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Palmer JR, Cozier YC, Rosenberg L. Research on Health Disparities: Strategies and Findings From the Black Women's Health Study. Am J Epidemiol 2023; 192:1806-1810. [PMID: 35136921 PMCID: PMC11004793 DOI: 10.1093/aje/kwac022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/24/2022] [Accepted: 02/01/2022] [Indexed: 01/10/2023] Open
Abstract
The American Journal of Epidemiology has been a platform for findings from the Black Women's Health Study (BWHS) that are relevant to health disparities. Topics addressed have included methods of follow-up of a large cohort of Black women, disparities in health-care delivery, modifiable risk factors for health conditions that disproportionately affect Black women, associations with exposures that are highly prevalent in Black women, and methods for genetic research. BWHS papers have also highlighted the importance of considering social context, including perceived experiences of racism, in understanding health disparities. In the future, BWHS investigators will contribute to documentation of the role that structural racism plays in health disparities.
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Affiliation(s)
| | | | - Lynn Rosenberg
- Correspondence to Dr. Lynn Rosenberg, Slone Epidemiology Center at Boston University, 72 East Concord Street L7, Boston, MA 02118 (e-mail: )
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Díaz-Zuluaga AM, Vélez JI, Cuartas M, Valencia J, Castaño M, Palacio JD, Arcos-Burgos M, López-Jaramillo C. Ancestry component as a major predictor of lithium response in the treatment of bipolar disorder. J Affect Disord 2023; 332:203-209. [PMID: 36997125 DOI: 10.1016/j.jad.2023.03.058] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 03/10/2023] [Accepted: 03/18/2023] [Indexed: 04/01/2023]
Abstract
BACKGROUND Bipolar Disorder (BD) represents the seventh major cause of disability life-years-adjusted. Lithium remains as a first-line treatment, but clinical improvement occurs only in 30 % of treated patients. Studies suggest that genetics plays a major role in shaping the individual response of BD patients to lithium. METHODS We used machine-learning techniques (Advance Recursive Partitioned Analysis, ARPA) to build a personalized prediction framework of BD lithium response using biological, clinical, and demographical data. Using the Alda scale, we classified 172 BD I-II patients as responders or non-responders to lithium treatment. ARPA methods were used to build individual prediction frameworks and to define variable importance. Two predictive models were evaluated: 1) demographic and clinical data, and 2) demographic, clinical and ancestry data. Model performance was assessed using Receiver Operating Characteristic (ROC) curves. RESULTS The predictive model including ancestry yield the best performance (sensibility = 84.6 %, specificity = 93.8 % and AUC = 89.2 %) compared to the model without ancestry (sensibility = 50 %, Specificity = 94.5 %, and AUC = 72.2 %). This ancestry component best predicted lithium individual response. Clinical variables such as disease duration, the number of depressive episodes, the total number of affective episodes, and the number of manic episodes were also important predictors. CONCLUSION Ancestry component is a major predictor and significantly improves the definition of individual Lithium response in BD patients. We provide classification trees with potential bench application in the clinical setting. While this prediction framework might be applied in specific populations, the used methodology might be of general use in precision and translational medicine.
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Affiliation(s)
- Ana M Díaz-Zuluaga
- Research Group in Psychiatry (GIPSI), Institute of Medical Research, Department of Psychiatry, Faculty of Medicine, University of Antioquia, Medellín, Antioquia, Colombia
| | - Jorge I Vélez
- Department of Industrial Engineering, Universidad del Norte, Km 5 vía Puerto Colombia, 081007 Barranquilla, Colombia
| | - Mauricio Cuartas
- Research Group Studies in Psychology, School of Humanities, Department of Psychology, EAFIT University, Medellín, Antioquia, Colombia
| | - Johanna Valencia
- Research Group in Psychiatry (GIPSI), Institute of Medical Research, Department of Psychiatry, Faculty of Medicine, University of Antioquia, Medellín, Antioquia, Colombia
| | - Mauricio Castaño
- Department of Mental Health and Human Behavior, Universidad de Caldas, Manizales, Caldas, Colombia
| | - Juan David Palacio
- Research Group in Psychiatry (GIPSI), Institute of Medical Research, Department of Psychiatry, Faculty of Medicine, University of Antioquia, Medellín, Antioquia, Colombia
| | - Mauricio Arcos-Burgos
- Research Group in Psychiatry (GIPSI), Institute of Medical Research, Department of Psychiatry, Faculty of Medicine, University of Antioquia, Medellín, Antioquia, Colombia
| | - Carlos López-Jaramillo
- Research Group in Psychiatry (GIPSI), Institute of Medical Research, Department of Psychiatry, Faculty of Medicine, University of Antioquia, Medellín, Antioquia, Colombia.
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3
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Mongiovi JM, Hong CC, Zirpoli GR, Khoury T, Omilian AR, Qin B, Bandera EV, Yao S, Ambrosone CB, Gong Z. Genetic Variants in COX2 and ALOX Genes and Breast Cancer Risk in White and Black Women. Front Oncol 2021; 11:679998. [PMID: 34249719 PMCID: PMC8263909 DOI: 10.3389/fonc.2021.679998] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/07/2021] [Indexed: 01/05/2023] Open
Abstract
COX and ALOX genes are involved in inflammatory processes and that may be related to breast cancer risk differentially between White and Black women. We evaluated distributions of genetic variants involved in COX2 and ALOX-related pathways and examined their associations with breast cancer risk among 1,275 White and 1,299 Black cases and controls who participated in the Women’s Circle of Health Study. Odds ratios (ORs) and 95% confidence intervals (CIs) were estimated using multivariable-adjusted logistic regression models. Our results showed differential associations of certain genetic variants with breast cancer according to menopausal and ER status in either White or Black women. In White women, an increased risk of breast cancer was observed for COX2-rs689470 (OR: 2.02, P = 0.01) in the dominant model, and was strongest among postmenopausal women (OR: 2.72, P = 0.02) and for estrogen receptor positive (ER+) breast cancers (OR: 2.60, P = 0.001). A reduced risk was observed for ALOX5-rs7099874 (OR: 0.75, P = 0.01) in the dominant model, and was stronger among postmenopausal women (OR: 0.68, P = 0.03) and for ER+ cancer (OR: 0.66, P = 0.001). Four SNPs (rs3840880, rs1126667, rs434473, rs1042357) in the ALOX12 gene were found in high LD (r2 >0.98) in White women and were similarly associated with reduced risk of breast cancer, with a stronger association among postmenopausal women and for ER− cancer. Among Black women, increased risk was observed for ALOX5-rs1369214 (OR: 1.44, P = 0.003) in the recessive model and was stronger among premenopausal women (OR: 1.57, P = 0.03) and for ER+ cancer (OR: 1.53, P = 0.003). Our study suggests that genetic variants of COX2 and ALOX genes are associated with breast cancer, and that these associations and genotype distributions differ in subgroups defined by menopausal and ER status between White and Black women. Findings may provide insights into the etiology of breast cancer and areas for further research into reasons for breast cancer differences between races.
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Affiliation(s)
- Jennifer M Mongiovi
- Department of Cancer Prevention & Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States.,Department of Epidemiology and Environmental Health, University at Buffalo, Buffalo, NY, United States
| | - Chi-Chen Hong
- Department of Cancer Prevention & Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Gary R Zirpoli
- Slone Epidemiology Center, Boston University, Boston, NY, United States
| | - Thaer Khoury
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Angela R Omilian
- Department of Cancer Prevention & Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Bo Qin
- Cancer Epidemiology and Health Outcomes, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States
| | - Elisa V Bandera
- Cancer Epidemiology and Health Outcomes, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States
| | - Song Yao
- Department of Cancer Prevention & Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Christine B Ambrosone
- Department of Cancer Prevention & Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Zhihong Gong
- Department of Cancer Prevention & Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
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4
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Sung H, DeSantis CE, Fedewa SA, Kantelhardt EJ, Jemal A. Breast cancer subtypes among Eastern‐African–born black women and other black women in the United States. Cancer 2019; 125:3401-3411. [DOI: 10.1002/cncr.32293] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 01/19/2023]
Affiliation(s)
- Hyuna Sung
- Surveillance and Health Services Research American Cancer Society Atlanta Georgia
| | - Carol E. DeSantis
- Surveillance and Health Services Research American Cancer Society Atlanta Georgia
| | - Stacey A. Fedewa
- Surveillance and Health Services Research American Cancer Society Atlanta Georgia
| | - Eva J. Kantelhardt
- Department of Gynecology, Institute of Medical Epidemiology, Biometrics and Informatics Martin‐Luther University Halle Germany
| | - Ahmedin Jemal
- Surveillance and Health Services Research American Cancer Society Atlanta Georgia
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Coignet MV, Zirpoli GR, Roberts MR, Khoury T, Bandera EV, Zhu Q, Yao S. Genetic variations, reproductive aging, and breast cancer risk in African American and European American women: The Women's Circle of Health Study. PLoS One 2017; 12:e0187205. [PMID: 29073238 PMCID: PMC5658184 DOI: 10.1371/journal.pone.0187205] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 10/16/2017] [Indexed: 11/18/2022] Open
Abstract
Reproductive aging phenotypes, including age at menarche (AM) and age at natural menopause (ANM), are well-established risk factors for breast cancer. In recent years, many genetic variants have been identified in association with AM and ANM in genome-wide association studies among European populations. Using data from the Women’s Circle of Health Study (WCHS) of 1,307 European-American (EA) and 1,365 African-American (AA) breast cancer cases and controls, we aimed to replicate 53 earlier GWAS variants for AM and ANM in AA and EA groups and to perform analyses on total and net reproductive lifespan (TRLS; NRLS). Breast cancer risk was also examined in relation to a polygenic risk score (PRS) for each of the reproductive aging phenotypes. We replicated a number of variants in EA women, including rs7759938 in LIN28B for AM and rs16991615 in MCM8 for ANM; whereas in the AA group, only one SNP (rs2947411 in TMEM18) for AM was directionally consistent and nominally significant. In analysis of TRLS and NRLS, several SNPs were significant, including rs466639 in RXRG that was associated with both phenotypes in both AA and EA groups. None of the PRS was associated with breast cancer risk. Given the paucity of data available among AA populations, our study contributes to the literature of genetics of reproductive aging in AA women and highlights the importance of cross population replication of GWAS variants.
