Replication of breast cancer susceptibility loci in whites and African Americans using a bayesian approach

American Journal of Epidemiology

Volumn 179, Issue 3, 2014, Pages 382-394

  O'Brien, Katie M ^a,b   Cole, Stephen R ^a   Poole, Charles ^a   Bensen, Jeannette T ^a,b   Herring, Amy H ^c   Engel, Lawrence S ^a   Millikan, Robert C ^a,b  

^a University of North Carolina at Chapel Hill   (United States)

^b UNIVERSITY OF NORTH CAROLINA   (United States)

^c UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL   (United States)

Author keywords

Bayesian analysis; breast cancer; genetics; genome wide association studies; GWAS replication; race; single nucleotide polymorphisms

Indexed keywords

ESTROGEN RECEPTOR ALPHA; FIBROBLAST GROWTH FACTOR RECEPTOR 2; HIGH MOBILITY GROUP B PROTEIN; MITOGEN ACTIVATED PROTEIN KINASE KINASE KINASE 1; RIBOSOME PROTEIN; ZINC FINGER PROTEIN;

AFRICAN AMERICAN; BAYESIAN ANALYSIS; CANCER; EPIDEMIOLOGY; GENOME; HEALTH RISK; MAXIMUM LIKELIHOOD ANALYSIS; PARTICIPATORY APPROACH; POLYMORPHISM; PUBLIC HEALTH;

ADULT; AFRICAN AMERICAN; AGED; ARTICLE; BAYES THEOREM; BREAST CANCER; CANCER GENETICS; CANCER SUSCEPTIBILITY; CONTROLLED STUDY; EUROPEAN AMERICAN; FEMALE; GENE LOCATION; GENE LOCUS; GENE REPLICATION; GENETIC ASSOCIATION; GENETIC RISK; GENETIC VARIABILITY; HUMAN; MAJOR CLINICAL STUDY; MIDDLE AGED; SINGLE NUCLEOTIDE POLYMORPHISM; TUMOR GENE; YOUNG ADULT;

CAROLINA; PUERTO RICO;

BAYESIAN ANALYSIS; BREAST CANCER; GENETICS; GENOME-WIDE ASSOCIATION STUDIES; GWAS REPLICATION; RACE; SINGLE NUCLEOTIDE POLYMORPHISMS;

ADULT; AFRICAN AMERICANS; AGED; BAYES THEOREM; BREAST NEOPLASMS; CASE-CONTROL STUDIES; EUROPEAN CONTINENTAL ANCESTRY GROUP; FEMALE; GENETIC MARKERS; GENOME-WIDE ASSOCIATION STUDY; HUMANS; LIKELIHOOD FUNCTIONS; LOGISTIC MODELS; MIDDLE AGED; NORTH CAROLINA; ODDS RATIO; POLYMORPHISM, SINGLE NUCLEOTIDE; REGISTRIES; RISK FACTORS; TUMOR MARKERS, BIOLOGICAL;

EID: 84892685499     PISSN: 00029262     EISSN: 14766256     Source Type: Journal    
DOI: 10.1093/aje/kwt258     Document Type: Article

References (67)

