni
- Department of General Surgery, Shanghai Zhabei District Shibei Hospital, Shanghai, People's Republic of China
| | - Qingyu Wu
- Department of General Surgery, Shanghai Zhabei District Shibei Hospital, Shanghai, People's Republic of China
- * E-mail: (QYW); (JS)
| | - Jie Sun
- Department of General Surgery, Shanghai Zhabei District Shibei Hospital, Shanghai, People's Republic of China
- * E-mail: (QYW); (JS)
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Assessing interactions between the association of common genetic variant at 1p11 (rs11249433) and hormone receptor status with breast cancer risk. PLoS One 2013; 8:e72487. [PMID: 23977306 PMCID: PMC3745461 DOI: 10.1371/journal.pone.0072487] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 07/10/2013] [Indexed: 02/07/2023] Open
Abstract
Background The association between rs11249433 polymorphism on 1p11 and breast cancer (BC) has been widely evaluated since it was first identified through genome-wide association approach. However, the results have been inconclusive. To investigate this inconsistency, we performed a meta-analysis of all available studies dealing with the relationship between the 1p11-rs11249433 polymorphism and BC. Methods Databases including Pubmed, SCOPUS, ISI web of knowledge, Embase and Cochrane databases were searched to find relevant studies. Odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the strength of association. The random-effects model was applied, addressing heterogeneity and publication bias. Results A total of 15 articles involving 90,291 cases and 137,525 controls were included. In a combined analysis, the summary per-allele odds ratio (OR) for BC of 1p11-rs11249433 polymorphism was 1.09 (95% CI: 1.06–1.12; P<10−5). Significant associations were also observed under dominant and recessive genetic models. In the subgroup analysis by ethnicity, significantly increased risks were found in Caucasians; whereas no significant associations were found among Asians and Africans. In addition, our data indicate that 1p11-rs11249433 polymorphism is involved in BC susceptibility and confer its effect primarily in estrogen receptor-positive and progesterone receptor-positive tumors. Conclusions In conclusion, this meta-analysis demonstrated that the G allele of 1p11-rs11249433 is a risk factor associated with increased breast cancer susceptibility, but these associations vary in different ethnic populations.
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Wu S, Cai J, Wang H, Zhang H, Yang W. Association between 1p11-rs11249433 polymorphism and breast cancer susceptibility: evidence from 15 case-control studies. PLoS One 2013; 8:e72526. [PMID: 23977314 PMCID: PMC3744559 DOI: 10.1371/journal.pone.0072526] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 07/15/2013] [Indexed: 01/10/2023] Open
Abstract
Genome-wide association studies have identified SNP rs11249433 at chromosome 1p11 as a new breast cancer (BC) susceptibility locus in populations of European descent. Since then, the relationship between 1p11- rs11249433 and breast cancer has been reported in various ethnic groups; however, these studies have yielded inconsistent results. To investigate this inconsistency, we performed a meta-analysis of 15 studies involving a total of 90,154 cases and 137,238 controls for 1p11-rs11249433 polymorphism to evaluate its effect on genetic susceptibility for breast cancer. An overall random effects odds ratio of 1.09 (95% CI: 1.06-1.12, P<10-5) was found for rs11249433-G variant. Significant results were also observed for heterozygous (OR=1.09, 95% CI: 1.05-1.12, P<10-5) and homozygote (OR=1.14, 95% CI: 1.08-1.21, P<10-5). There was strong evidence of heterogeneity, which largely disappeared after stratification by ethnicity. After stratified by ethnicity, significant associations were found among Caucasians. However, no significant associations were detected among East Asian and African populations. In addition, we found that rs11249433 polymorphism on 1p11 confer risk, exclusively for ER-positive tumors with per-allele OR of 1.13 (95% CI: 1.08-1.18; P <10-5) compared to ER-negative tumors of 1.01 (95% CI: 0.98-1.04; P=0.49). Similar results were also observed when stratified by PR status. Our findings demonstrated that rs11249433-G allele is a risk-conferring factor for the development of breast cancer, especially in Caucasians.