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Affiliation(s)
- Marie V. Coignet
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, United States of America
| | - Gary Robert Zirpoli
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, United States of America
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Michelle R. Roberts
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, United States of America
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States of America
| | - Thaer Khoury
- Department of Pathology, Roswell Park Cancer Institute, Buffalo, NY, United States of America
| | - Elisa V. Bandera
- Cancer Prevention and Control Program, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, United States of America
| | - Qianqian Zhu
- Department of Biostatistics, Roswell Park Cancer Institute, Buffalo, NY, United States of America
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, United States of America
- * E-mail:
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Hellwege J, Keaton J, Giri A, Gao X, Velez Edwards DR, Edwards TL. Population Stratification in Genetic Association Studies. CURRENT PROTOCOLS IN HUMAN GENETICS 2017; 95:1.22.1-1.22.23. [PMID: 29044472 PMCID: PMC6007879 DOI: 10.1002/cphg.48] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Population stratification (PS) is a primary consideration in studies of genetic determinants of human traits. Failure to control for PS may lead to confounding, causing a study to fail for lack of significant results, or resources to be wasted following false-positive signals. Here, historical and current approaches for addressing PS when performing genetic association studies in human populations are reviewed. Methods for detecting the presence of PS, including global and local ancestry methods, are described. Also described are approaches for accounting for PS when calculating association statistics, such that measures of association are not confounded. Many traits are being examined for the first time in minority populations, which may inherently feature PS. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Jacklyn Hellwege
- Vanderbilt Genetics Institute, Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center,
Nashville, TN 37203, USA
| | - Jacob Keaton
- Vanderbilt Genetics Institute, Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center,
Nashville, TN 37203, USA
| | - Ayush Giri
- Vanderbilt Genetics Institute, Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center,
Nashville, TN 37203, USA
| | - Xiaoyi Gao
- Department of Ophthalmology and Preventive Medicine, Keck School of Medicine, University of Southern California, Los
Angeles, CA 90033, USA
| | - Digna R. Velez Edwards
- Vanderbilt Genetics Institute, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center,
Nashville, TN 37203, USA
| | - Todd L. Edwards
- Vanderbilt Genetics Institute, Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center,
Nashville, TN 37203, USA
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Roberts MR, Sucheston-Campbell LE, Zirpoli GR, Higgins M, Freudenheim JL, Bandera EV, Ambrosone CB, Yao S. Single nucleotide variants in metastasis-related genes are associated with breast cancer risk, by lymph node involvement and estrogen receptor status, in women with European and African ancestry. Mol Carcinog 2017; 56:1000-1009. [PMID: 27597141 PMCID: PMC5310990 DOI: 10.1002/mc.22565] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 07/29/2016] [Accepted: 09/04/2016] [Indexed: 01/01/2023]
Abstract
Single nucleotide polymorphisms (SNPs) in pathways influencing lymph node (LN) metastasis and estrogen receptor (ER) status in breast cancer may partially explain inter-patient variability in prognosis. We examined 154 SNPs in 12 metastasis-related genes for associations with breast cancer risk, stratified by LN and ER status, in European-American (EA) and African-American (AA) women. Two-thousand six hundred and seventy-one women enrolled in the Women's Circle of Health Study were genotyped. Pathway analyses were conducted using the adaptive rank truncated product (ARTP) method, with pARTP ≤ 0.10 as significant. Multi-allelic risk scores were created for the ARTP-significant gene(s). Single-SNP and risk score associations were modeled using logistic regression, with false discovery rate (FDR) P-value adjustment. Although single-SNP associations were not significant at pFDR < 0.05, several genes were significant in the ARTP analyses. In AA women, significant ARTP gene-level associations included CDH1 with LN+ (pARTP = 0.10; multi-allelic OR = 1.13, 95%CI 1.07-1.19, pFDR = 0.0003) and SIPA1 with ER- breast cancer (pARTP = 0.10; multi-allelic OR = 1.16, 95%CI 1.02-1.31, pFDR = 0.03). In EA women, MTA2 was associated with overall breast cancer risk (pARTP = 0.004), regardless of ER status, and with LN- disease (pARTP = 0.01). Also significant were SATB1 in ER- (pARTP = 0.03; multi-allelic OR = 1.12, 95%CI 1.05-1.20, pFDR = 0.003) and KISS1 in LN- (pARTP = 0.10; multi-allelic OR = 1.18, 95%CI 1.08-1.29, pFDR = 0.002) analyses. Among LN+ cases, significant ARTP associations were observed for SNAI1, CD82, NME1, and CTNNB1 (multi-allelic OR = 1.09, 95%CI 1.04-1.14, pFDR = 0.001). Our findings suggest that variants in several metastasis genes may affect breast cancer risk by LN or ER status, although verification in larger studies is required. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Michelle R. Roberts
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY
- Department of Epidemiology and Environmental Health, University at Buffalo, Buffalo, NY
| | | | - Gary R. Zirpoli
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Michael Higgins
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY
| | - Jo L. Freudenheim
- Department of Epidemiology and Environmental Health, University at Buffalo, Buffalo, NY
| | | | | | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY
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8
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Wise LA, Palmer JR, Rosenberg L, Haddad SA, Ruiz-Narváez EA. FASN, dietary fat intake, and risk of uterine leiomyomata in the Black Women's Health Study. Fertil Steril 2016; 106:1136-1141. [PMID: 27375065 PMCID: PMC5048502 DOI: 10.1016/j.fertnstert.2016.06.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 06/08/2016] [Accepted: 06/08/2016] [Indexed: 12/31/2022]
Abstract
OBJECTIVE To replicate results from a previous genome-wide association study of European ancestry women, in which a positive association was found between uterine leiomyomata (UL) and rs4247357, a single-nucleotide polymorphism located near the fatty acid synthase (FASN) gene. DESIGN Prospective cohort study. SETTING Not applicable. PATIENT(S) African-American women aged 23-50 years, who were premenopausal and had an intact uterus in 1997. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) We genotyped rs4247357 among 2,301 incident UL cases and 3,005 controls from the Black Women's Health Study (1997-2011). Odds ratios (ORs) and 95% confidence intervals (CI) were estimated using logistic regression with control for age, geographic region of residence, and percent European ancestry using a panel of validated ancestry informative markers. RESULT(S) Overall, rs4247357 was not associated with UL risk. Relative to the CC genotype, ORs were 1.04 (95% CI 0.92-1.19) for the AC genotype and 1.09 (95% CI 0.93-1.29) for the AA genotype. A positive association was found, however, among those with higher European ancestry (≥40%). Relative to the CC genotype, ORs were 2.03 (95% CI 1.12-3.69) for the AC genotype and 2.44 (95% CI 1.20-4.96) for the AA genotype. Dietary fat intake also appeared to modify the FASN-UL association. CONCLUSION(S) Although there was little overall association between rs4247357 and UL risk, a positive association was observed among women with ≥40% European ancestry. Direct sequencing of this genomic region might be warranted to determine whether rs4247357, or some other variant, is causally related to UL.
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Affiliation(s)
- Lauren A Wise
- Slone Epidemiology Center at Boston University, Boston, Massachusetts; Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts.