1. Hindorff LA, MacArthur J, Morales J, et al. A catalog of published genome-wide association studies. Bethesda, MD: National Human Genome Research Institute, National Institutes of Health; 2013. (www.genome.gov/gwastudies). (Accessed January 13, 2013).
2. Chen F, Chen GK, Millikan RC, et al. Fine-mapping of breast cancer susceptibility loci characterizes genetic risk in African Americans. Hum Mol Genet. 2011;20(22):4491-4503.
3. Hutter CM, Young AM, Ochs-Balcom HM, et al. Replication of breast cancer GWAS susceptibility loci in the Women's Health Initiative African American SHARe Study. Cancer Epidemiol Biomarkers Prev. 2011;20(9):1950-1959.
4. Campa D, Kaaks R, Le Marchand L, et al. Interactions between genetic variants and breast cancer risk factors in the breast and prostate cancer cohort consortium. J Natl Cancer Inst. 2011; 103(16):1252-1263.
5. Zheng W, Cai Q, Signorello LB, et al. Evaluation of 11 breast cancer susceptibility loci in African-American women. Cancer Epidemiol Biomarkers Prev. 2009;18(10):2761-2764.
6. Stacey SN, Sulem P, Zanon C, et al. Ancestry-shift refinement mapping of the C6orf97-ESR1 breast cancer susceptibility locus. PLoS Genet. 2010;6(7):e1001029.
7. Rebbeck TR, DeMichele A, Tran TV, et al. Hormone-dependent effects of FGFR2 and MAP3K1 in breast cancer susceptibility in a population-based sample of postmenopausal African-American and European-American women. Carcinogenesis. 2009;30(2):269-274.
8. Udler MS, Meyer KB, Pooley KA, et al. FGFR2 variants and breast cancer risk: fine-scale mapping using African American studies and analysis of chromatin conformation. Hum Mol Genet. 2009;18(9):1692-1703.
9. Ruiz-Narvaez EA, Rosenberg L, Rotimi CN, et al. Genetic variants on chromosome 5p12 are associated with risk of breast cancer in African American women: the Black Women's Health Study. Breast Cancer Res Treat. 2010;123(2):525-530.
10. Ruiz-Narváez EA, Rosenberg L, Cozier YC, et al. Polymorphisms in the TOX3/LOC643714 locus and risk of breast cancer in African-American women. Cancer Epidemiol Biomarkers Prev. 2010;19(5):1320-1327.
11. Palmer JR, Ruiz-Narvaez EA, Rotimi CN, et al. Genetic susceptibility loci for subtypes of breast cancer in an African American population. Cancer Epidemiol Biomarkers Prev. 2013;22(1):127-134.
12. Huo D, Zheng Y, Ogundiran TO, et al. Evaluation of 19 susceptibility loci of breast cancer in women of African ancestry. Carcinogenesis. 2012;33(4):835-840.
13. Carey LA, Perou CM, Livasy CA, et al. Race, breast cancer subtypes, and survival in the Carolina Breast Cancer Study. JAMA. 2006;295(21):2492-2502.
14. Huo D, Ikpatt F, Khramtsov A, et al. Population differences in breast cancer: survey in indigenous African women reveals over-representation of triple-negative breast cancer. J Clin Oncol. 2009;27(27):4515-4521.
15. Lund MJ, Trivers KF, Porter PL, et al. Race and triple negative threats to breast cancer survival: a population-based study in Atlanta, GA. Breast Cancer Res Treat. 2009;113(2):357-370.
16. Millikan RC, Newman B, Tse C, et al. Epidemiology of basal-like breast cancer. Breast Cancer Res Treat. 2008;109(1):123-139.
17. Surveillance Epidemiology and End Results. US cancer morality statistics. Bethesda, MD: National Cancer Institute, National Institutes of Health; 2013. (http://seer.cancer.gov/canques/mortality.html). (Accessed January 9, 2013).
18. Haiman CA, Stram DO. Exploring genetic susceptibility to cancer in diverse populations. Curr Opin Genet Dev. 2010; 20(3):330-335.
19. Hinch AG, Tandon A, Patterson N, et al. The landscape of recombination in African Americans. Nature. 2011;476(7359): 170-175.
20. Hunter DJ. Lessons from genome-wide association studies for epidemiology. Epidemiology. 2012;23(3):363-367.
21. Hung RJ, Brennan P, Malaveille C, et al. Using hierarchical modeling in genetic association studies with multiple markers: application to a case-control study of bladder cancer. Cancer Epidemiol Biomarkers Prev. 2004;13(6):1013- 1021.