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Affiliation(s)
- Sheng Wu
- Department of General Surgery, Zhongshan Hospital, Qingpu Branch, Fudan University, Shanghai, People’s Republic of China
| | - Jungang Cai
- Department of General Surgery, Zhongshan Hospital, Qingpu Branch, Fudan University, Shanghai, People’s Republic of China
| | - Hong Wang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, People’s Republic of China
- * E-mail: (HW); (HWZ)
| | - Hongwei Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, People’s Republic of China
- * E-mail: (HW); (HWZ)
| | - Weige Yang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, People’s Republic of China
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Gu C, Zhou L, Yu J. Quantitative assessment of 2q35-rs13387042 polymorphism and hormone receptor status with breast cancer risk. PLoS One 2013; 8:e66979. [PMID: 23894282 PMCID: PMC3718795 DOI: 10.1371/journal.pone.0066979] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 05/15/2013] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The association between rs13387042 polymorphism on 2q35 and breast cancer (BC) has been widely evaluated since it was first identified through genome-wide association approach. However, the results have been inconclusive. To investigate this inconsistency, we performed a meta-analysis of all available studies dealing with the relationship between the 2q35-rs13387042 polymorphism and BC. METHODS Databases including MEDLINE, PubMed, EMBASE, ISI web of science and CNKI (China National Knowledge Infrastructure) were searched to find relevant studies. Odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the strength of association. The random-effects model was applied, addressing heterogeneity and publication bias. RESULTS A total of 24 articles involving 99,772 cases and 164,985 controls were included. In a combined analysis, the summary per-allele odds ratio (OR) for BC of 2q35-rs13387042 polymorphism was 1.13 (95% CI: 1.11-1.16; P<10(-5)). Significant associations were also detected under co-dominant, dominant and recessive genetic models. In the subgroup analysis by ethnicity, significantly increased risks were found in Asians, Caucasians and Hispanic whites for the polymorphism in all comparisons; whereas no significant associations were found among Africans. In addition, we find 2q35-rs13387042 polymorphism conferred significantly risks for both ER-positive and ER-negative tumors. Furthermore, significant associations were also detected both in PR-positive and PR-negative cancer. CONCLUSIONS Our findings demonstrated that rs13387042-A allele is a risk-conferring factors for the development of BC, especially in Asians, Caucasians and Hispanic whites.
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Affiliation(s)
- Chao Gu
- Department of General Surgery, Jinshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Liang Zhou
- Department of General Surgery, Jinshan Hospital, Fudan University, Shanghai, People's Republic of China
| | - Jianping Yu
- Department of General Surgery, Jinshan Hospital, Fudan University, Shanghai, People's Republic of China
- * E-mail:
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Swett RJ, Elias A, Miller JA, Dyson GE, Andrés Cisneros G. Hypothesis driven single nucleotide polymorphism search (HyDn-SNP-S). DNA Repair (Amst) 2013; 12:733-40. [PMID: 23830898 DOI: 10.1016/j.dnarep.2013.06.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 05/27/2013] [Accepted: 06/11/2013] [Indexed: 12/28/2022]
Abstract
The advent of complete-genome genotyping across phenotype cohorts has provided a rich source of information for bioinformaticians. However the search for SNPs from this data is generally performed on a study-by-study case without any specific hypothesis of the location for SNPs that are predictive for the phenotype. We have designed a method whereby very large SNP lists (several gigabytes in size), combining several genotyping studies at once, can be sorted and traced back to their ultimate consequence in protein structure. Given a working hypothesis, researchers are able to easily search whole genome genotyping data for SNPs that link genetic locations to phenotypes. This allows a targeted search for correlations between phenotypes and potentially relevant systems, rather than utilizing statistical methods only. HyDn-SNP-S returns results that are less data dense, allowing more thorough analysis, including haplotype analysis. We have applied our method to correlate DNA polymerases to cancer phenotypes using four of the available cancer databases in dbGaP. Logistic regression and derived haplotype analysis indicates that ~80SNPs, previously overlooked, are statistically significant. Derived haplotypes from this work link POLL to breast cancer and POLG to prostate cancer with an increase in incidence of 3.01- and 9.6-fold, respectively. Molecular dynamics simulations on wild-type and one of the SNP mutants from the haplotype of POLL provide insights at the atomic level on the functional impact of this cancer related SNP. Furthermore, HyDn-SNP-S has been designed to allow application to any system. The program is available upon request from the authors.
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Affiliation(s)
- Rebecca J Swett
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202, USA
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Shi J, Sung H, Zhang B, Lu W, Choi JY, Xiang YB, Kim MK, Iwasaki M, Long J, Ji BT, Park SK, Zheng Y, Tsugane S, Yoo KY, Wang W, Noh DY, Han W, Kim SW, Lee MH, Lee JW, Lee JY, Shen CY, Matsuo K, Ahn SH, Gao YT, Shu XO, Cai Q, Kang D, Zheng W. New breast cancer risk variant discovered at 10q25 in East Asian women. Cancer Epidemiol Biomarkers Prev 2013; 22:1297-303. [PMID: 23677579 PMCID: PMC3720126 DOI: 10.1158/1055-9965.epi-12-1393] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Recently, 41 new genetic susceptibility loci for breast cancer risk were identified in a genome-wide association study (GWAS) conducted in European descendants. Most of these risk variants have not been directly replicated in Asian populations. METHODS We evaluated nine of those nonreplication loci in East Asians to identify new risk variants for breast cancer in these regions. First, we analyzed single-nucleotide polymorphisms (SNP) in these regions using data from two GWAS conducted among Chinese and Korean women, including 5,083 cases and 4,376 controls (stage 1). In each region, we selected an SNP showing the strongest association with breast cancer risk for replication in an independent set of 7,294 cases and 9,404 controls of East Asian descents (stage 2). Logistic regression models were used to calculate adjusted ORs and 95% confidence intervals (CI) as a measure of the association of breast cancer risk and genetic variants. RESULTS Two SNPs were replicated in stage 2 at P < 0.05: rs1419026 at 6q14 [per allele OR, 1.07; 95% confidence interval (CI), 1.03-1.12; P = 3.0 × 10(-4)] and rs941827 at 10q25 (OR, 0.92, 95% CI, 0.89-0.96; P = 5.3 × 10(-5)). The association with rs941827 remained highly statistically significant after adjusting for the risk variant identified initially in women of European ancestry (OR, 0.88; 95% CI, 0.82-0.97; P = 5.3 × 10(-5)). CONCLUSION We identified a new breast cancer risk variant at 10q25 in East Asian women. IMPACT Results from this study improve the understanding of the genetic basis for breast cancer.