| | - Julie R Palmer
- Slone Epidemiology Center at Boston University, Boston, Massachusetts
| | - Lynn Rosenberg
- Slone Epidemiology Center at Boston University, Boston, Massachusetts
| | - Stephen A Haddad
- Slone Epidemiology Center at Boston University, Boston, Massachusetts
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Wyszynski A, Hong CC, Lam K, Michailidou K, Lytle C, Yao S, Zhang Y, Bolla MK, Wang Q, Dennis J, Hopper JL, Southey MC, Schmidt MK, Broeks A, Muir K, Lophatananon A, Fasching PA, Beckmann MW, Peto J, Dos-Santos-Silva I, Sawyer EJ, Tomlinson I, Burwinkel B, Marme F, Guénel P, Truong T, Bojesen SE, Nordestgaard BG, González-Neira A, Benitez J, Neuhausen SL, Brenner H, Dieffenbach AK, Meindl A, Schmutzler RK, Brauch H, Nevanlinna H, Khan S, Matsuo K, Ito H, Dörk T, Bogdanova NV, Lindblom A, Margolin S, Mannermaa A, Kosma VM, Wu AH, Van Den Berg D, Lambrechts D, Wildiers H, Chang-Claude J, Rudolph A, Radice P, Peterlongo P, Couch FJ, Olson JE, Giles GG, Milne RL, Haiman CA, Henderson BE, Dumont M, Teo SH, Wong TY, Kristensen V, Zheng W, Long J, Winqvist R, Pylkäs K, Andrulis IL, Knight JA, Devilee P, Seynaeve C, García-Closas M, Figueroa J, Klevebring D, Czene K, Hooning MJ, van den Ouweland AMW, Darabi H, Shu XO, Gao YT, Cox A, Blot W, Signorello LB, Shah M, Kang D, Choi JY, Hartman M, Miao H, Hamann U, Jakubowska A, Lubinski J, Sangrajrang S, McKay J, Toland AE, Yannoukakos D, Shen CY, Wu PE, Swerdlow A, Orr N, Simard J, Pharoah PDP, Dunning AM, Chenevix-Trench G, Hall P, Bandera E, Amos C, Ambrosone C, Easton DF, Cole MD. An intergenic risk locus containing an enhancer deletion in 2q35 modulates breast cancer risk by deregulating IGFBP5 expression. Hum Mol Genet 2016; 25:3863-3876. [PMID: 27402876 PMCID: PMC5216618 DOI: 10.1093/hmg/ddw223] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 06/11/2016] [Accepted: 07/04/2016] [Indexed: 12/20/2022] Open
Abstract
Breast cancer is the most diagnosed malignancy and the second leading cause of cancer mortality in females. Previous association studies have identified variants on 2q35 associated with the risk of breast cancer. To identify functional susceptibility loci for breast cancer, we interrogated the 2q35 gene desert for chromatin architecture and functional variation correlated with gene expression. We report a novel intergenic breast cancer risk locus containing an enhancer copy number variation (enCNV; deletion) located approximately 400Kb upstream to IGFBP5, which overlaps an intergenic ERα-bound enhancer that loops to the IGFBP5 promoter. The enCNV is correlated with modified ERα binding and monoallelic-repression of IGFBP5 following oestrogen treatment. We investigated the association of enCNV genotype with breast cancer in 1,182 cases and 1,362 controls, and replicate our findings in an independent set of 62,533 cases and 60,966 controls from 41 case control studies and 11 GWAS. We report a dose-dependent inverse association of 2q35 enCNV genotype (percopy OR = 0.68 95%CI 0.55-0.83, P = 0.0002; replication OR = 0.77 95% CI 0.73-0.82, P = 2.1 × 10-19) and identify 13 additional linked variants (r2 > 0.8) in the 20Kb linkage block containing the enCNV (P = 3.2 × 10-15 - 5.6 × 10-17). These associations were independent of previously reported 2q35 variants, rs13387042/rs4442975 and rs16857609, and were stronger for ER-positive than ER-negative disease. Together, these results suggest that 2q35 breast cancer risk loci may be mediating their effect through IGFBP5.
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Affiliation(s)
- Asaf Wyszynski
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Chi-Chen Hong
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | | | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Christian Lytle
- Molecular Biology Core Facility, Dartmouth College, Hanover, NH 03755 USA
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Yali Zhang
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Melissa C Southey
- Department of Pathology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Marjanka K Schmidt
- Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, 1066 CX Amsterdam, The Netherlands
| | - Annegien Broeks
- Wellcome Trust Centre for Human Genetics and Oxford Biomedical Research Centre, University of Oxford, OX3 7BN, UK
| | - Kenneth Muir
- Division of Health Sciences, Warwick Medical school, Warwick University, Coventry, CV4 7AL, UK
- Institute of Population Health, University of Manchester, Manchester, M13 9PL, UK
| | - Artitaya Lophatananon
- Department of Obstetrics and Gynecology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Peter A Fasching
- University Breast Center Franconia, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, 91054 Erlangen, Germany
- David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Matthias W Beckmann
- University Breast Center Franconia, Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, 91054 Erlangen, Germany
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Isabel Dos-Santos-Silva
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Elinor J Sawyer
- Research Oncology, Division of Cancer Studies, King's College London, Guy's Hospital, London, SE1 9RT, UK
| | - Ian Tomlinson
- Wellcome Trust Centre for Human Genetics and Oxford Biomedical Research Centre, University of Oxford, OX3 7BN, UK
| | - Barbara Burwinkel
- Department of Obstetrics and Gynecology, University of Heidelberg, 69120 Heidelberg, Germany
- Molecular Epidemiology Group, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Frederik Marme
- Department of Obstetrics and Gynecology, University of Heidelberg, 69120 Heidelberg, Germany
- National Center for Tumor Diseases, University of Heidelberg, 69120 Heidelberg, Germany
| | - Pascal Guénel
- Inserm (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer, 94807 Villejuif, France
- University Paris-Sud, UMRS 1018, 94807 Villejuif, France
| | - Thérèse Truong
- Inserm (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer, 94807 Villejuif, France
- University Paris-Sud, UMRS 1018, 94807 Villejuif, France
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev Hospital, Copenhagen University Hospital, 2730 Herlev, Denmark
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, 2730 Herlev, Denmark
| | - Børge G Nordestgaard
- Copenhagen General Population Study, Herlev Hospital, Copenhagen University Hospital, 2730 Herlev, Denmark
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, 2730 Herlev, Denmark
| | - Anna González-Neira
- Human Genotyping-CEGEN Unit, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Javier Benitez
- Human Genetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), 46010 Valencia, Spain
| | | | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Aida Karina Dieffenbach
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Alfons Meindl
- Division of Gynaecology and Obstetrics, Technische Universität München, 81675 Munich, Germany
| | - Rita K Schmutzler
- Division of Molecular Gyneco-Oncology, Department of Gynaecology and Obstetrics, University Hospital of Cologne, 50931 Cologne, Germany
- Center of Familial Breast and Ovarian Cancer, University Hospital of Cologne, 50931 Cologne, Germany
- Center for Integrated Oncology (CIO), University Hospital of Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376 Stuttgart, Germany
- University of Tübingen, 72074 Tübingen, Germany
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, FI-00029 HUS, Finland
| | - Sofia Khan
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, FI-00029 HUS, Finland
| | - Keitaro Matsuo
- Department of Preventive Medicine, Kyushu University Faculty of Medical Sciences, Fukuoka, Japan
| | - Hidemi Ito
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Aichi, 464-8681, Japan
| | - Thilo Dörk
- Department of Obstetrics and Gynaecology, Hannover Medical School, 30625 Hannover, Germany
| | - Natalia V Bogdanova
- Department of Radiation Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm SE-17177, Sweden
| | - Sara Margolin
- Department of Oncology - Pathology, Karolinska Institutet, Stockholm SE-17177, Sweden
| | - Arto Mannermaa
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, FI-70211 Kuopio, Finland
- Cancer Center of Eastern Finland, University of Eastern Finland, FI-70211 Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, 70210 Kuopio, Finland
| | - Veli-Matti Kosma
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, FI-70211 Kuopio, Finland
- Cancer Center of Eastern Finland, University of Eastern Finland, FI-70211 Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, 70210 Kuopio, Finland
| | - Anna H Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - David Van Den Berg
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Diether Lambrechts
- Vesalius Research Center (VRC), VIB, 3000 Leuven, Belgium
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, 3000 Leuven, Belgium
| | - Hans Wildiers
- Multidisciplinary Breast Center, Department of General Medical Oncology, University Hospitals Leuven, B-3000 Leuven, Belgium
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), 20133 Milan, Italy
| | - Paolo Peterlongo
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, 20139 Milan, Italy
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Janet E Olson
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Graham G Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Roger L Milne
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Brian E Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Martine Dumont
- Centre Hospitalier Universitaire de Québec Research Center and Laval University, QC, G1V 4G2, Canada
| | - Soo Hwang Teo
- Cancer Research Initiatives Foundation, Sime Darby Medical Centre, 47500 Subang Jaya, Selangor, Malaysia
- Breast Cancer Research Unit, University Malaya Cancer Research Institute, University Malaya Medical Centre (UMMC), 59100 Kuala Lumpur, Malaysia
| | - Tien Y Wong
- Singapore Eye Research Institute, National University of Singapore, Singapore 168751
| | - Vessela Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, N-0310 Oslo, Norway
- Institute of Clinical Medicine, University of Oslo (UiO), 0450 Oslo, Norway
- Department of Clinical Molecular Biology (EpiGen), University of Oslo (UiO), 0450 Oslo, Norway
| | - Wei Zheng
- 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
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Department of Clinical Chemistry and Biocenter Oulu, University of Oulu, NordLab Oulu/Oulu University Hospital, FI-90220 Oulu, Finland
| | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Department of Clinical Chemistry and Biocenter Oulu, University of Oulu, NordLab Oulu/Oulu University Hospital, FI-90220 Oulu, Finland
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Julia A Knight
- Prosserman Centre for Health Research, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Peter Devilee
- Department of Human Genetics & Department of Pathology, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
| | - Caroline Seynaeve
- Family Cancer Clinic, Department of Medical Oncology, Erasmus MC-Daniel den Hoed Cancer Center, 3075 EA Rotterdam, The Netherlands
| | - Montserrat García-Closas
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, SM2 5NG, UK
