Risk of GWAS-identified genetic variants for breast cancer in a Chinese population: A multiple interaction analysis

Breast Cancer Research and Treatment

Volumn 142, Issue 3, 2013, Pages 637-644

  Chen, Wei ^a   Song, Haiping ^a   Zhong, Rong ^a   Zhu, Beibei ^a   Guo, Hui ^a   Lou, Jiao ^a   Shen, Na ^a   Li, Jiaoyuan ^a   Chen, Xueqin ^a   Liu, Cheng ^a   Ming, Jie ^a   Huang, Tao ^a   Miao, Xiaoping ^a  

^a HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

Breast cancer; Genome wide association study; Multifactor dimensionality reduction; Random forest; Single nucleotide polymorphism

Indexed keywords

ACCURACY; ADULT; ALLELE; ARTICLE; BREAST CANCER; CANCER RISK; CANCER SUSCEPTIBILITY; CHINESE; CONTROLLED STUDY; FEMALE; GENE DOSAGE; GENETIC ASSOCIATION; HETEROZYGOTE; HUMAN; LOGISTIC REGRESSION ANALYSIS; MAJOR CLINICAL STUDY; MULTIFACTOR DIMENSIONALITY REDUCTION; PRIORITY JOURNAL; RANDOM FOREST; SINGLE NUCLEOTIDE POLYMORPHISM; VALIDATION STUDY;

AGED; ASIAN CONTINENTAL ANCESTRY GROUP; BREAST NEOPLASMS; CASE-CONTROL STUDIES; CHINA; FEMALE; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MIDDLE AGED; POLYMORPHISM, SINGLE NUCLEOTIDE; RECEPTORS, ESTROGEN; RECEPTORS, PROGESTERONE; RISK;

EID: 84890304969     PISSN: 01676806     EISSN: 15737217     Source Type: Journal    
DOI: 10.1007/s10549-013-2775-8     Document Type: Article

References (26)

