Fine-mapping of breast cancer susceptibility loci characterizes genetic risk in African Americans

Human Molecular Genetics

Volumn 20, Issue 22, 2011, Pages 4491-4503

  Chen, Fang ^a   Chen, Gary K ^a   Millikan, Robert C ^b   John, Esther M ^c,d   Ambrosone, Christine B ^e   Bernstein, Leslie ^f   Zheng, Wei ^g   Hu, Jennifer J ^h   Ziegler, Regina G ⁱ   Deming, Sandra L ^g   Bandera, Elisa V ^j   Nyante, Sarah ^b   Palmer, Julie R ^k   Rebbeck, Timothy R ^l   Ingles, Sue A ^a   Press, Michael F ^a   Rodriguez Gil, Jorge L ^h   Chanock, Stephen J ⁱ   Le Marchand, Loïc ^m   Kolonel, Laurence N ^m   Henderson, Brian E ^a   Stram, Daniel O ^a   Haiman, Christopher A ^a   more..

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^b IL   (United States)

^c NORTHERN CALIFORNIA CANCER CENTER   (United States)

^d STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^e ROSWELL PARK CANCER INSTITUTE   (United States)

^f CITY OF HOPE NATIONAL MEDICAL CENTER   (United States)

^g VANDERBILT INGRAM CANCER CENTER   (United States)

^h UNIVERSITY OF MIAMI   (United States)

ⁱ NATIONAL CANCER INSTITUTE   (United States)

^j RUTGERS CANCER INSTITUTE OF NEW JERSEY   (United States)

^k BOSTON UNIVERSITY   (United States)

^l UNIVERSITY OF PENNSYLVANIA   (United States)

^m UNIVERSITY OF HAWAII CANCER CENTER   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; AFRICAN AMERICAN; AGED; ALLELE; ARTICLE; BREAST CANCER; CANCER RISK; CANCER SUSCEPTIBILITY; CONTROLLED STUDY; FEMALE; GENE LOCUS; GENE MAPPING; GENETIC ASSOCIATION; GENETIC RISK; GENETIC VARIABILITY; HUMAN; MAJOR CLINICAL STUDY; PRIORITY JOURNAL;

EID: 80054878612     PISSN: 09646906     EISSN: 14602083     Source Type: Journal    
DOI: 10.1093/hmg/ddr367     Document Type: Article

References (55)