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Affiliation(s)
- Jiajun Shi
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Hyuna Sung
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Ben Zhang
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Wei Lu
- Shanghai Center for Disease Control and Prevention, Shanghai, China
| | - Ji-Yeob Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Yong-Bing Xiang
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
| | - Mi Kyung Kim
- Cancer Epidemiology Division, Breast Cancer Center, National Cancer Center, Korea
- Department of Surgery, College of Medicine, University of Ulsan, Asan Medical Center, Korea
| | - Motoki Iwasaki
- Epidemiology and Prevention Division, Research Center for Cancer Prevention and Screening, National Cancer Center, Tokyo, Japan
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Bu-Tian Ji
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda, Maryland, USA
| | - Sue K. Park
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Ying Zheng
- Shanghai Center for Disease Control and Prevention, Shanghai, China
| | - Shoichiro Tsugane
- Epidemiology and Prevention Division, Research Center for Cancer Prevention and Screening, National Cancer Center, Tokyo, Japan
| | - Keun-Young Yoo
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Wenjing Wang
- Shanghai Center for Disease Control and Prevention, Shanghai, China
| | - Dong-Young Noh
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Wonshik Han
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
- Department of Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Sung-Won Kim
- Department of Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Min Hyuk Lee
- Department of Surgery, Soonchunhynag University Hospital, Korea
| | - Jong Won Lee
- Department of Surgery, University of Ulsan College of Medicine and Asan Medical Center, Seoul, Korea
| | - Jong-Young Lee
- Center for Genome Science, Korea National Institute of Health, Osong Health Technology Administration Complex, Chungcheongbuk-do, Korea
| | - Chen-Yang Shen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- College of Public Health, China Medical University, Taichung, Taiwan
| | - Keitaro Matsuo
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Sei-Hyun Ahn
- Cancer Epidemiology Division, Breast Cancer Center, National Cancer Center, Korea
- Department of Surgery, College of Medicine, University of Ulsan, Asan Medical Center, Korea
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
| | - Xiao Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Daehee Kang
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
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Kravitz E, Laitman Y, Hassin-Baer S, Inzelberg R, Friedman E. Parkinson's Disease Genes Do Not Segregate with Breast Cancer Genes' Loci. Cancer Epidemiol Biomarkers Prev 2013; 22:1464-72. [DOI: 10.1158/1055-9965.epi-13-0472] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Long J, Zhang B, Signorello LB, Cai Q, Deming-Halverson S, Shrubsole MJ, Sanderson M, Dennis J, Michailidou K, Michailiou K, Easton DF, Shu XO, Blot WJ, Zheng W. Evaluating genome-wide association study-identified breast cancer risk variants in African-American women. PLoS One 2013; 8:e58350. [PMID: 23593120 PMCID: PMC3620157 DOI: 10.1371/journal.pone.0058350] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 02/03/2013] [Indexed: 12/25/2022] Open
Abstract
Genome-wide association studies (GWAS), conducted mostly in European or Asian descendants, have identified approximately 67 genetic susceptibility loci for breast cancer. Given the large differences in genetic architecture between the African-ancestry genome and genomes of Asians and Europeans, it is important to investigate these loci in African-ancestry populations. We evaluated index SNPs in all 67 breast cancer susceptibility loci identified to date in our study including up to 3,300 African-American women (1,231 cases and 2,069 controls), recruited in the Southern Community Cohort Study (SCCS) and the Nashville Breast Health Study (NBHS). Seven SNPs were statistically significant (P ≤ 0.05) with the risk of overall breast cancer in the same direction as previously reported: rs10069690 (5p15/TERT), rs999737 (14q24/RAD51L1), rs13387042 (2q35/TNP1), rs1219648 (10q26/FGFR2), rs8170 (19p13/BABAM1), rs17817449 (16q12/FTO), and rs13329835 (16q23/DYL2). A marginally significant association (P<0.10) was found for three additional SNPs: rs1045485 (2q33/CASP8), rs4849887 (2q14/INHBB), and rs4808801 (19p13/ELL). Three additional SNPs, including rs1011970 (9p21/CDKN2A/2B), rs941764 (14q32/CCDC88C), and rs17529111 (6q14/FAM46A), showed a significant association in analyses conducted by breast cancer subtype. The risk of breast cancer was elevated with an increasing number of risk variants, as measured by quintile of the genetic risk score, from 1.00 (reference), to 1.75 (1.30-2.37), 1.56 (1.15-2.11), 2.02 (1.50-2.74) and 2.63 (1.96-3.52), respectively, (P = 7.8 × 10(-10)). Results from this study highlight the need for large genetic studies in AAs to identify risk variants impacting this population.