1. Jemal A, Bray F, Center MM, Ferlay J, Ward E, Forman D (2011) Global cancer statistics. CA Cancer J Clin 61(2):69-90. doi: 10.3322/caac.20107
2. Benson JR, Jatoi I (2012) The global breast cancer burden. Future Oncol 8(6):697-702. doi: 10.2217/fon.12.61
3. Sun T, Miao X, Wang J, Tan W, Zhou Y, Yu C, Lin D (2004) Functional Phe31Ile polymorphism in Aurora A and risk of breast carcinoma. Carcinogenesis 25(11):2225-2230. doi: 10.1093/carcin/bgh244
4. Liu L, Yuan P, Wu C, Zhang X, Guo H, Zhong R, Xu Y, Wu J, Duan S, Rui R, Wu T, Nie S, Miao X, Lin D (2011) A functional -77T>C polymorphism in XRCC1 is associated with risk of breast cancer. Breast Cancer Res Treat 125(2):479-487. doi: 10.1007/s10549-010-0959-z
5. Murabito JM, Rosenberg CL, Finger D, Kreger BE, Levy D, Splansky GL, Antman K, Hwang SJ (2007) A genome-wide association study of breast and prostate cancer in the NHLBI's Framingham Heart Study. BMC Med Genet 8(Suppl 1):S6. doi: 10.1186/1471-2350-8-S1-S6
6. Turnbull C, Ahmed S, Morrison J, Pernet D, Renwick A, Maranian M, Seal S, Ghoussaini M, Hines S, Healey CS, Hughes D, Warren-Perry M, Tapper W, Eccles D, Evans DG, Hooning M, Schutte M, van den Ouweland A, Houlston R, Ross G, Langford C, Pharoah PD, Stratton MR, Dunning AM, Rahman N, Easton DF (2010) Genome-wide association study identifies five new breast cancer susceptibility loci. Nat Genet 42(6):504-507. doi: 10.1038/ng.586
7. Stacey SN, Manolescu A, Sulem P, Thorlacius S, Gudjonsson SA, Jonsson GF, Jakobsdottir M, Bergthorsson JT, Gudmundsson J, Aben KK, Strobbe LJ, Swinkels DW, van Engelenburg KC, Henderson BE, Kolonel LN, Le Marchand L, Millastre E, Andres R, Saez B, Lambea J, Godino J, Polo E, Tres A, Picelli S, Rantala J, Margolin S, Jonsson T, Sigurdsson H, Jonsdottir T, Hrafnkelsson J, Johannsson J, Sveinsson T, Myrdal G, Grimsson HN, Sveinsdottir SG, Alexiusdottir K, Saemundsdottir J, Sigurdsson A, Kostic J, Gudmundsson L, Kristjansson K, Masson G, Fackenthal JD, Adebamowo C, Ogundiran T, Olopade OI, Haiman CA, Lindblom A, Mayordomo JI, Kiemeney LA, Gulcher JR, Rafnar T, Thorsteinsdottir U, Johannsson OT, Kong A, Stefansson K (2008) Common variants on chromosome 5p12 confer susceptibility to estrogen receptor-positive breast cancer. Nat Genet 40(6):703-706. doi: 10.1038/ng.131
8. Stacey SN, Manolescu A, Sulem P, Rafnar T, Gudmundsson J, Gudjonsson SA, Masson G, Jakobsdottir M, Thorlacius S, Helgason A, Aben KK, Strobbe LJ, Albers-Akkers MT, Swinkels DW, Henderson BE, Kolonel LN, Le Marchand L, Millastre E, Andres R, Godino J, Garcia-Prats MD, Polo E, Tres A, Mouy M, Saemundsdottir J, Backman VM, Gudmundsson L, Kristjansson K, Bergthorsson JT, Kostic J, Frigge ML, Geller F, Gudbjartsson D, Sigurdsson H, Jonsdottir T, Hrafnkelsson J, Johannsson J, Sveinsson T, Myrdal G, Grimsson HN, Jonsson T, von Holst S, Werelius B, Margolin S, Lindblom A, Mayordomo JI, Haiman CA, Kiemeney LA, Johannsson OT, Gulcher JR, Thorsteinsdottir U, Kong A, Stefansson K (2007) Common variants on chromosomes 2q35 and 16q12 confer susceptibility to estrogen receptor-positive breast cancer. Nat Genet 39(7):865-869. doi: 10.1038/ng2064