1. Easton, D.F., Pooley, K.A., Dunning, A.M., Pharoah, P.D., Thompson, D., Ballinger, D.G., Struewing, J.P., Morrison, J., Field, H., Luben, R. et al. (2007) Genome-wide association study identifies novel breast cancer susceptibility loci. Nature, 447, 1087-1093.
2. Stacey, S.N., Manolescu, A., Sulem, P., Rafnar, T., Gudmundsson, J., Gudjonsson, S.A., Masson, G., Jakobsdottir, M., Thorlacius, S., Helgason, A. et al. (2007) Common variants on chromosomes 2q35 and 16q12 confer susceptibility to estrogen receptor-positive breast cancer. Nat. Genet., 39, 865-869.
3. Hunter, D.J., Kraft, P., Jacobs, K.B., Cox, D.G., Yeager, M., Hankinson, S.E., Wacholder, S., Wang, Z., Welch, R., Huntchinson, A. et al. (2007) A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer. Nat. Genet., 39, 870-874.
4. Stacey, S.N., Manolescu, A., Sulem, P., Thorlacius, S., Gudjonsson, S.A., Jonsson, G.F., Jakobsdottir, M., Bergthorsson, J.T., Gudmundsson, J., Aben, K.K. et al. (2008) Common variants on chromosome 5p12 confer susceptibility to estrogen receptor-positive breast cancer. Nat. Genet., 40, 703-706.
5. Zheng, W., Long, J., Gao, Y.T., Li, C., Zheng, Y., Xiang, Y.B., Wen, W., Levy, S., Deming, S.L., Haines, J.L. et al. (2009) Genome-wide association study identifies a new breast cancer susceptibility locus at 6q25.1. Nat. Genet., 41, 324-328.
6. Thomas, G., Jacobs, K.B., Kraft, P., Yeager, M., Wacholder, S., Cox, D.G., Hankinson, S.E., Hutchinson, A., Wang, Z., Yu, K. et al. (2009) A multistage genome-wide association study in breast cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1). Nat. Genet., 41, 579-584.
7. Ahmed, S., Thomas, G., Ghoussaini, M., Healey, C.S., Humphreys, M.K., Platte, R., Morrison, J., Maranian, M., Pooley, K.A., Luben, R. et al. (2009) Newly discovered breast cancer susceptibility loci on 3p24 and 17q23.2. Nat. Genet., 41, 585-590.
8. Turnbull, C., Shahana, A., Morrison, J., Pernet, D., Renwick, A., Maranian, M., Seal, S., Ghoussaini, M., Hines, S., Healey, C.S. et al. (2010) Genome-wide association study identifies five new breast cancer susceptibility loci. Nat. Genet., 42, 504-507.
9. Antoniou, A.C., Wang, X., Fredericksen, Z.S., McGuffog, L., Tarrell, R., Sinilnikova, O.M., Healey, S., Morrison, J., Kartsonaki, C., Lesnick, T. et al. (2010) A locus on 19p13 modifies risk of breast cancer in BRCA1 mutation carriers and is associated with hormone receptor-negative breast cancer in the general population. Nat. Genet., 42, 885-892.
10. Fletcher, O., Johnson, N., Orr, N., Hosking, F.J., Gibson, L.J., Walker, K., Zelenika, D., Gut, I., Heath, S., Palles, C. et al. (2011) Novel breast cancer susceptibility locus at 9q31.2: results of a genome-wide association study. J. Natl Cancer Inst., 103, 425-435.
11. Pepe, M.S. and Janes, H.E. (2008) Gauging the performance of SNPs, biomarkers, and clinical factors for predicting risk of breast cancer. J. Natl Cancer Inst., 100, 978-979.
12. Gail, M.H. (2008) Discriminatory accuracy from single-nucleotide polymorphisms in models to predict breast cancer risk. J. Natl Cancer Inst., 100, 1037-1041.
13. Pharoah, P.D., Antoniou, A., Bobrow, M., Zimmern, R.L., Easton, D.F. and Ponder, B.A. (2002) Polygenic susceptibility to breast cancer and implications for prevention. Nat. Genet., 31, 33-36.
14. Chen, F., Stram, D.O., Le Marchand, L., Monroe, K.R., Kolonel, L.N., Henderson, B.E. and Haiman, C.A. (2010) Caution in generalizing known genetic risk markers for breast cancer across all ethnic/racial populations. Eur. J. Hum. Genet., 19, 243-245.