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Affiliation(s)
- Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America.
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Fejerman L, Stern MC, Ziv E, John EM, Torres-Mejia G, Hines LM, Wolff R, Wang W, Baumgartner KB, Giuliano AR, Slattery ML. Genetic ancestry modifies the association between genetic risk variants and breast cancer risk among Hispanic and non-Hispanic white women. Carcinogenesis 2013; 34:1787-93. [PMID: 23563089 DOI: 10.1093/carcin/bgt110] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Hispanic women in the USA have lower breast cancer incidence than non-Hispanic white (NHW) women. Genetic factors may contribute to this difference. Breast cancer genome-wide association studies (GWAS) conducted in women of European or Asian descent have identified multiple risk variants. We tested the association between 10 previously reported single nucleotide polymorphisms (SNPs) and risk of breast cancer in a sample of 4697 Hispanic and 3077 NHW women recruited as part of three population-based case-control studies of breast cancer. We used stratified logistic regression analyses to compare the associations with different genetic variants in NHWs and Hispanics classified by their proportion of Indigenous American (IA) ancestry. Five of 10 SNPs were statistically significantly associated with breast cancer risk. Three of the five significant variants (rs17157903-RELN, rs7696175-TLR1 and rs13387042-2q35) were associated with risk among Hispanics but not in NHWs. The odds ratio (OR) for the heterozygous at 2q35 was 0.75 [95% confidence interval (CI) = 0.50-1.15] for low IA ancestry and 1.38 (95% CI = 1.04-1.82) for high IA ancestry (P interaction 0.02). The ORs for association at RELN were 0.87 (95% CI = 0.59-1.29) and 1.69 (95% CI = 1.04-2.73), respectively (P interaction 0.03). At the TLR1 locus, the ORs for women homozygous for the rare allele were 0.74 (95% CI = 0.42-1.31) and 1.73 (95% CI = 1.19-2.52) (P interaction 0.03). Our results suggest that the proportion of IA ancestry modifies the magnitude and direction of the association of 3 of the 10 previously reported variants. Genetic ancestry should be considered when assessing risk in women of mixed descent and in studies designed to discover causal mutations.
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Affiliation(s)
- Laura Fejerman
- Department of Medicine, Division of General Internal Medicine, Institute for Human Genetics and Helen Diller Family Comprehensive Cancer Center, University of California-San Francisco, CA 94158, USA.
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McCarthy AM, Armstrong K, Handorf E, Boghossian L, Jones M, Chen J, Demeter MB, McGuire E, Conant EF, Domchek SM. Incremental impact of breast cancer SNP panel on risk classification in a screening population of white and African American women. Breast Cancer Res Treat 2013; 138:889-98. [PMID: 23474973 DOI: 10.1007/s10549-013-2471-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 02/26/2013] [Indexed: 11/25/2022]
Abstract
Breast cancer risk prediction remains imperfect, particularly among non-white populations. This study examines the impact of including single-nucleotide polymorphism (SNP) alleles in risk prediction for white and African American women undergoing screening mammogram. Using a prospective cohort study, standard risk information and buccal swabs were collected at the time of screening mammography. A 12 SNP panel was performed by deCODE genetics. Five-year and lifetime risks incorporating SNPs were calculated by multiplying estimated Breast Cancer Risk Assessment Tool (BCRAT) risk by the total genetic risk ratio. Concordance between the BCRAT and the combined model (BCRAT + SNPs) in identifying high-risk women was measured using the kappa statistic. SNP data were available for 810 women (39 % African American, 55 % white). The mean BCRAT 5-year risk was 1.71 % for whites and 1.18 % for African Americans. Mean genetic risk ratios were 1.09 in whites and 1.29 in African Americans. Among whites, three SNPs had higher frequencies, and among African Americans, seven SNPs had higher and four had lower high-risk allele frequencies than previously reported. Agreement between the BCRAT and the combined model was relatively low for identifying high-risk women (5-year κ = 0.54, lifetime κ = 0.36). Addition of SNPs had the greatest effect among African Americans, with 12.4 % identified as having high-5-year risk by BCRAT, but 33 % by the combined model. A greater proportion of African Americans were reclassified as having high-5-year risk than whites using the combined model (21 vs. 10 %). The addition of SNPs to the BCRAT reclassifies the high-risk status of some women undergoing screening mammography, particularly African Americans. Further research is needed to determine the clinical validity and utility of the SNP panel for use in breast cancer risk prediction, particularly among African Americans for whom these risk alleles have generally not been validated.