9. Easton DF, Pooley KA, Dunning AM, Pharoah PD, Thompson D, Ballinger DG, Struewing JP, Morrison J, Field H, Luben R, Wareham N, Ahmed S, Healey CS, Bowman R, Meyer KB, Haiman CA, Kolonel LK, Henderson BE, Le Marchand L, Brennan P, Sangrajrang S, Gaborieau V, Odefrey F, Shen CY, Wu PE, Wang HC, Eccles D, Evans DG, Peto J, Fletcher O, Johnson N, Seal S, Stratton MR, Rahman N, Chenevix-Trench G, Bojesen SE, Nordestgaard BG, Axelsson CK, Garcia-Closas M, Brinton L, Chanock S, Lissowska J, Peplonska B, Nevanlinna H, Fagerholm R, Eerola H, Kang D, Yoo KY, Noh DY, Ahn SH, Hunter DJ, Hankinson SE, Cox DG, Hall P, Wedren S, Liu J, Low YL, Bogdanova N, Schurmann P, Dork T, Tollenaar RA, Jacobi CE, Devilee P, Klijn JG, Sigurdson AJ, Doody MM, Alexander BH, Zhang J, Cox A, Brock IW, MacPherson G, Reed MW, Couch FJ, Goode EL, Olson JE, Meijers-Heijboer H, van den Ouweland A, Uitterlinden A, Rivadeneira F, Milne RL, Ribas G, Gonzalez-Neira A, Benitez J, Hopper JL, McCredie M, Southey M, Giles GG, Schroen C, Justenhoven C, Brauch H, Hamann U, Ko YD, Spurdle AB, Beesley J, Chen X, Mannermaa A, Kosma VM, Kataja V, Hartikainen J, Day NE, Cox DR, Ponder BA (2007) Genome-wide association study identifies novel breast cancer susceptibility loci. Nature 447(7148):1087-1093. doi: 10.1038/nature05887
10. Thomas G, Jacobs KB, Kraft P, Yeager M, Wacholder S, Cox DG, Hankinson SE, Hutchinson A, Wang Z, Yu K, Chatterjee N, Garcia-Closas M, Gonzalez-Bosquet J, Prokunina-Olsson L, Orr N, Willett WC, Colditz GA, Ziegler RG, Berg CD, Buys SS, McCarty CA, Feigelson HS, Calle EE, Thun MJ, Diver R, Prentice R, Jackson R, Kooperberg C, Chlebowski R, Lissowska J, Peplonska B, Brinton LA, Sigurdson A, Doody M, Bhatti P, Alexander BH, Buring J, Lee IM, Vatten LJ, Hveem K, Kumle M, Hayes RB, Tucker M, Gerhard DS, Fraumeni JF Jr, Hoover RN, Chanock SJ, Hunter DJ (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(5):579-584. doi: 10.1038/ng.353
11. Li J, Humphreys K, Heikkinen T, Aittomaki K, Blomqvist C, Pharoah PD, Dunning AM, Ahmed S, Hooning MJ, Martens JW, van den Ouweland AM, Alfredsson L, Palotie A, Peltonen-Palotie L, Irwanto A, Low HQ, Teoh GH, Thalamuthu A, Easton DF, Nevanlinna H, Liu J, Czene K, Hall P (2011) A combined analysis of genome-wide association studies in breast cancer. Breast Cancer Res Treat 126(3):717-727. doi: 10.1007/s10549-010-1172-9
12. Kim HC, Lee JY, Sung H, Choi JY, Park SK, Lee KM, Kim YJ, Go MJ, Li L, Cho YS, Park M, Kim DJ, Oh JH, Kim JW, Jeon JP, Jeon SY, Min H, Kim HM, Park J, Yoo KY, Noh DY, Ahn SH, Lee MH, Kim SW, Lee JW, Park BW, Park WY, Kim EH, Kim MK, Han W, Lee SA, Matsuo K, Shen CY, Wu PE, Hsiung CN, Kim HL, Han BG, Kang D (2012) A genome-wide association study identifies a breast cancer risk variant in ERBB4 at 2q34: results from the Seoul Breast Cancer Study. Breast Cancer Res 14(2):R56. doi: 10.1186/bcr3158
13. Hunter DJ, Kraft P, Jacobs KB, Cox DG, Yeager M, Hankinson SE, Wacholder S, Wang Z, Welch R, Hutchinson A, Wang J, Yu K, Chatterjee N, Orr N, Willett WC, Colditz GA, Ziegler RG, Berg CD, Buys SS, McCarty CA, Feigelson HS, Calle EE, Thun MJ, Hayes RB, Tucker M, Gerhard DS, Fraumeni JF Jr, Hoover RN, Thomas G, Chanock SJ (2007) A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer. Nat Genet 39(7):870-874. doi: 10.1038/ng2075