- Breakthrough Breast Cancer Research Centre, Division of Breast Cancer Research, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Jonine Figueroa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA
| | - Daniel Klevebring
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm SE-17177, Sweden
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm SE-17177, Sweden
| | - Maartje J Hooning
- Department of Medical Oncology, Erasmus University Medical Center, 3075 EA Rotterdam, The Netherlands
| | - Ans M W van den Ouweland
- Department of Clinical Genetics, Erasmus University Medical Center, 3075 EA Rotterdam, The Netherlands
| | - Hatef Darabi
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm SE-17177, Sweden
| | - 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
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Xuhui, Shanghai, China
| | - Angela Cox
- CRUK/YCR Sheffield Cancer Research Centre, Department of Oncology, University of Sheffield, Sheffield, S10 2RX, UK
| | - William Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
- International Epidemiology Institute, Rockville, MD 20850, USA
| | - Lisa B Signorello
- Division of Cancer Prevention, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, CB1 8RN, UK
| | - Daehee Kang
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul 110-799, Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 151-742, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 110-799, Korea
| | - Ji-Yeob Choi
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 151-742, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 110-799, Korea
| | - Mikael Hartman
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117597
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore 117597
| | - Hui Miao
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117597
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, 70-115 Szczecin, Poland
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, 70-115 Szczecin, Poland
| | | | - James McKay
- International Agency for Research on Cancer, 69372 Lyon, CEDEX 08, France
| | - Amanda E Toland
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, IRRP, National Centre for Scientific Research "Demokritos", Aghia Paraskevi Attikis, 153 10 Athens, Greece
| | - Chen-Yang Shen
- Taiwan Biobank, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
- School of Public Health, China Medical University, Taichung 404, Taiwan
| | - Pei-Ei Wu
- Taiwan Biobank, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, SM2 5NG, UK
- Division of Breast Cancer Research, Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Nick Orr
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Jacques Simard
- Centre Hospitalier Universitaire de Québec Research Center and Laval University, QC, G1V 4G2, Canada
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, CB1 8RN, UK
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, CB1 8RN, UK
| | - Georgia Chenevix-Trench
- Department of Genetics, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm SE-17177, Sweden
| | - Elisa Bandera
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901 USA
| | - Chris Amos
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Christine Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Michael D Cole
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
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Cheng TYD, Shankar J, Zirpoli G, Roberts MR, Hong CC, Bandera EV, Ambrosone CB, Yao S. Genetic variants in the mTOR pathway and interaction with body size and weight gain on breast cancer risk in African-American and European American women. Cancer Causes Control 2016; 27:965-76. [PMID: 27314662 DOI: 10.1007/s10552-016-0774-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 06/07/2016] [Indexed: 11/30/2022]
Abstract
PURPOSE Positive energy imbalance and growth factors linked to obesity promote the phosphatidylinositol 3-kinase/AKT/mammalian target of rapamycin (mTOR) pathway. As the obesity-breast cancer associations differ between European American (EA) and African-American (AA) women, we investigated genetic variants in the mTOR pathway and breast cancer risk in these two racial groups. METHODS We examined 400 single-nucleotide polymorphisms (SNPs) in 31 mTOR pathway genes in the Women's Circle of Health Study with 1263 incident breast cancers (645 EA, 618 AA) and 1382 controls (641 EA, 741 AA). Multivariable logistic regression was performed separately within racial groups. Effect modification was assessed for measured body size and weight gain since age 20. RESULTS In EA women, variants in FRAP1 rs12125777 (intron), PRR5L rs3740958 (synonymous coding), and CDKAL1 rs9368197 (intron) were associated with increased breast cancer risk, while variants in RPTOR rs9900506 (intron) were associated with decreased risk (nominal p-trend for functional and FRAP1 SNPs or p adjusted for correlated test [p ACT] < 0.05). For AA women, variants in RPTOR rs3817293 (intron), PIK3R1 rs7713645 (intron), and CDKAL1 rs9368197 were associated with decreased breast cancer risk. The significance for FRAP1 rs12125777 and RPTOR rs9900506 in EA women did not hold after correction for multiple comparisons. The risk associated with FRAP1 rs12125777 was higher among EAs who had body mass index ≥30 kg/m(2) (odds ratio = 7.69, 95 % CI 2.11-28.0; p-interaction = 0.007) and gained weight ≥35 lb since age 20 (odds ratio = 3.34, 95 % CI 1.42-7.85; p-interaction = 0.021), compared to their counterparts. CONCLUSIONS The mTOR pathway may be involved in breast cancer carcinogenesis differently for EA and AA women.
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Affiliation(s)
- Ting-Yuan David Cheng
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Elm & Carlton Sts., Buffalo, NY, 14263, USA.
| | | | - Gary Zirpoli
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Elm & Carlton Sts., Buffalo, NY, 14263, USA
| | - Michelle R Roberts
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Chi-Chen Hong
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Elm & Carlton Sts., Buffalo, NY, 14263, USA
| | - Elisa V Bandera
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Elm & Carlton Sts., Buffalo, NY, 14263, USA
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Elm & Carlton Sts., Buffalo, NY, 14263, USA
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11
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Oetjens MT, Brown-Gentry K, Goodloe R, Dilks HH, Crawford DC. Population Stratification in the Context of Diverse Epidemiologic Surveys Sans Genome-Wide Data. Front Genet 2016; 7:76. [PMID: 27200085 PMCID: PMC4858524 DOI: 10.3389/fgene.2016.00076] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 04/18/2016] [Indexed: 01/01/2023] Open
Abstract
Population stratification or confounding by genetic ancestry is a potential cause of false associations in genetic association studies. Estimation of and adjustment for genetic ancestry has become common practice thanks in part to the availability of ancestry informative markers on genome-wide association study (GWAS) arrays. While array data is now widespread, these data are not ubiquitous as several large epidemiologic and clinic-based studies lack genome-wide data. One such large epidemiologic-based study lacking genome-wide data accessible to investigators is the National Health and Nutrition Examination Surveys (NHANES), population-based cross-sectional surveys of Americans linked to demographic, health, and lifestyle data conducted by the Centers for Disease Control and Prevention. DNA samples (n = 14,998) were extracted from biospecimens from consented NHANES participants between 1991-1994 (NHANES III, phase 2) and 1999-2002 and represent three major self-identified racial/ethnic groups: non-Hispanic whites (n = 6,634), non-Hispanic blacks (n = 3,458), and Mexican Americans (n = 3,950). We as the Epidemiologic Architecture for Genes Linked to Environment study genotyped candidate gene and GWAS-identified index variants in NHANES as part of the larger Population Architecture using Genomics and Epidemiology I study for collaborative genetic association studies. To enable basic quality control such as estimation of genetic ancestry to control for population stratification in NHANES san genome-wide data, we outline here strategies that use limited genetic data to identify the markers optimal for characterizing genetic ancestry. From among 411 and 295 autosomal SNPs available in NHANES III and NHANES 1999-2002, we demonstrate that markers with ancestry information can be identified to estimate global ancestry. Despite limited resolution, global genetic ancestry is highly correlated with self-identified race for the majority of participants, although less so for ethnicity. Overall, the strategies outlined here for a large epidemiologic study can be applied to other datasets accessible for genotype-phenotype studies but are sans genome-wide data.
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Affiliation(s)
- Matthew T. Oetjens
- Center for Human Genetics Research Vanderbilt University, NashvilleTN, USA
| | | | - Robert Goodloe
- Center for Human Genetics Research Vanderbilt University, NashvilleTN, USA
| | | | - Dana C. Crawford
- Department of Epidemiology and Biostatistics, Institute for Computational Biology, Case Western Reserve University, ClevelandOH, USA
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12
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Gong Z, Yao S, Zirpoli G, Cheng TYD, Roberts M, Khoury T, Ciupak G, Davis W, Pawlish K, Jandorf L, Bovbjerg DH, Bandera EV, Ambrosone CB. Genetic variants in one-carbon metabolism genes and breast cancer risk in European American and African American women. Int J Cancer 2015; 137:666-77. [PMID: 25598430 PMCID: PMC4437886 DOI: 10.1002/ijc.29434] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 12/22/2014] [Indexed: 02/03/2023]
Abstract
Folate-mediated one-carbon metabolism plays critical roles in DNA synthesis, repair and DNA methylation. The impact of single nucleotide polymorphisms (SNPs) in folate-metabolizing enzymes has been investigated in risk of breast cancer among European or Asian populations, but not among women of African ancestry. We conducted a comprehensive analysis of SNPs in eleven genes involved in one-carbon metabolism and risk of breast cancer in 1,275 European-American (EA) and 1,299 African-American (AA) women who participated in the Women's Circle of Health Study. Allele frequencies varied significantly between EA and AA populations. A number of these SNPs, specifically in genes including MTR, MTRR, SHMT1, TYMS and SLC19A1, were associated with overall breast cancer risk, as well as risk by estrogen receptor (ER) status, in either EA or AA women. Associations appeared to be modified by dietary folate intake. Although single-SNP associations were not statistically significant after correcting for multiple comparisons, polygenetic score analyses revealed significant associations with breast cancer risk. Per unit increase of the risk score was associated with a modest 19 to 50% increase in risk of breast cancer overall, ER positive or ER negative cancer (all p < 0.0005) in EAs or AAs. In summary, our data suggest that one-carbon metabolizing gene polymorphisms could play a role in breast cancer and that may differ between EA and AA women.