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Affiliation(s)
- Anne Marie McCarthy
- Perelman School of Medicine, University of Pennsylvania, 423 Guardian Drive, Room 1009, Philadelphia, PA 19104, USA.
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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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Chen F, Chen GK, Stram DO, Millikan RC, Ambrosone CB, John EM, Bernstein L, Zheng W, Palmer JR, Hu JJ, Rebbeck TR, Ziegler RG, Nyante S, Bandera EV, Ingles SA, Press MF, Ruiz-Narvaez EA, Deming SL, Rodriguez-Gil JL, Demichele A, Chanock SJ, Blot W, Signorello L, Cai Q, Li G, Long J, Huo D, Zheng Y, Cox NJ, Olopade OI, Ogundiran TO, Adebamowo C, Nathanson KL, Domchek SM, Simon MS, Hennis A, Nemesure B, Wu SY, Leske MC, Ambs S, Hutter CM, Young A, Kooperberg C, Peters U, Rhie SK, Wan P, Sheng X, Pooler LC, Van Den Berg DJ, Le Marchand L, Kolonel LN, Henderson BE, Haiman CA. A genome-wide association study of breast cancer in women of African ancestry. Hum Genet 2013; 132:39-48. [PMID: 22923054 PMCID: PMC3749077 DOI: 10.1007/s00439-012-1214-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 07/31/2012] [Indexed: 01/30/2023]
Abstract
Genome-wide association studies (GWAS) in diverse populations are needed to reveal variants that are more common and/or limited to defined populations. We conducted a GWAS of breast cancer in women of African ancestry, with genotyping of >1,000,000 SNPs in 3,153 African American cases and 2,831 controls, and replication testing of the top 66 associations in an additional 3,607 breast cancer cases and 11,330 controls of African ancestry. Two of the 66 SNPs replicated (p < 0.05) in stage 2, which reached statistical significance levels of 10(-6) and 10(-5) in the stage 1 and 2 combined analysis (rs4322600 at chromosome 14q31: OR = 1.18, p = 4.3 × 10(-6); rs10510333 at chromosome 3p26: OR = 1.15, p = 1.5 × 10(-5)). These suggestive risk loci have not been identified in previous GWAS in other populations and will need to be examined in additional samples. Identification of novel risk variants for breast cancer in women of African ancestry will demand testing of a substantially larger set of markers from stage 1 in a larger replication sample.
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Affiliation(s)
- Fang Chen
- Department of Preventive Medicine, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 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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Palmer JR, Ruiz-Narvaez EA, Rotimi CN, Cupples LA, Cozier YC, Adams-Campbell LL, Rosenberg L. Genetic susceptibility loci for subtypes of breast cancer in an African American population. Cancer Epidemiol Biomarkers Prev 2012; 22:127-34. [PMID: 23136140 DOI: 10.1158/1055-9965.epi-12-0769] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Most genome-wide association studies (GWAS) have been carried out in European ancestry populations; no risk variants for breast cancer have been identified solely from African ancestry GWAS data. Few GWAS hits have replicated in African ancestry populations. METHODS In a nested case-control study of breast cancer in the Black Women's Health Study (1,199 cases/1,948 controls), we evaluated index single-nucleotide polymorphisms (SNP) in 21 loci from GWAS of European or Asian ancestry populations, overall, in subtypes defined by estrogen receptor (ER) and progesterone receptor (PR) status (ER+/PR+, n = 336; ER-/PR-, n = 229), and in triple-negative breast cancer (TNBC, N = 81). To evaluate the contribution of genetic factors to population differences in breast cancer subtype, we also examined global percent African ancestry. RESULTS Index SNPs in five loci were replicated, including three associated with ER-/PR- breast cancer (TERT rs10069690 in 5p15.33, rs704010 in 10q22.3, and rs8170 in 19p13.11): per allele ORs were 1.29 [95% confidence interval (CI) 1.04-1.59], P = 0.02, 1.52 (95% CI 1.12-2.08), P = 0.01, and 1.30 (95% CI 1.01-1.68), P = 0.04, respectively. Stronger associations were observed for TNBC. Furthermore, cases in the highest quintile of percent African ancestry were three times more likely to have TNBC than ER+/PR+ cancer. CONCLUSIONS These findings provide the first confirmation of the TNBC SNP rs8170 in an African ancestry population, and independent confirmation of the TERT ER- SNP. Furthermore, the risk of developing ER- breast cancer, particularly TNBC, increased with increasing proportion of global African ancestry. IMPACT The findings illustrate the importance of genetic factors in the disproportionately high occurrence of TNBC in African American women.