22. Conti DV, Witte JS. Hierarchical modeling of linkage disequilibrium: genetic structure and spatial relations. Am J Hum Genet. 2003;72(2):351-363.
23. Stephens M, Balding DJ. Bayesian statistical methods for genetic association studies. Nat Rev Genet. 2009;10(10): 681-690.
24. Newcombe PJ, Reck BH, Sun J, et al. A comparison of Bayesian and frequentist approaches to incorporating external information for the prediction of prostate cancer risk. Genet Epidemiol. 2012;36(1):71-83.
25. Quintana MA, Berstein JL, Thomas DC, et al. Incorporating model uncertainty in detecting rare variants: the Bayesian risk index. Genet Epidemiol. 2011;35(7):638-649.
26. Wakefield J. Bayes factors for genome-wide association studies: comparison with P-values. Genet Epidemiol. 2009;33(1):79-86.
27. Fridley BL, Serie D, Jenkins G, et al. Bayesian mixture models for the incorporation of prior knowledge to inform genetic association studies. Genet Epidemiol. 2010;34(5):418-426.
28. Aldrich TE, Vann D, Moorman PG, et al. Rapid reporting of cancer incidence in a population-based study of breast cancer: one constructive use of a central cancer registry. Breast Cancer Res Treat. 1995;35(1):61-64.
29. Weinberg CR, Sandler DP. Randomized recruitment in case-control studies. Am J Epidemiol. 1991;134(4):421-432.
30. Easton DF, Pooley KA, Dunning AM, et al. Genome-wide association study identifies novel breast cancer susceptibility loci. Nature. 2007;447(7148):1087- 1093.
31. Gold B, Kirchhoff T, Stefanov S, et al. Genome-wide association study provides evidence for a breast cancer risk locus at 6q22.33. Proc Natl Acad Sci USA. 2008;105(11): 4340-4345.
32. Hunter DJ, Kraft P, Jacobs KB, et al. A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer. Nat Genet. 2007;39(7):870-874.
33. Long J, Cai Q, Shu X, et al. Identification of a functional genetic variant at 16q12.1 for breast cancer risk: results from the Asia Breast Cancer Consortium. PLoS Genet. 2010;6(6): e1001002.
34. Stacey SN, Manolescu A, Sulem P, et al. Common variants on chromosomes 2q35 and 16q12 confer susceptibility to estrogen receptor-positive breast cancer. Nat Genet. 2007;39(7): 865-869.
35. Thomas G, Jacobs KB, Kraft P, et al. A multistage genome-wide association study in breast cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1). Nat Genet. 2009;41(5):579-584.
36. Turnbull C, Ahmed S, Morrison J, et al. Genome-wide association study identifies five new breast cancer susceptibility loci. Nat Genet. 2010;42(6):504-507.
37. Zheng W, Long J, Gao Y, et al. Genome-wide association study identifies a new breast cancer susceptibility locus at 6q25.1. Nat Genet. 2009;41(3):324-328.
38. Ahmed S, Thomas G, Ghoussaini M, et al. Newly discovered breast cancer susceptibility loci on 3p24 and 17q23.2. Nat Genet. 2009;41(5):585-590.
39. Stacey SN, Manolescu A, Sulem P, et al. Common variants on chromosome 5p12 confer susceptibility to estrogen receptor-positive breast cancer. Nat Genet. 2008;40(6):703-706.
40. Zhang B, Beeghly-Fadiel A, Long J, et al. Genetic variants associated with breast-cancer risk: comprehensive research synopsis, meta-analysis, and epidemiological evidence. Lancet Oncol. 2011;12(5):477-488.
41. Thomas DC, Witte JS. Point: Population stratification: A problem for case-control studies of candidate-gene associations? Cancer Epidemiol Biomarkers Prev. 2002;11(6): 505-512.
42. Barnholtz-Sloan JS, McEvoy B, Shriver MD, et al. Ancestry estimation and correction for population stratification in molecular epidemiologic association studies. Cancer Epidemiol Biomarkers Prev. 2008;17(3):471-477.
43. Nyante SJ, Gammon MD, Kaufman JS, et al. Common genetic variation in adiponectin, leptin, and leptin receptor and association with breast cancer subtypes. Breast Cancer Res Treat. 2011;129(2):593-606.