15. Zheng, W., Cai, Q., Signorello, L.B., Long, J., Hargreaves, M.K., Deming, S.L., Li, G., Li, C., Cui, Y. and Blot, W.J. (2009) Evaluation of 11 breast cancer susceptibility loci in African-American women. Cancer Epidemiol. Biomarkers Prev., 18, 2761-2764.
16. Ruiz-Narvaez, E.A., Rosenberg, L., Cozier, Y.C., Cupples, L.A., Adams-Campbell, L.L. and Palmer, J.R. (2010) Polymorphisms in the TOX3/LOC643714 locus and risk of breast cancer in African-American women. Cancer Epidemiol. Biomarkers Prev., 19, 1320-1327.
17. Stacey, S.N., Sulem, P., Zanon, C., Gudjonsson, S.A., Thorleifsson, G., Helgason, A., Jonasdottir, A., Besenbacher, S., Kostic, J.P., Fackenthal, J.D. et al. (2010) Ancestry-shift refinement mapping of the C6orf97-ESR1 breast cancer susceptibility locus. PLoS Genet., 6, e1001029.
18. Garcia-Closas, M., Hall, P., Nevanlinna, H., Pooley, K., Morrison, J., Richesson, D.A., Bojesen, S.E., Nordestgaard, B.G., Axelsson, C.K., Arias, J.I. et al. (2008) Heterogeneity of breast cancer associations with five susceptibility loci by clinical and pathological characteristics. PLoS Genet., 4, e1000054.
19. Pasaniuc, B., Zaitlen, N., Lettre, G., Chen, G., Tandon, A., Kao, L., Ruczinski, I., Fornage, M., Siscovick, D., Zhu, X. et al. (2011) Enhanced statistical tests for GWAS in admixed populations: assessment using African Americans from CARe and a breast cancer consortium. PLoS Genet., 7, e1001371.
20. Fejerman, L., Haiman, C.A., Reich, D., Tandon, A., Deo, R.C., John, E.M., Ingles, S.A., Ambrosone, C.B., Bovbjerg, D.H., Jandorf, L.H. et al. (2009) An admixture scan in 1484 African American women with breast cancer. Cancer Epidemiol. Biomarkers Prev., 18, 3110-3117.
21. Milne, R.L., Benitez, J., Nevanlinna, H., Heikkinen, T., Aittomaki, K., Blomqvist, C., Arias, J.I., Zamora, M.P., Burwinkel, B., Bartram, C.R. et al. (2009) Risk of estrogen receptor-positive and -negative breast cancer and single-nucleotide polymorphism 2q35-rs13387042. J. Natl Cancer Inst., 101, 1012-1018.
22. Udler, M.S., Meyer, K.B., Pooley, K.A., Karlins, E., Struewing, J.P., Zhang, J., Doody, D.R., MacArthur, S., Tyrer, J., Pharoah, P.D. et al. (2009) FGFR2 variants and breast cancer risk: fine-scale mapping using African American studies and analysis of chromatin conformation. Hum. Mol. Genet., 18, 1692-1703.
23. Jia, L., Landan, G., Pomerantz, M., Jaschek, R., Herman, P., Reich, D., Yan, C., Khalid, O., Kantoff, P., Oh, W. et al. (2009) Functional enhancers at the gene-poor 8q24 cancer-linked locus. PLoS Genet., 5, e1000597.
24. Freedman, M.L. (2006) Admixture mapping identifies 8q24 as a prostate cancer risk locus in African-American men. Proc. Natl Acad. Sci. USA, 103, 14068-14073.
25. Ghoussaini, M., Song, H., Koessler, T., Al Olama, A.A., Kote-Jarai, Z., Driver, K.E., Pooley, K.A., Ramus, S.J., Kjaer, S.K., Hogdall, E. et al. (2008) Multiple loci with different cancer specificities within the 8q24 gene desert. J. Natl Cancer Inst., 100, 962-966.
26. Kiemeney, L.A., Thorlacius, S., Sulem, P., Geller, F., Aben, K.K., Stacey, S.N., Gudmundsson, J., Jakobsdottir, M., Bergthorsson, J.T., Sigurdsson, A. et al. (2008) Sequence variant on 8q24 confers susceptibility to urinary bladder cancer. Nat. Genet., 40, 1307-1312.
27. Goode, E.L., Chenevix-Trench, G., Song, H., Ramus, S.J., Notaridou, M., Lawrenson, K., Widschwendter, M., Vierkant, R.A., Larson, M.C., Kjaer, S.K. et al. (2010) A genome-wide association study identifies susceptibility loci for ovarian cancer at 2q31 and 8q24. Nat. Genet., 42, 874-879.