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Affiliation(s)
- Zhihong Gong
- Department of Cancer Prevention & Control, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Song Yao
- Department of Cancer Prevention & Control, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Gary Zirpoli
- Department of Cancer Prevention & Control, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Ting-Yuan David Cheng
- Department of Cancer Prevention & Control, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Michelle Roberts
- Department of Cancer Prevention & Control, Roswell Park Cancer Institute, Buffalo, NY, USA
- Department of Epidemiology and Environmental Health, University at Buffalo, Buffalo, NY, USA
| | - Thaer Khoury
- Department of Pathology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Gregory Ciupak
- Department of Cancer Prevention & Control, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Warren Davis
- Department of Cancer Prevention & Control, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Karen Pawlish
- New Jersey State Cancer Registry, New Jersey Department of Health, Trenton, NJ, USA
| | - Lina Jandorf
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Elisa V. Bandera
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
- Rutgers School of Public Health, Piscataway, NJ, USA
| | - Christine B. Ambrosone
- Department of Cancer Prevention & Control, Roswell Park Cancer Institute, Buffalo, NY, USA
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13
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Admixture mapping of genetic variants for uterine fibroids. J Hum Genet 2015; 60:533-8. [PMID: 26040208 PMCID: PMC4583808 DOI: 10.1038/jhg.2015.60] [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: 02/09/2015] [Revised: 04/28/2015] [Accepted: 05/07/2015] [Indexed: 01/05/2023]
Abstract
Uterine leiomyoma (UL) are benign neoplasms arising from the smooth muscle cells of the uterus. One of the established risk factors for UL is African American ethnicity. Studies have consistently shown that African Americans have 2-3 times higher risk compared with that of non-Hispanic Whites. However, there is still no adequate explanation for the higher risk among African Americans. To investigate the genetic contribution to the observed difference between the African American and European American populations, we conducted an admixture scan in 525 eligible African American women participants to the NIEHS uterine fibroid study (NIEHS-UFS). In models with no stratification, we found multiple genomic regions showing significant and suggestive evidence of association, with chromosomal band 2q32.2 at rs256552 showing the highest score (Z-score = 7.86, Bonferroni adjusted p-value = 5.5×10-12) consistent with the suggestive evidence reported for this genomic region in the Black Women's Health Study. However, in models stratified by the body mass index (BMI) covariate, chromosomal 1q42.2 was the sole genomic region that consistently showed suggestive associations across the BMI categories tested (Z-scores ≤ -3.96, Bonferroni adjusted p-values ≤ 0.107). In age-stratified models, a significant association was observed in the older category (age > 40) reaching a Z-score of 6.44 (Bonferroni-adjusted p-value = 1.64 × 10-7) at rs256552. The mean percentage of European ancestry among cases was lower than that among controls in the NIEHS-UFS study. However, our study did not show a significant association between mean percentage of European ancestry and UL.
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14
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Wise LA, Ruiz-Narváez EA, Haddad SA, Rosenberg L, Palmer JR. Polymorphisms in vitamin D-related genes and risk of uterine leiomyomata. Fertil Steril 2014; 102:503-510.e1. [PMID: 24890271 DOI: 10.1016/j.fertnstert.2014.04.037] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 04/23/2014] [Accepted: 04/23/2014] [Indexed: 01/08/2023]
Abstract
OBJECTIVE To investigate uterine leiomyomata (UL) incidence in relation to polymorphisms in genes involved in vitamin D metabolism and skin pigmentation. Rates of UL are 2-3 times higher in African Americans than in European Americans. Recent studies suggest that vitamin D deficiency is associated with an increased risk of UL. DESIGN Nested case-control study. SETTING Not applicable. PATIENT(S) Two thousand two hundred thirty-two premenopausal women first diagnosed with UL confirmed by ultrasound or surgery during 1997-2011 (cases) and 2,432 premenopausal women never diagnosed with UL through 2011 (controls). INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) Self-reported UL. We used logistic regression to estimate odds ratios (OR) and 95% confidence intervals (CI) for the association between each polymorphism and UL, controlling for age, geographic region, and ancestry. RESULT(S) Three of 12 polymorphisms were associated with UL at the nominal significance level: rs4944957 and rs12800438 near DHCR7 and rs6058017 in ASIP. After correction for multiple hypothesis testing, two single nucleotide polymorphisms remained significantly associated with UL (rs12800438 and rs6058017). Compared with the AA genotype for rs12800438 (correlated with higher serum 25[OH]D levels), ORs were 1.09 (95% CI, 0.92, 1.29) and 1.23 (95% CI, 1.03, 1.47) for the GA and GG genotypes, respectively. Compared with the AA genotype for rs6058017 (correlated with lighter skin pigmentation), ORs were 1.01 (95% CI, 0.83, 1.22) and 1.18 (95% CI, 0.97, 1.44) for the GA and GG genotypes, respectively. CONCLUSION(S) Our data support the hypothesis that vitamin D deficiency is involved in UL etiology.
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Affiliation(s)
- Lauren A Wise
- Slone Epidemiology Center at Boston University, Boston, Massachusetts.
| | | | - Stephen A Haddad
- Slone Epidemiology Center at Boston University, Boston, Massachusetts
| | - Lynn Rosenberg
- Slone Epidemiology Center at Boston University, Boston, Massachusetts
| | - Julie R Palmer
- Slone Epidemiology Center at Boston University, Boston, Massachusetts
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15
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Moubarac JC. Persisting problems related to race and ethnicity in public health and epidemiology research. Rev Saude Publica 2014; 47:104-15. [PMID: 23703136 DOI: 10.1590/s0034-89102013000100014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 09/18/2012] [Indexed: 11/22/2022] Open
Abstract
A recent and comprehensive review of the use of race and ethnicity in research that address health disparities in epidemiology and public health is provided. First it is described the theoretical basis upon which race and ethnicity differ drawing from previous work in anthropology, social science and public health. Second, it is presented a review of 280 articles published in high impacts factor journals in regards to public health and epidemiology from 2009-2011. An analytical grid enabled the examination of conceptual, theoretical and methodological questions related to the use of both concepts. The majority of articles reviewed were grounded in a theoretical framework and provided interpretations from various models. However, key problems identified include a) a failure from researchers to differentiate between the concepts of race and ethnicity; b) an inappropriate use of racial categories to ascribe ethnicity; c) a lack of transparency in the methods used to assess both concepts; and d) failure to address limits associated with the construction of racial or ethnic taxonomies and their use. In conclusion, future studies examining health disparities should clearly establish the distinction between race and ethnicity, develop theoretically driven research and address specific questions about the relationships between race, ethnicity and health. One argue that one way to think about ethnicity, race and health is to dichotomize research into two sets of questions about the relationship between human diversity and health.
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Affiliation(s)
- Jean-Claude Moubarac
- Departamento de Nutrição, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo, SP, Brasil.
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16
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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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17
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Quan L, Gong Z, Yao S, Bandera EV, Zirpoli G, Hwang H, Roberts M, Ciupak G, Davis W, Sucheston L, Pawlish K, Bovbjerg DH, Jandorf L, Cabasag C, Coignet JG, Ambrosone CB, Hong CC. Cytokine and cytokine receptor genes of the adaptive immune response are differentially associated with breast cancer risk in American women of African and European ancestry. Int J Cancer 2013; 134:1408-21. [PMID: 23996684 DOI: 10.1002/ijc.28458] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 07/18/2013] [Accepted: 08/13/2013] [Indexed: 12/21/2022]
Abstract
Disparities in breast cancer biology are evident between American women of African ancestry (AA) and European ancestry (EA) and may be due, in part, to differences in immune function. To assess the potential role of constitutional host immunity on breast carcinogenesis, we tested associations between breast cancer risk and 47 single nucleotide polymorphisms (SNPs) in 26 cytokine-related genes of the adaptive immune system using 650 EA (n = 335 cases) and 864 AA (n = 458 cases) women from the Women's Circle of Health Study (WCHS). With additional participant accrual to the WCHS, promising SNPs from the initial analysis were evaluated in a larger sample size (1,307 EAs and 1,365 AAs). Multivariate logistic regression found SNPs in genes important for T helper type 1 (Th1) immunity (IFNGR2 rs1059293, IL15RA rs2296135, LTA rs1041981), Th2 immunity (IL4R rs1801275), and T regulatory cell-mediated immunosuppression (TGFB1 rs1800469) associated with breast cancer risk, mainly among AAs. The combined effect of these five SNPs was highly significant among AAs (P-trend = 0.0005). When stratified by estrogen receptor (ER) status, LTA rs1041981 was associated with ER-positive breast cancers among EAs and marginally among AAs. Only among AA women, IL15 rs10833 and IL15RA rs2296135 were associated with ER-positive tumors, and IL12RB1 rs375947, IL15 rs10833 and TGFB1 rs1800469 were associated with ER-negative tumors. Our study systematically identified genetic variants in the adaptive immune response pathway associated with breast cancer risk, which appears to differ by ancestry groups, menopausal status and ER status.
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Affiliation(s)
- Lei Quan
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY
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18
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Wise LA, Palmer JR, Ruiz-Narvaez E, Reich DE, Rosenberg L. Is the observed association between dairy intake and fibroids in African Americans explained by genetic ancestry? Am J Epidemiol 2013; 178:1114-9. [PMID: 23825169 DOI: 10.1093/aje/kwt091] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Uterine leiomyomata are a major source of gynecological morbidity and are 2-3 times more prevalent in African Americans than European Americans. In an earlier report, we found that dairy intake was inversely associated with uterine leiomyomata among African Americans. Because African Americans are more likely to have lactose intolerance and avoid dairy products, the observed association might have been confounded by genetic ancestry. This report reevaluates the dairy-uterine leiomyomata association after accounting for genetic ancestry among 1,968 cases and 2,183 noncases from the Black Women's Health Study (1997-2007). Dairy intake was estimated by using food frequency questionnaires in 1995 and 2001. Percent European ancestry was estimated by using a panel of ancestry informative markers. Incidence rate ratios and 95% confidence intervals were estimated by using Cox regression, with adjustment for potential confounders and percent European ancestry. Incidence rate ratios comparing 1, 2, 3, and ≥4 servings/day with <1 serving/day of dairy products were 0.95 (95% confidence interval (CI): 0.85, 1.06), 0.75 (95% CI: 0.61, 0.92), 0.77 (95% CI: 0.57, 1.04), and 0.59 (95% CI: 0.41, 0.86), respectively (Ptrend = 0.0003). These effect estimates were similar to those obtained without control for ancestry. The findings suggest that the observed inverse association between dairy consumption and uterine leiomyomata in African Americans is not explained by percent European ancestry.