14. Fletcher O, Johnson N, Orr N, Hosking FJ, Gibson LJ, Walker K, Zelenika D, Gut I, Heath S, Palles C, Coupland B, Broderick P, Schoemaker M, Jones M, Williamson J, Chilcott-Burns S, Tomczyk K, Simpson G, Jacobs KB, Chanock SJ, Hunter DJ, Tomlinson IP, Swerdlow A, Ashworth A, Ross G, dos Santos Silva I, Lathrop M, Houlston RS, Peto J (2011) Novel breast cancer susceptibility locus at 9q31.2: results of a genome-wide association study. J Natl Cancer Inst 103(5):425-435. doi: 10.1093/jnci/djq563
15. Zheng W, Long J, Gao YT, Li C, Zheng Y, Xiang YB, Wen W, Levy S, Deming SL, Haines JL, Gu K, Fair AM, Cai Q, Lu W, Shu XO (2009) Genome-wide association study identifies a new breast cancer susceptibility locus at 6q25.1. Nat Genet 41(3):324-328. doi: 10.1038/ng.318
16. Zhong R, Liu L, Zou L, Sheng W, Zhu B, Xiang H, Chen W, Chen J, Rui R, Zheng X, Yin J, Duan S, Yang B, Sun J, Lou J, Xie D, Xu Y, Nie S, Miao X (2013) Genetic variations in the TGFbeta signaling pathway, smoking and risk of colorectal cancer in a Chinese population. Carcinogenesis 34(4):936-942. doi: 10.1093/carcin/bgs395
17. Lin HY, Chen YA, Tsai YY, Qu X, Tseng TS, Park JY (2012) TRM: a powerful two-stage machine learning approach for identifying SNP-SNP interactions. Ann Hum Genet 76(1):53-62. doi: 10.1111/j.1469-1809.2011.00692.x
18. Hahn LW, Ritchie MD, Moore JH (2003) Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactions. Bioinformatics 19(3):376-382
19. Ritchie MD, Hahn LW, Roodi N, Bailey LR, Dupont WD, Parl FF, Moore JH (2001) Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer. Am J Hum Genet 69(1):138-147. doi: 10.1086/321276
20. Liu L, Wu C, Wang Y, Zhong R, Wang F, Zhang X, Duan S, Lou J, Yu D, Tan W, Yuan J, Wu T, Nie S, Miao X, Lin D (2011) Association of candidate genetic variations with gastric cardia adenocarcinoma in Chinese population: a multiple interaction analysis. Carcinogenesis 32(3):336-342. doi: 10.1093/carcin/bgq264
21. Liu L, Wu J, Zhong R, Wu C, Zou L, Yang B, Chen W, Zhu B, Duan S, Yu D, Tan W, Nie S, Lin D, Miao X (2012) Multi-loci analysis reveals the importance of genetic variations in sensitivity of platinum-based chemotherapy in non-small-cell lung cancer. Mol Carcinog. doi: 10.1002/mc.21942
22. Chen W, Zhong R, Ming J, Zou L, Zhu B, Lu X, Ke J, Zhang Y, Liu L, Miao X, Huang T (2012) The SLC4A7 variant rs4973768 is associated with breast cancer risk: evidence from a case-control study and a meta-analysis. Breast Cancer Res Treat 136(3):847-857. doi: 10.1007/s10549-012-2309-9
23. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A, Cho JH, Guttmacher AE, Kong A, Kruglyak L, Mardis E, Rotimi CN, Slatkin M, Valle D, Whittemore AS, Boehnke M, Clark AG, Eichler EE, Gibson G, Haines JL, Mackay TF, McCarroll SA, Visscher PM (2009) Finding the missing heritability of complex diseases. Nature 461(7265):747-753. doi: 10.1038/nature08494
24. Bloom JS, Ehrenreich IM, Loo WT, Lite TL, Kruglyak L (2013) Finding the sources of missing heritability in a yeast cross. Nature 494(7436):234-237. doi: 10.1038/nature11867
25. Barzan D, Veldwijk MR, Herskind C, Li Y, Zhang B, Sperk E, Du WD, Zhang XJ, Wenz F (2013) Comparison of genetic variation of breast cancer susceptibility genes in Chinese and German populations. Eur J Hum Genet. doi: 10.1038/ejhg.2013.38
26. Kumar S, Flacke JP, Kostin S, Appukuttan A, Reusch HP, Ladilov Y (2011) SLC4A7 sodium bicarbonate co-transporter controls mitochondrial apoptosis in ischaemic coronary endothelial cells. Cardiovasc Res 89(2):392-400. doi: 10.1093/cvr/cvq330