28. Crowther-Swanepoel, D., Broderick, P., Di Bernardo, M.C., Dobbins, S.E., Torres, M., Mansouri, M., Ruiz-Ponte, C., Enjuanes, A., Rosenquist, R., Carracedo, A. et al. (2010) Common variants at 2q37.3, 8q24.21, 15q21.3 and 16q24.1 influence chronic lymphocytic leukemia risk. Nat. Genet., 42, 132-136.
29. Salinas, C.A., Kwon, E., Carlson, C.S., Koopmeiners, J.S., Feng, Z., Karyadi, D.M., Ostrander, E.A. and Stanford, J.L. (2008) Multiple independent genetic variants in the 8q24 region are associated with prostate cancer risk. Cancer Epidemiol. Biomarkers Prev., 17, 1203-1213.
30. Gudmundsson, J., Sulem, P., Gudbjartsson, D.F., Blondal, T., Gylfason, A., Agnarsson, B.A., Benediktsdottir, K.R., Magnusdottir, D.N., Orlygsdottir, G., Jakobsdottir, M. et al. (2009) Genome-wide association and replication studies identify four variants associated with prostate cancer susceptibility. Nat. Genet., 41, 1122-1126.
31. Gudmundsson, J., Sulem, P., Manolescu, A., Amundadottir, L.T., Gudbjartsson, D., Helgason, A., Rafnar, T., Bergthorsson, J.T., Agnarsson, B.A., Baker, A. et al. (2007) Genome-wide association study identifies a second prostate cancer susceptibility variant at 8q24. Nat. Genet., 39, 631-637.
32. Yeager, M., Orr, N., Hayes, R.B., Jacobs, K.B., Kraft, P., Wacholder, S., Minichiello, M.J., Fearnhead, P., Yu, K., Chatterjee, N. et al. (2007) Genome-wide association study of prostate cancer identifies a second risk locus at 8q24. Nat. Genet., 39, 645-649.
33. Yeager, M., Chatterjee, N., Ciampa, J., Jacobs, K.B., Gonzalez-Bosquet, J., Hayes, R.B., Kraft, P., Wacholder, S., Orr, N., Berndt, S. et al. (2009) Identification of a new prostate cancer susceptibility locus on chromosome 8q24. Nat. Genet., 41, 1055-1057.
34. Al Olama, A.A., Kote-Jarai, Z., Giles, G.G., Guy, M., Morrison, J., Severi, G., Leongamornlert, D.A., Tymrakiewicz, M., Jhavar, S., Saunders, E. et al. (2009) Multiple loci on 8q24 associated with prostate cancer susceptibility. Nat. Genet., 41, 1058-1060.
35. Haiman, C.A., Patterson, N., Freedman, M.L., Myers, S.R., Pike, M.C., Waliszewska, A., Neubauer, J., Tandon, A., Schirmer, C., McDonald, G.J. et al. (2007) Multiple regions within 8q24 independently affect risk for prostate cancer. Nat. Genet., 39, 638-644.
36. Long, J., Cai, Q., Shu, X.O., Qu, S., Li, C., Zheng, Y., Gu, K., Wang, W., Xiang, Y.B., Cheng, J. et al. (2010) Identification of a functional genetic variant at 16q12.1 for breast cancer risk: results from the Asia Breast Cancer Consortium. PLoS Genet., 6, e1001002.
37. Waters, K.M., Stram, D.O., Hassanein, M.T., Le Marchand, L., Wilkens, L.R., Maskarinec, G., Monroe, K.R., Kolonel, L.N., Altshuler, D., Henderson, B.E. et al. (2010) Consistent association of type 2 diabetes risk variants found in Europeans in diverse racial and ethnic groups. PLoS Genet., 6, e1001078.
38. Waters, K.M., Le Marchand, L., Kolonel, L.N., Monroe, K.R., Stram, D.O., Henderson, B.E. and Haiman, C.A. (2009) Generalizability of associations from prostate cancer genome-wide association studies in multiple populations. Cancer Epidemiol. Biomarkers Prev., 18, 1285-1289.
39. Sharma, M., Li, X., Wang, Y., Zarnegar, M., Huang, C.-Y., Palvimo, J.J., Lim, B. and Sun, Z. (2003) hZimp10 is an androgen receptor co-activator and forms a complex with SUMO-1 at replication foci. EMBO J., 22, 6101-6114.
40. Li, X., Thyssen, G., Beliakoff, J. and Sun, Z. (2006) The novel PIAS-like protein hZimp10 enhances Smad transcriptional activity. J. Biol. Chem., 281, 23748-23756.
41. Lee, J., Beliakoff, J. and Sun, Z. (2007) The novel PIAS-like protein hZimp10 is a transcriptional co-activator of the p53 tumor suppressor. Nucleic Acids Res., 35, 4523-4534.