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19
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Gong Z, Quan L, Yao S, Zirpoli G, Bandera EV, Roberts M, Coignet JG, Cabasag C, Sucheston L, Hwang H, Ciupak G, Davis W, Pawlish K, Jandorf L, Bovbjerg DH, Ambrosone CB, Hong CC. Innate immunity pathways and breast cancer Risk in African American and European-American women in the Women's Circle of Health Study (WCHS). PLoS One 2013; 8:e72619. [PMID: 23991131 PMCID: PMC3749137 DOI: 10.1371/journal.pone.0072619] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 07/12/2013] [Indexed: 01/18/2023] Open
Abstract
African American (AA) women are more likely than European American (EA) women to be diagnosed with early, aggressive breast cancer. Possible differences in innate immune pathways (e.g., inflammatory responses) have received little attention as potential mechanisms underlying this disparity. We evaluated distributions of selected genetic variants in innate immune pathways in AA and EA women, and examined their associations with breast cancer risk within the Women's Circle of Health Study (WCHS). In stage I of the study (864 AA and 650 EA women) we found that genotype frequencies for 35 of 42 tested SNPs (18 candidate genes) differed between AAs and EAs (corroborated by ancestry informative markers). Among premenopausal AA women, comparing variant allele carriers to non-carriers, reduced breast cancer risk was associated with CXCL5-rs425535 (OR=0.61, P=0.02), while among EA women, there were associations with TNFA-rs1799724 (OR =2.31, P =0.002) and CRP-rs1205 (OR=0.54, P=0.01). For postmenopausal women, IL1B-rs1143627 (OR=1.80, P=0.02) and IL1B-rs16944 (OR=1.85, P =0.02) were associated with risk among EA women, with significant associations for TNFA-rs1799724 limited to estrogen receptor (ER) positive cancers (OR=2.0, P =0.001). However, none of the SNPs retained significance after Bonferroni adjustment for multiple testing at the level of P0.0012 (0.05/42) except for TNFA-rs1799724 in ER positive cancers. In a stage II validation (1,365 AA and 1,307 EA women), we extended evaluations for four SNPs (CCL2-rs4586, CRP-rs1205, CXCL5-rs425535, and IL1RN-rs4251961), which yielded similar results. In summary, distributions of variants in genes involved in innate immune pathways were found to differ between AA and EA populations, and showed differential associations with breast cancer according to menopausal or ER status. These results suggest that immune adaptations suited to ancestral environments may differentially influence breast cancer risk among EA and AA women.
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Affiliation(s)
- Zhihong Gong
- Roswell Park Cancer Institute, Buffalo, New York, USA.
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20
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Aldrich MC, Selvin S, Wrensch MR, Sison JD, Hansen HM, Quesenberry CP, Seldin MF, Barcellos LF, Buffler PA, Wiencke JK. Socioeconomic status and lung cancer: unraveling the contribution of genetic admixture. Am J Public Health 2013; 103:e73-80. [PMID: 23948011 DOI: 10.2105/ajph.2013.301370] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
OBJECTIVES We examined the relationship between genetic ancestry, socioeconomic status (SES), and lung cancer among African Americans and Latinos. METHODS We evaluated SES and genetic ancestry in a Northern California lung cancer case-control study (1998-2003) of African Americans and Latinos. Lung cancer case and control participants were frequency matched on age, gender, and race/ethnicity. We assessed case-control differences in individual admixture proportions using the 2-sample t test and analysis of covariance. Logistic regression models examined associations among genetic ancestry, socioeconomic characteristics, and lung cancer. RESULTS Decreased Amerindian ancestry was associated with higher education among Latino control participants and greater African ancestry was associated with decreased education among African lung cancer case participants. Education was associated with lung cancer among both Latinos and African Americans, independent of smoking, ancestry, age, and gender. Genetic ancestry was not associated with lung cancer among African Americans. CONCLUSIONS Findings suggest that socioeconomic factors may have a greater impact than genetic ancestry on lung cancer among African Americans. The genetic heterogeneity and recent dynamic migration and acculturation of Latinos complicate recruitment; thus, epidemiological analyses and findings should be interpreted cautiously.
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Affiliation(s)
- Melinda C Aldrich
- At the time of the study, Melinda C. Aldrich was with the Division of Epidemiology, School of Public Health, University of California, Berkeley. Steve Selvin is with the Division of Biostatistics, School of Public Health, University of California, Berkeley. Margaret R. Wrensch, Helen M. Hansen, and John K. Wiencke are with the Department of Neurologic Surgery, University of California, San Francisco. Jennette D. Sison was with the Department of Neurologic Surgery, University of California, San Francisco. Charles P. Quesenberry Jr, is with the Division of Research, Kaiser Permanente, Oakland, CA. Michael F. Seldin is with the Departments of Biological Chemistry and Medicine, University of California, Davis. Lisa F. Barcellos and Patricia A. Buffler are with the Division of Epidemiology, School of Public Health, University of California, Berkeley
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21
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Isobe N, Gourraud PA, Harbo HF, Caillier SJ, Santaniello A, Khankhanian P, Maiers M, Spellman S, Cereb N, Yang S, Pando MJ, Piccio L, Cross AH, De Jager PL, Cree BAC, Hauser SL, Oksenberg JR. Genetic risk variants in African Americans with multiple sclerosis. Neurology 2013; 81:219-27. [PMID: 23771490 PMCID: PMC3770164 DOI: 10.1212/wnl.0b013e31829bfe2f] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 04/04/2013] [Indexed: 01/26/2023] Open
Abstract
OBJECTIVES To assess the association of established multiple sclerosis (MS) risk variants in 3,254 African Americans (1,162 cases and 2,092 controls). METHODS Human leukocyte antigen (HLA)-DRB1, HLA-DQB1, and HLA-A alleles were typed by molecular techniques. Single nucleotide polymorphism (SNP) genotyping was conducted for 76 MS-associated SNPs and 52 ancestry informative marker SNPs selected throughout the genome. Self-declared ancestry was refined by principal component analysis of the ancestry informative marker SNPs. An ancestry-adjusted multivariate model was applied to assess genetic associations. RESULTS The following major histocompatibility complex risk alleles were replicated: HLA-DRB1*15:01 (odds ratio [OR] = 2.02 [95% confidence interval: 1.54-2.63], p = 2.50e-07), HLA-DRB1*03:01 (OR = 1.58 [1.29-1.94], p = 1.11e-05), as well as HLA-DRB1*04:05 (OR = 2.35 [1.26-4.37], p = 0.007) and the African-specific risk allele of HLA-DRB1*15:03 (OR = 1.26 [1.05-1.51], p = 0.012). The protective association of HLA-A*02:01 was confirmed (OR = 0.72 [0.55-0.93], p = 0.013). None of the HLA-DQB1 alleles were associated with MS. Using a significance threshold of p < 0.01, outside the major histocompatibility complex region, 8 MS SNPs were also found to be associated with MS in African Americans. CONCLUSION MS genetic risk in African Americans only partially overlaps with that of Europeans and could explain the difference of MS prevalence between populations.
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Affiliation(s)
- Noriko Isobe
- Department of Neurology, School of Medicine, University of California, San Francisco, CA, USA
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Kodaman N, Aldrich MC, Smith JR, Signorello LB, Bradley K, Breyer J, Cohen SS, Long J, Cai Q, Giles J, Bush WS, Blot WJ, Matthews CE, Williams SM. A small number of candidate gene SNPs reveal continental ancestry in African Americans. Ann Hum Genet 2013; 77:56-66. [PMID: 23278390 DOI: 10.1111/j.1469-1809.2012.00738.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 09/18/2012] [Indexed: 11/30/2022]
Abstract
Using genetic data from an obesity candidate gene study of self-reported African Americans and European Americans, we investigated the number of Ancestry Informative Markers (AIMs) and candidate gene SNPs necessary to infer continental ancestry. Proportions of African and European ancestry were assessed with STRUCTURE (K = 2), using 276 AIMs. These reference values were compared to estimates derived using 120, 60, 30, and 15 SNP subsets randomly chosen from the 276 AIMs and from 1144 SNPs in 44 candidate genes. All subsets generated estimates of ancestry consistent with the reference estimates, with mean correlations greater than 0.99 for all subsets of AIMs, and mean correlations of 0.99 ± 0.003; 0.98 ± 0.01; 0.93 ± 0.03; and 0.81 ± 0.11 for subsets of 120, 60, 30, and 15 candidate gene SNPs, respectively. Among African Americans, the median absolute difference from reference African ancestry values ranged from 0.01 to 0.03 for the four AIMs subsets and from 0.03 to 0.09 for the four candidate gene SNP subsets. Furthermore, YRI/CEU Fst values provided a metric to predict the performance of candidate gene SNPs. Our results demonstrate that a small number of SNPs randomly selected from candidate genes can be used to estimate admixture proportions in African Americans reliably.