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Affiliation(s)
- Julie R Palmer
- Slone Epidemiology Center at Boston University, 1010 Commonwealth Avenue, Boston, MA 02215, USA.
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42
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Three novel functional polymorphisms in the promoter of FGFR2 gene and breast cancer risk: a HuGE review and meta-analysis. Breast Cancer Res Treat 2012; 136:885-97. [DOI: 10.1007/s10549-012-2300-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 10/12/2012] [Indexed: 10/27/2022]
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Chen W, Zhong R, Ming J, Zou L, Zhu B, Lu X, Ke J, Zhang Y, Liu L, Miao X, Huang T. The SLC4A7 variant rs4973768 is associated with breast cancer risk: evidence from a case-control study and a meta-analysis. Breast Cancer Res Treat 2012; 136:847-57. [PMID: 23117855 DOI: 10.1007/s10549-012-2309-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 10/19/2012] [Indexed: 11/26/2022]
Abstract
Recent genome-wide association study has identified a genetic variant rs4973768, located in 3'-UTR of solute carrier family 4, sodium bicarbonate cotransporter, member 7 (SLC4A7), was associated with increased risk of breast cancer (BC). However, several following replication studies cannot yield consistent results. We thus conducted a hospital-based case-control study including 485 patients and 514 controls, combined a meta-analysis including 108,632 cases and 135,818 controls to explore the relationship between this variant and BC risk. Our case-control study showed that rs4973768 was significantly associated with increased BC risk with the odds ratio (OR) of 1.29 (95 % confidence interval [CI]: 1.04-1.60) under the allelic model. In addition, the meta-analysis also indicated that the variant slightly increased the risk of BC with the pooled OR of the per-allele effect being 1.08 (95 % CI: 1.04-1.11) although with significant heterogeneity between studies. Stratified analyses showed that ethnicity, sample size, and study design may explain part of the heterogeneity. Moreover, the bioinformatics analysis suggested that this variant may influence the transcriptional capacity of SLC4A7. In summary, our results showed that the SLC4A7 variant, rs4973768, is associated with risk of BC although the underlying biologic mechanism warrants further studies.
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Affiliation(s)
- Wei Chen
- Ministry of Education Key Lab of Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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44
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Ruiz-Narváez EA, Rosenberg L, Yao S, Rotimi CN, Cupples AL, Bandera EV, Ambrosone CB, Adams-Campbell LL, Palmer JR. Fine-mapping of the 6q25 locus identifies a novel SNP associated with breast cancer risk in African-American women. Carcinogenesis 2012; 34:287-91. [PMID: 23104177 DOI: 10.1093/carcin/bgs334] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The rs2046210 single nucleotide polymorphism (SNP) in the 6q25.1 region was identified in a breast cancer genome-wide association study of Chinese women. The SNP has been replicated in European ancestry populations, but replication efforts have failed in African ancestry populations. We evaluated a total of 13 tagging SNPs in the linkage disequilibrium block around rs2046210 in a case-control study of breast cancer nested within the Black Women's Health Study, which included 1191 cases and 1941 controls. Replication of initial significant findings was carried out in 665 cases and 821 controls of African ancestry from the Women's Circle of Health Study (WCHS). No significant association was found for rs2046210 in univariate analysis. A new SNP, rs2046211, was significantly associated with reduced risk of breast cancer and was replicated in data from WCHS. In joint analyses that included both SNPs, the rs2046210-A allele was associated with increased risk of breast cancer [odds ratio (OR) = 1.14; 95% confidence interval (CI) = 1.02-1.28], and the rs2046211-G allele was associated with reduced risk (OR = 0.80; 95% CI = 0.67-0.95). Haplotype analysis confirmed these results and showed that the rs2046210-A allele is present in high-risk (rs2046211-C/rs2046210-A) and low-risk (rs2046211-G/rs2046210-A) haplotypes. Our results confirm the importance of 6q25.1 as a breast cancer susceptibility region. We replicated the rs2046210 association, after accounting for the haplotype background that included rs2046211 in African-American women, and we report the presence of a novel signal that is tagged by rs2046211.