42. Udler, M.S., Ahmed, S., Healey, C.S., Meyer, K., Struewing, J., Maranian, M., Kwon, E.M., Zhang, J., Tyrer, J., Karlins, E. et al. (2010) Fine scale mapping of the breast cancer 16q12 locus. Hum. Mol. Genet., 19, 2507-2515.
43. Broeks, A., Schmidt, M.K., Sherman, M.E., Couch, F.J., Hopper, J.L., Dite, G.S., Apicella, C., Smith, L.D., Hammet, F., Southey, M.C. et al. (2011) Low penetrance breast cancer susceptibility loci are associated with specific breast tumor subtypes: findings from the Breast Cancer Association Consortium. Hum. Mol. Genet., 20, 3289-3303.
44. Kolonel, L.N., Henderson, B.E., Hankin, J.H., Nomura, A.M., Wilkens, L.R., Pike, M.C., Stram, D.O., Monroe, K.R., Earle, M.E. and Nagamine, F.S. (2000) A multiethnic cohort in Hawaii and Los Angeles: baseline characteristics. Am. J. Epidemiol., 151, 346-357.
45. Marchbanks, P.A.,McDonald, J.A.,Wilson,H.G.,Burnett,N.M.,Daling, J.R., Bernstein, L., Malone, K.E., Strom, B.L., Norman, S.A., Weiss, L.K. et al. (2002) The NICHD Women's Contraceptive and Reproductive Experiences Study: methods and operational results. Ann. Epidemiol., 12, 213-221.
46. Ambrosone, C.B., Ciupak, G.L., Bandera, E.V., Jandorf, L., Bovbjerg, D.H., Zirpoli, G., Pawlish, K., Godbold, J., Furberg, H., Fatone, A. et al. (2009) Conducting molecular epidemiological research in the age of HIPAA: a multi-institutional case-control study of breast cancer in African-American and European-American women. J. Oncol., 2009, 871250.
47. John, E.M., Schwartz, G.G., Koo, J., Wang, W. and Ingles, S.A. (2007) Sun exposure, vitamin D receptor gene polymorphisms, and breast cancer risk in a multiethnic population. Am. J. Epidemiol., 166, 1409-1419.
48. John, E.M., Hopper, J.L., Beck, J.C., Knight, J.A., Neuhausen, S.L., Senie, R.T., Ziogas, A., Andrulis, I.L., Anton-Culver, H., Boyd, N. et al. (2004) The Breast Cancer Family Registry: an infrastructure for cooperative multinational, interdisciplinary and translational studies of the genetic epidemiology of breast cancer. Breast Cancer Res., 6, R375-R389.
49. Newman, B., Moorman, P.G., Millikan, R., Qaqish, B.F., Geradts, J., Aldrich, T.E. and Liu, E.T. (1995) The Carolina Breast Cancer Study: integrating population-based epidemiology and molecular biology. Breast Cancer Res. Treat, 35, 51-60.
50. Prorok, P.C., Andriole, G.L., Bresalier, R.S., Buys, S.S., Chia, D., Crawford, E.D., Fogel, R., Gelmann, E.P., Gilbert, F., Hasson, M.A. et al. (2000) Design of the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial. Control Clin. Trials, 21, 273S-309S.
51. Smith, T.R., Levine, E.A., Freimanis, R.I., Akman, S.A., Allen, G.O., Hoang, K.N., Liu-Mares, W. and Hu, J.J. (2008) Polygenic model of DNA repair genetic polymorphisms in human breast cancer risk. Carcinogenesis, 29, 2132-2138.
52. Price, A.L., Patterson, N.J., Plenge, R.M., Weinblatt, M.E., Shadick, N.A. and Reich, D. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet., 38, 904-909.
53. Price, A.L., Tandon, A., Patterson, N., Barnes, K.C., Rafaels, N., Ruczinski, I., Beaty, T.H., Mathias, R., Reich, D. and Myers, S. (2009) Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genet., 5, e1000519.
54. Li, Y., Willer, C., Sanna, S. and Abecasis, G. (2009) Genotype imputation. Annu. Rev. Genomics Hum. Genet., 10, 387-406.
55. Pruim, R.J., Welch, R.P., Sanna, S., Teslovich, T.M., Chines, P.S., Gliedt, T.P., Boehnke, M., Abecasis, G.R. and Willer, C.J. (2010) LocusZoom: regional visualization of genome-wide association scan results. Bioinformatics, 26, 2336-2337.