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Affiliation(s)
- Nuri Kodaman
- Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
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23
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Demerath EW, Liu CT, Franceschini N, Chen G, Palmer JR, Smith EN, Chen CTL, Ambrosone CB, Arnold AM, Bandera EV, Berenson GS, Bernstein L, Britton A, Cappola AR, Carlson CS, Chanock SJ, Chen W, Chen Z, Deming SL, Elks CE, Evans MK, Gajdos Z, Henderson BE, Hu JJ, Ingles S, John EM, Kerr KF, Kolonel LN, Le Marchand L, Lu X, Millikan RC, Musani SK, Nock NL, North K, Nyante S, Press MF, Rodriquez-Gil JL, Ruiz-Narvaez EA, Schork NJ, Srinivasan SR, Woods NF, Zheng W, Ziegler RG, Zonderman A, Heiss G, Gwen Windham B, Wellons M, Murray SS, Nalls M, Pastinen T, Rajkovic A, Hirschhorn J, Adrienne Cupples L, Kooperberg C, Murabito JM, Haiman CA. Genome-wide association study of age at menarche in African-American women. Hum Mol Genet 2013; 22:3329-46. [PMID: 23599027 DOI: 10.1093/hmg/ddt181] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
African-American (AA) women have earlier menarche on average than women of European ancestry (EA), and earlier menarche is a risk factor for obesity and type 2 diabetes among other chronic diseases. Identification of common genetic variants associated with age at menarche has a potential value in pointing to the genetic pathways underlying chronic disease risk, yet comprehensive genome-wide studies of age at menarche are lacking for AA women. In this study, we tested the genome-wide association of self-reported age at menarche with common single-nucleotide polymorphisms (SNPs) in a total of 18 089 AA women in 15 studies using an additive genetic linear regression model, adjusting for year of birth and population stratification, followed by inverse-variance weighted meta-analysis (Stage 1). Top meta-analysis results were then tested in an independent sample of 2850 women (Stage 2). First, while no SNP passed the pre-specified P < 5 × 10(-8) threshold for significance in Stage 1, suggestive associations were found for variants near FLRT2 and PIK3R1, and conditional analysis identified two independent SNPs (rs339978 and rs980000) in or near RORA, strengthening the support for this suggestive locus identified in EA women. Secondly, an investigation of SNPs in 42 previously identified menarche loci in EA women demonstrated that 25 (60%) of them contained variants significantly associated with menarche in AA women. The findings provide the first evidence of cross-ethnic generalization of menarche loci identified to date, and suggest a number of novel biological links to menarche timing in AA women.
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Affiliation(s)
- Ellen W Demerath
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA.
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Cozier Y, Ruiz-Narvaez E, McKinnon C, Berman J, Rosenberg L, Palmer J. Replication of genetic loci for sarcoidosis in US black women: data from the Black Women's Health Study. Hum Genet 2013; 132:803-10. [PMID: 23543185 DOI: 10.1007/s00439-013-1292-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 03/18/2013] [Indexed: 01/08/2023]
Abstract
In the United States, incidence and mortality from sarcoidosis, a chronic, granulomatous disease, are increased in black women. In data from the Black Women's Health Study, a follow-up of US black women, we assessed two SNPs (rs2076530 and rs9268480) previously identified in the BTNL2 gene (chromosome 6p21), of which rs4424066 and rs3817963 are perfect proxies, to determine if they represent independent signals of disease risk. We also assessed whether local ancestry in four genomic regions previously identified through admixture mapping was associated with sarcoidosis. Finally, we assessed the relation of global percent African ancestry to risk. We conducted a nested case-control study of 486 sarcoidosis cases and 943 age- and geography-matched controls. Both BTNL2 SNPs were associated with risk of sarcoidosis in separate models, but in a combined analysis the increased risk was due to the A-allele of the rs3817963 SNP; each copy of the A-allele was associated with a 40 % increase in risk of sarcoidosis (p = 0.02) and was confirmed by our haplotypic analysis. Local African ancestry around the rs30533 ancestry informative marker at chromosome 5q31 was associated with a 29 % risk reduction (p = 0.01). Therefore, we adjusted our analysis of global African ancestry for number of copies of African alleles in rs30533. Subjects in the highest quintile of percent African ancestry had a 54 % increased risk of sarcoidosis. The present results from a population of African-American women support the role of the BTNL2 gene and the 5q31 locus in the etiology of sarcoidosis, and also demonstrate that percent African ancestry is associated with disease risk.
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Affiliation(s)
- Yvette Cozier
- Slone Epidemiology Center, Boston University, Boston, USA.
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25
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Chen CY, Pollack S, Hunter DJ, Hirschhorn JN, Kraft P, Price AL. Improved ancestry inference using weights from external reference panels. ACTA ACUST UNITED AC 2013; 29:1399-406. [PMID: 23539302 DOI: 10.1093/bioinformatics/btt144] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION Inference of ancestry using genetic data is motivated by applications in genetic association studies, population genetics and personal genomics. Here, we provide methods and software for improved ancestry inference using genome-wide single nucleotide polymorphism (SNP) weights from external reference panels. This approach makes it possible to leverage the rich ancestry information that is available from large external reference panels, without the administrative and computational complexities of re-analyzing the raw genotype data from the reference panel in subsequent studies. RESULTS We extensively validate our approach in multiple African American, Latino American and European American datasets, making use of genome-wide SNP weights derived from large reference panels, including HapMap 3 populations and 6546 European Americans from the Framingham Heart Study. We show empirically that our approach provides much greater accuracy than either the prevailing ancestry-informative marker (AIM) approach or the analysis of genome-wide target genotypes without a reference panel. For example, in an independent set of 1636 European American genome-wide association study samples, we attained prediction accuracy (R(2)) of 1.000 and 0.994 for the first two principal components using our method, compared with 0.418 and 0.407 using 150 published AIMs or 0.955 and 0.003 by applying principal component analysis directly to the target samples. We finally show that the higher accuracy in inferring ancestry using our method leads to more effective correction for population stratification in association studies. AVAILABILITY The SNPweights software is available online at http://www.hsph.harvard.edu/faculty/alkes-price/software/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Chia-Yen Chen
- Department of Epidemiology, Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, 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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Wise LA, Ruiz-Narvaez EA, Palmer JR, Cozier YC, Tandon A, Patterson N, Radin RG, Rosenberg L, Reich D. African ancestry and genetic risk for uterine leiomyomata. Am J Epidemiol 2012; 176:1159-68. [PMID: 23161897 DOI: 10.1093/aje/kws276] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Rates of uterine leiomyomata (UL) are 2-3 times higher in African Americans than in European Americans. It is unclear whether inherited factors explain the ethnic disparity. To investigate the presence of risk alleles for UL that are highly differentiated in frequency between African Americans and European Americans, the authors conducted an admixture-based genome-wide scan of 2,453 UL cases confirmed by ultrasound or surgery in the Black Women's Health Study (1997-2009), a national prospective cohort study. Controls (n = 2,102) were women who did not report a UL diagnosis through 2009. Mean percentage of European ancestry was significantly lower among cases (20.00%) than among controls (21.63%; age-adjusted mean difference = -1.76%, 95% confidence interval: -2.40, -1.12; P < 0.0001), and the association was stronger in younger cases. Admixture analyses showed suggestive evidence of association at chromosomes 2, 4, and 10. The authors also genotyped a dense set of tag single nucleotide polymorphisms at different loci associated with UL in Japanese women but failed to replicate the associations. This suggests that genetic variation for UL differs in populations with and without African ancestry. The admixture findings further indicate that no single highly differentiated locus is responsible for the ethnic disparity in UL, raising the possibility that multiple variants jointly contribute to the higher incidence of UL in African Americans.
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Affiliation(s)
- Lauren A Wise
- Slone Epidemiology Center at Boston University, 1010 Commonwealth Avenue, 4th Floor, Boston, MA 02215, USA.
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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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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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Abstract
Sarcoidosis is a chronic granulomatous disease with a wide spectrum of symptoms. Genome-wide association studies in European populations have reported significant associations between sarcoidosis and single nucleotide polymorphisms (SNPs) located in the inter-genic region between the C10ORF67 and OTUD1 genes on chromosome 10p12, and the ANXA11 gene (chromosome 10q22). We carried out fine-mapping at 10p12 and 10q22 to assess associations of genetic variants in those regions with sarcoidosis risk in African American women, based on 486 sarcoidosis cases and 943 age- and geography-matched controls in a nested case-control study within the Black Women’s Health Study. There were no significant associations with variants of the ANXA11 gene (P=0.17). Haplotypic analyses of the C10ORF67-OTUD1 inter-genic region revealed a strong inverse association of the variants rs1398024 and rs11013452 with sarcoidosis (OR=0.52; P=0.01). Both SNPs are located inside a ~300 kb low recombination region of chromosome 10p12, suggesting that both SNPs are tagging the same causal variant. Our top SNP (rs11013452) is located inside a smaller LD block in HapMap YRI, further narrowing the position of the causal SNP to a region of ~ 8kb on chromosome 10p12. The present findings confirm the potential importance of the 10p12 locus in the etiology of sarcoidosis.
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Baumgartel K, Zelazny J, Timcheck T, Snyder C, Bell M, Conley YP. Molecular genomic research designs. ANNUAL REVIEW OF NURSING RESEARCH 2012; 29:1-26. [PMID: 22891496 DOI: 10.1891/0739-6686.29.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Genetic and genomic research approaches have the capability to expand our understanding of the complex pathophysiology of disease susceptibility, susceptibility to complications related to disease, trajectory of recovery from acquired injuries and infections, patient response to interventions and therapeutics, as well as informing diagnoses and prognoses. Nurse scientists are actively involved in all of these fields of inquiry, and the goal of this chapter is to assist with incorporation of genetic and genomic trajectories into their research and facilitate the design and execution of these studies. New studies that are going to embark on recruitment, phenotyping, and sample collection will benefit from forethought about research design to ensure that it addresses the research questions or hypotheses being tested. Studies that will use existing data or samples will also benefit from forethought about research design for the same reason but will also address the fact that some designs may not be feasible with the available data or samples. This chapter discusses candidate gene association, genome-wide association, candidate gene expression, global gene expression, and epigenetic/epigenomic study designs. Information provided includes rationale for selecting an appropriate study design, important methodology considerations for each design, key technologies available to accomplish each type of study, and online resources available to assist in executing each type of study design.