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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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Microsatellites in the estrogen receptor (ESR1, ESR2) and androgen receptor (AR) genes and breast cancer risk in African American and Nigerian women. PLoS One 2012; 7:e40494. [PMID: 22792352 PMCID: PMC3394707 DOI: 10.1371/journal.pone.0040494] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 06/08/2012] [Indexed: 01/02/2023] Open
Abstract
Genetic variants in hormone receptor genes may be crucial predisposing factors for breast cancer, and microsatellites in the estrogen receptor (ESR1, ESR2) and androgen receptor (AR) genes have been suggested to play a role. We studied 258 African-American (AA) women with breast cancer and 259 hospital-based controls, as well as 349 Nigerian (NG) female breast cancer patients and 296 community controls. Three microsatellites, ESR1_TA, ESR2_CA and AR_CAG, in the ESR1, ESR2 and AR genes, respectively, were genotyped. Their repeat lengths were then analyzed as continuous and dichotomous variables. Analyses of continuous variables showed no association with breast cancer risk in either AA or NG at ESR1_TA; AA cases had shorter repeats in the long allele of ESR2_CA than AA controls (Mann-Whitney P= 0.036; logistic regression P = 0.04, OR= 0.91, 95% CI 0.83-1.00), whereas NG patients had longer repeats in the short allele than NG controls (Mann-Whitney P= 0.0018; logistic regression P= 0.04, OR= 1.06, 95% CI 1.00-1.11); and AA cases carried longer repeats in the short allele of AR_CAG than AA controls (Mann-Whitney P= 0.038; logistic regression P = 0.03, OR= 1.08, 95% CI 1.01-1.15). When allele sizes were categorized as dichotomous variables, we discovered that women with two long alleles of ESR2_CA had increased risk of breast cancer (OR = 1.38, 95% CI 1.10-1.74; P = 0.006). This is the first study to investigate these three microsatellites in hormonal receptor genes in relation to breast cancer risk in an indigenous African population. After adjusting for multiple-testing, our findings suggest that ESR2_CA is associated with breast cancer risk in Nigerian women, whereas ESR1_TA and AR_CAG seem to have no association with the disease among African American or Nigerian women.
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Chang WC, Woon PY, Hsu YW, Yang S, Chiu YC, Hou MF. The association between single-nucleotide polymorphisms of ORAI1 gene and breast cancer in a Taiwanese population. ScientificWorldJournal 2012; 2012:916587. [PMID: 22778704 PMCID: PMC3385595 DOI: 10.1100/2012/916587] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2012] [Accepted: 04/10/2012] [Indexed: 12/18/2022] Open
Abstract
Background. Breast cancer is the most common malignancy in women. There is increasing evidence suggesting that ORAI1, components of store-operated calcium channel, play a pivotal role in breast cancer progression and metastasis. Methods. A total of 384 female patients with breast cancer were included in this study. We selected five representative tagging ORAI1 SNPs from HapMap database with minimum allele frequency (MAF) >10%. Genotyping was performed using TaqMan allelic discrimination assay. Chi-square (χ2) test was used to analyze statistical differences among control and patient groups in genotype and allelic frequencies. Results. Two of the ORAI1 SNPs (rs12320939 and rs12313273) were associated with estrogen receptors positive in breast cancer patients under the recessive model. When the Bonferroni correction was performed, the significance still existed. In addition, rs12320939 also associated with the lymph nodal involvement. Conclusion. We showed that genetic polymorphisms of ORAI1 associated strongly with lymph nodal involvement and estrogen receptors (ERs) positive breast cancer patients in a Taiwanese population.
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Affiliation(s)
- Wei-Chiao Chang
- Department of Medical Genetics, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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48
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Shields AE, Crown WH. Looking to the future: incorporating genomic information into disparities research to reduce measurement error and selection bias. Health Serv Res 2012; 47:1387-410. [PMID: 22515190 PMCID: PMC3418832 DOI: 10.1111/j.1475-6773.2012.01413.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE To extend recent conceptual and methodological advances in disparities research to include the incorporation of genomic information in analyses of racial/ethnic disparities in health care and health outcomes. DATA SOURCES Published literature on human genetic variation, the role of genetics in disease and response to treatment, and methodological developments in disparities research. STUDY DESIGN We present a conceptual framework for incorporating genomic information into the Institute of Medicine definition of racial/ethnic disparities in health care, identify key concepts used in disparities research that can be informed by genomics research, and illustrate the incorporation of genomic information into current methods using the example of HER-2 mutations guiding care for breast cancer. PRINCIPAL FINDINGS Genomic information has not yet been incorporated into disparities research, though it has direct relevance to concepts of race/ethnicity, health status, appropriate care, and socioeconomic status. The HER-2 example demonstrates how available genetic information can be incorporated into current disparities methods to reduce selection bias and measurement error. Advances in health information infrastructure may soon make standardized genetic information more available to health services researchers. CONCLUSION Genomic information can refine measurement of racial/ethnic disparities in health care and health outcomes and should be included wherever possible in disparities research.
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Affiliation(s)
- Alexandra E Shields
- Harvard/MGH Center for Genomics, Vulnerable Populations and Health Disparities, and Mongan Institute for Health Policy, Massachusetts General Hospital, Boston, MA, USA.