44. Bortsov AV, Millikan RC, Belfer I, et al. μ-Opioid receptor gene A118G polymorphism predicts survival in patients with breast cancer. Anesthesiology. 2012;116(4):896-902.
45. Gill J. Bayesian Methods: A Social and Behavioral Sciences Approach. 2nd ed. New York, NY: CRC Press; 2002.
46. Greenland S. Bayesian perspectives for epidemiological research. II. Regression analysis. Int J Epidemiol. 2007;36(1): 195-202.
47. Greenland S. Bayesian perspectives for epidemiological research: I. Foundations and basic methods. Int J Epidemiol. 2006;35(3):765-775.
48. Chen GK, Witte JS. Enriching the analysis of genomewide association studies with hierarchical modeling. Am J Hum Genet. 2007;81(2):397-404.
49. Greenland S. Principles of multilevel modelling. Int J Epidemiol. 2000;29(1):158-167.
50. Hung RJ, Baragatti M, Thomas D, et al. Inherited predisposition of lung cancer: a hierarchical modeling approach to DNA repair and cell cycle control pathways. Cancer Epidemiol Biomarkers Prev. 2007;16(12):2736-2744.
51. Gabriel SB, Schaffner SF, Nguyen H, et al. The structure of haplotype blocks in the human genome. Science. 2002; 296(5576):2225-2229.
52. Barrett JC. Haploview: visualization and analysis of SNP genotype data. Cold Spring Harb Protoc. 2009;2009(10):71.
53. Hall IJ, Moorman PG, Millikan RC, et al. Comparative analysis of breast cancer risk factors among African-American women and white women. Am J Epidemiol. 2005;161(1): 40-51.
54. Barnholtz-Sloan JS, Shetty PB, Guan X, et al. FGFR2 and other loci identified in genome-wide association studies are associated with breast cancer in African-American and younger women. Carcinogenesis. 2010;31(8):1417-1423.
55. Milne RL, Goode EL, García-Closas M, et al. Confirmation of 5p12 as a susceptibility locus for progesterone-receptor-positive, lower grade breast cancer. Cancer Epidemiol Biomarkers Prev. 2011;20(10):2222-2231.
56. Li J, Humphreys K, Heikkinen T, et al. A combined analysis of genome-wide association studies in breast cancer. Breast Cancer Res Treat. 2011;126(3):717-727.
57. Fletcher O, Johnson N, Orr N, et al. Novel breast cancer susceptibility locus at 9q31.2: results of a genome-wide association study. J Natl Cancer Inst. 2011;103(5):425-435.
58. Huang Y, Ballinger DG, Dai JY, et al. Genetic variants in the MRPS30 region and postmenopausal breast cancer risk. Genome Med. 2011;3(6):42.
59. Milne RL, Gaudet MM, Spurdle AB, et al. Assessing interactions between the associations of common genetic susceptibility variants, reproductive history and body mass index with breast cancer risk in the breast cancer association consortium: a combined case-control study. Breast Cancer Res. 2010;12(6):R110.
60. Bhatti P, Doody MM, Rajaraman P, et al. Novel breast cancer risk alleles and interaction with ionizing radiation among US radiologic technologists. Radiat Res. 2010;173(2):214-224.
61. Higginbotham KS, Breyer JP, McReynolds KM, et al. A multistage genetic association study identifies breast cancer risk loci at 10q25 and 16q24. Cancer Epidemiol Biomarkers Prev. 2012;21(9):1565-1573.
62. Udler MS, Ahmed S, Healey CS, et al. Fine scale mapping of the breast cancer 16q12 locus. Hum Mol Genet. 2010;19(12): 2507-2515.
63. Cai Q, Wen W, Qu S, et al. Replication and functional genomic analyses of the breast cancer susceptibility locus at 6q25.1 generalize its importance in women of Chinese, Japanese, and European ancestry. Cancer Res. 2011;71(4):1344-1355.
64. MacLehose RF, Dunson DB, Herring AH, et al. Bayesian methods for highly correlated exposure data. Epidemiology. 2007;18(2):199-207.
65. Hamra GB, Maclehose RF, Cole SR. Sensitivity analyses for sparse-data problems-using weakly informative bayesian priors. Epidemiology. 2013;24(2):233-239.
66. Furberg H, Millikan R, Dressler L, et al. Tumor characteristics in African American and white women. Breast Cancer Res Treat. 2001;68(1):33-43.
67. Kerlikowske K. Epidemiology of ductal carcinoma in situ. J Natl Cancer Inst Monogr. 2010;2010(41):139-141.