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Reding KW, Carlson CS, Kahsai O, Chen CC, McDavid A, Doody DR, Chen C, Ornelas I, Lowe K, Bernstein L, Weiss L, McDonald JA, Simon MS, Strom B, Marchbanks PA, Burkman R, Spirtas R, Liff JM, Malone KE. Examination of ancestral informative markers and self-reported race with tumor characteristics of breast cancer among Black and White women. Breast Cancer Res Treat 2012; 134:801-9. [PMID: 22648732 DOI: 10.1007/s10549-012-2099-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2012] [Accepted: 05/15/2012] [Indexed: 10/28/2022]
Abstract
African American (AA) women have a higher mortality from breast cancer (BC) compared to European American (EA) women. This may be due to the higher proportion of AA women with tumors that are diagnosed at more advanced stages and are characterized as being estrogen receptor negative (ER-)/progesterone receptor negative (PR-). Our study sought to determine whether self-reported race and percent African ancestry were associated with BC tumor characteristics. In a multi-center, population-based case-control study of BC, we determined percent African ancestry using ancestry informative markers (AIM) among women self-reporting race as AA or Black. BC tumor characteristics were associated with self-reported race (including a 30 % reduction in ER+/PR+ tumors [95 % confidence interval [CI]: 0.6-0.9] and a 1.5-fold increased risk of high grade [95 % CI: 1.2-1.9] for AA women compared to EA women). AIMs among AA women were not associated with BC tumor characteristics (AA women with ≥95 % versus <80 % African ancestry, odds ratio [OR] = 1.0 for ER+/PR+ [95 % CI: 0.6-1.8] and OR = 0.9 for high-grade tumors [95 % CI: 0.6-1.4]). Similar findings were observed for BC stage. While BC subtypes were associated with self-reported race, BC subtypes were not associated with percent African ancestry. These study results suggest that subtle differences in percent African ancestry are less important than the overall presence of African ancestry in relation to BC tumor characteristics.
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Affiliation(s)
- Kerryn W Reding
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Mail Stop M4-B874, Seattle, WA 98109-1024, USA.
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Fang C, Cohen HW, Billett HH. Race, ABO blood group, and venous thromboembolism risk: not black and white. Transfusion 2012; 53:187-92. [PMID: 22536799 DOI: 10.1111/j.1537-2995.2012.03665.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
BACKGROUND The rate of venous thromboembolism (VTE) has been reported to be higher in blacks compared to whites. Non-O blood groups have also been associated with a significantly higher VTE risk. Given that a higher proportion of blacks have O blood group, one might have expected that black individuals would have fewer VTEs. STUDY DESIGN AND METHODS In this study, we analyzed race, sex, age, ABO or Rh blood group, and VTE risk in 60,982 black and white patients admitted over a span of 10 years. RESULTS The overall occurrence of VTEs was 7.6%, higher in males (8.7% males vs. 7.2% females), higher in non-O blood groups (8.5% non-O vs. 6.9% O blood group), and increased with age (5.8% <65 years, 11.3% ≥65 years). No difference in VTE rate was noted with Rh antigen positivity. When stratified by age, VTE rate was consistently higher in blacks and non-O blood groups. No difference was detected among the various non-O blood groups. To assess the potential confounder of comorbidities, we stratified patients according to Charlson comorbidity score. In a subgroup of healthy patients with age-independent Charlson comorbidity scores of 0 (n = 28,387), blacks still had an increased VTE risk and this risk was still higher with increasing age and in those with non-O blood groups. CONCLUSION We conclude that black race and non-O blood groups have increased VTE risk when stratified for age and that associated comorbidities do not explain these differences.
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Affiliation(s)
- Chunhui Fang
- Department of Medicine, Jacobi Medical Center, the Department of Epidemiology and Public Health, Albert Einstein College of Medicine, and the Division of Hematology, Department of Medicine, Montefiore Medical Center, Bronx, New York, USA
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Genetic ancestry, self-reported race and ethnicity in African Americans and European Americans in the PCaP cohort. PLoS One 2012; 7:e30950. [PMID: 22479307 PMCID: PMC3313995 DOI: 10.1371/journal.pone.0030950] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 12/27/2011] [Indexed: 11/19/2022] Open
Abstract
Background Family history and African-American race are important risk factors for both prostate cancer (CaP) incidence and aggressiveness. When studying complex diseases such as CaP that have a heritable component, chances of finding true disease susceptibility alleles can be increased by accounting for genetic ancestry within the population investigated. Race, ethnicity and ancestry were studied in a geographically diverse cohort of men with newly diagnosed CaP. Methods Individual ancestry (IA) was estimated in the population-based North Carolina and Louisiana Prostate Cancer Project (PCaP), a cohort of 2,106 incident CaP cases (2063 with complete ethnicity information) comprising roughly equal numbers of research subjects reporting as Black/African American (AA) or European American/Caucasian/Caucasian American/White (EA) from North Carolina or Louisiana. Mean genome wide individual ancestry estimates of percent African, European and Asian were obtained and tested for differences by state and ethnicity (Cajun and/or Creole and Hispanic/Latino) using multivariate analysis of variance models. Principal components (PC) were compared to assess differences in genetic composition by self-reported race and ethnicity between and within states. Results Mean individual ancestries differed by state for self-reporting AA (p = 0.03) and EA (p = 0.001). This geographic difference attenuated for AAs who answered “no” to all ethnicity membership questions (non-ethnic research subjects; p = 0.78) but not EA research subjects, p = 0.002. Mean ancestry estimates of self-identified AA Louisiana research subjects for each ethnic group; Cajun only, Creole only and both Cajun and Creole differed significantly from self-identified non-ethnic AA Louisiana research subjects. These ethnicity differences were not seen in those who self-identified as EA. Conclusions Mean IA differed by race between states, elucidating a potential contributing factor to these differences in AA research participants: self-reported ethnicity. Accurately accounting for genetic admixture in this cohort is essential for future analyses of the genetic and environmental contributions to CaP.
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Wise LA, Palmer JR, Reich D, Cozier YC, Rosenberg L. Hair relaxer use and risk of uterine leiomyomata in African-American women. Am J Epidemiol 2012; 175:432-40. [PMID: 22234483 PMCID: PMC3282879 DOI: 10.1093/aje/kwr351] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 09/09/2011] [Indexed: 11/13/2022] Open
Abstract
Hair relaxers are used by millions of black women, possibly exposing them to various chemicals through scalp lesions and burns. In the Black Women's Health Study, the authors assessed hair relaxer use in relation to uterine leiomyomata incidence. In 1997, participants reported on hair relaxer use (age at first use, frequency, duration, number of burns, and type of formulation). From 1997 to 2009, 23,580 premenopausal women were followed for incident uterine leiomyomata. Multivariable Cox regression was used to estimate incidence rate ratios and 95% confidence intervals. During 199,991 person-years, 7,146 cases of uterine leiomyomata were reported as confirmed by ultrasound (n = 4,630) or surgery (n = 2,516). The incidence rate ratio comparing ever with never use of relaxers was 1.17 (95% confidence interval (CI): 1.06, 1.30). Positive trends were observed for frequency of use (P(trend) < 0.001), duration of use (P(trend) = 0.015), and number of burns (P(trend) < 0.001). Among long-term users (≥10 years), the incidence rate ratios for frequency of use categories 3-4, 5-6, and ≥7 versus 1-2 times/year were 1.04 (95% CI: 0.92, 1.19), 1.12 (95% CI: 0.99, 1.27), and 1.15 (95% CI: 1.01, 1.31), respectively (P(trend) = 0.002). Risk was unrelated to age at first use or type of formulation. These findings raise the hypothesis that hair relaxer use increases uterine leiomyomata risk.
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Affiliation(s)
- Lauren A Wise
- Slone Epidemiology Center, Boston University, Massachusetts 02215, USA.
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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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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, Huo D. Lack of association between common single nucleotide polymorphisms in the TERT-CLPTM1L locus and breast cancer in women of African ancestry. Breast Cancer Res Treat 2011; 132:341-5. [PMID: 22134622 DOI: 10.1007/s10549-011-1890-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 11/18/2011] [Indexed: 11/26/2022]
Abstract
As one of the most common cancers worldwide, breast cancer places an extraordinary burden on the populations of African ancestry. Common SNPs in the TERT-CLPTM1L locus have been reported to be associated with several types of cancer, including breast cancer. We sought to investigate whether the previously reported common single nucleotide polymorphisms (SNPs) in the TERT-CLPTM1L locus could also contribute to the breast cancer risk in women of African ancestry. We genotyped eleven SNPs in 2,892 women of African descent but were unable to detect any significant association between TERT-CLPTM1L SNPs and their predispositions for breast cancer risk. Given the differences in linkage disequilibrium patterns across populations, our findings suggest that larger independent studies from diverse populations are expected to evaluate the importance of the TERT-CLPTM1L locus in breast cancer.
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Affiliation(s)
- Yonglan Zheng
- Department of Medicine, The University of Chicago, 900 E 57th Street, KCBD Building 8113D, Chicago, IL 60637, USA.
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