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Kim HC, Lee JY, Sung H, Choi JY, Park SK, Lee KM, Kim YJ, Go MJ, Li L, Cho YS, Park M, Kim DJ, Oh JH, Kim JW, Jeon JP, Jeon SY, Min H, Kim HM, Park J, Yoo KY, Noh DY, Ahn SH, Lee MH, Kim SW, Lee JW, Park BW, Park WY, Kim EH, Kim MK, Han W, Lee SA, Matsuo K, Shen CY, Wu PE, Hsiung CN, Lee JY, Kim HL, Han BG, Kang D. A genome-wide association study identifies a breast cancer risk variant in ERBB4 at 2q34: results from the Seoul Breast Cancer Study. Breast Cancer Res 2012; 14:R56. [PMID: 22452962 PMCID: PMC3446390 DOI: 10.1186/bcr3158] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 03/07/2012] [Accepted: 03/27/2012] [Indexed: 12/16/2022] Open
Abstract
Introduction Although approximately 25 common genetic susceptibility loci have been identified to be independently associated with breast cancer risk through genome-wide association studies (GWAS), the genetic risk variants reported to date only explain a small fraction of the heritability of breast cancer. Furthermore, GWAS-identified loci were primarily identified in women of European descent. Methods To evaluate previously identified loci in Korean women and to identify additional novel breast cancer susceptibility variants, we conducted a three-stage GWAS that included 6,322 cases and 5,897 controls. Results In the validation study using Stage I of the 2,273 cases and 2,052 controls, seven GWAS-identified loci [5q11.2/MAP3K1 (rs889312 and rs16886165), 5p15.2/ROPN1L (rs1092913), 5q12/MRPS30 (rs7716600), 6q25.1/ESR1 (rs2046210 and rs3734802), 8q24.21 (rs1562430), 10q26.13/FGFR2 (rs10736303), and 16q12.1/TOX3 (rs4784227 and rs3803662)] were significantly associated with breast cancer risk in Korean women (Ptrend < 0.05). To identify additional genetic risk variants, we selected the most promising 17 SNPs in Stage I and replicated these SNPs in 2,052 cases and 2,169 controls (Stage II). Four SNPs were further evaluated in 1,997 cases and 1,676 controls (Stage III). SNP rs13393577 at chromosome 2q34, located in the Epidermal Growth Factor Receptor 4 (ERBB4) gene, showed a consistent association with breast cancer risk with combined odds ratios (95% CI) of 1.53 (1.37-1.70) (combined P for trend = 8.8 × 10-14). Conclusions This study shows that seven breast cancer susceptibility loci, which were previously identified in European and/or Chinese populations, could be directly replicated in Korean women. Furthermore, this study provides strong evidence implicating rs13393577 at 2q34 as a new risk variant for breast cancer.
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Affiliation(s)
- Hyung-cheol Kim
- Center for Genome Science, National Institute of Health, Osong Health Technology Administration Complex, Chungcheongbuk-do, 363-951, Korea
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Huo D, Zheng Y, Ogundiran TO, Adebamowo C, Nathanson KL, Domchek SM, Rebbeck TR, Simon MS, John EM, Hennis A, Nemesure B, Wu SY, Leske MC, Ambs S, Niu Q, Zhang J, Cox NJ, Olopade OI. Evaluation of 19 susceptibility loci of breast cancer in women of African ancestry. Carcinogenesis 2012; 33:835-40. [PMID: 22357627 DOI: 10.1093/carcin/bgs093] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Multiple breast cancer susceptibility loci have been identified in genome-wide association studies (GWAS) in populations of European and Asian ancestry using array chips optimized for populations of European ancestry. It is important to examine whether these loci are associated with breast cancer risk in women of African ancestry. We evaluated 25 single nucleotide polymorphisms (SNPs) at 19 loci in a pooled case-control study of breast cancer, which included 1509 cases and 1383 controls. Cases and controls were enrolled in Nigeria, Barbados and the USA; all women were of African ancestry. We found significant associations for three SNPs, which were in the same direction and of similar magnitude as those reported in previous fine-mapping studies in women of African ancestry. The allelic odds ratios were 1.24 [95% confidence interval (CI): 1.04-1.47; P = 0.018] for the rs2981578-G allele (10q26/FGFR2), 1.34 (95% CI: 1.10-1.63; P = 0.0035) for the rs9397435-G allele (6q25) and 1.12 (95% CI: 1.00-1.25; P = 0.04) for the rs3104793-C allele (16q12). Although a significant association was observed for an additional index SNP (rs3817198), it was in the opposite direction to prior GWAS studies. In conclusion, this study highlights the complexity of applying current GWAS findings across racial/ethnic groups, as none of GWAS-identified index SNPs could be replicated in women of African ancestry. Further fine-mapping studies in women of African ancestry will be needed to reveal additional and causal variants for breast cancer.
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Affiliation(s)
- Dezheng Huo
- Department of Health Studies, University of Chicago, 5841 South Maryland Avenue, MC 2007, Chicago, IL 60637, USA.
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