Assessing SNP-SNP Interactions among DNA Repair, Modification and Metabolism Related Pathway Genes in Breast Cancer Susceptibility

PLoS ONE

Volumn 8, Issue 6, 2013, Pages

  Sapkota, Yadav ^a,b   Mackey, John R ^a,b   Lai, Raymond ^b   Franco Villalobos, Conrado ^b   Lupichuk, Sasha ^c,e   Robson, Paula J ^b,d   Kopciuk, Karen ^c   Cass, Carol E ^a,b   Yasui, Yutaka ^b   Damaraju, Sambasivarao ^a,b  

^a CROSS CANCER INSTITUTE   (Canada)

^b UNIVERSITY OF ALBERTA   (Canada)

^c UNIVERSITY OF CALGARY   (Canada)

^d ALBERTA HEALTH SERVICES   (Canada)

^e TOM BAKER CANCER CENTRE   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; AGED; APEX1 GENE; ARTICLE; BODY MASS; BRCA2 GENE; BREAST CANCER; BREAST CARCINOGENESIS; CANADA; CANCER RISK; CANCER SUSCEPTIBILITY; CAUCASIAN; CONTROLLED STUDY; DNA METABOLISM; DNA MODIFICATION; DNA REPAIR; EPISTASIS; FEMALE; GENE FREQUENCY; GENE FUNCTION; GENE INTERACTION; GENE LOCUS; GENETIC ASSOCIATION; GENETIC VARIABILITY; HUMAN; MAJOR CLINICAL STUDY; MBD2 GENE; MDM2 GENE; MLH1 GENE; RPAP1 GENE; SINGLE NUCLEOTIDE POLYMORPHISM; TUMOR GENE; BREAST TUMOR; GENETIC PREDISPOSITION; GENETICS; METABOLISM; MIDDLE AGED; SIGNAL TRANSDUCTION; STATISTICAL MODEL;

ADULT; AGED; BREAST NEOPLASMS; DNA REPAIR; FEMALE; GENETIC PREDISPOSITION TO DISEASE; HUMANS; LOGISTIC MODELS; MIDDLE AGED; POLYMORPHISM, SINGLE NUCLEOTIDE; SIGNAL TRANSDUCTION;

EID: 84878634812     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0064896     Document Type: Article

References (44)

1. Collaborative Group on Hormonal Factors in Breast Cancer (2001) Familial breast cancer: Collaborative reanalysis of individual data from 52 epidemiological studies including 58,209 women with breast cancer and 101,986 women without the disease. Lancet 358: 1389-1399.
2. Lichtenstein P, Holm NV, Verkasalo PK, Iliadou A, Kaprio J, et al. (2000) Environmental and heritable factors in the causation of cancer-analyses of cohorts of twins from sweden, denmark, and finland. The New England Journal of Medicine 343: 78-85.
3. Hall JM, Lee MK, Newman B, Morrow JE, Anderson LA, et al. (1990) Linkage of early-onset familial breast cancer to chromosome 17q21. Science (New York, N.Y.) 250: 1684-1689.
4. Wooster R, Bignell G, Lancaster J, Swift S, Seal S, et al. (1995) Identification of the breast cancer susceptibility gene BRCA2. Nature 378: 789-792.
5. Renwick A, Thompson D, Seal S, Kelly P, Chagtai T, et al. (2006) ATM mutations that cause ataxia-telangiectasia are breast cancer susceptibility alleles. Nature Genetics 38: 873-875.
6. Liaw D, Marsh DJ, Li J, Dahia PL, Wang SI, et al. (1997) Germline mutations of the PTEN gene in cowden disease, an inherited breast and thyroid cancer syndrome. Nature Genetics 16: 64-67.
7. Malkin D, Li FP, Strong LC, Fraumeni JF, Nelson CE, et al. (1990) Germ line p53 mutations in a familial syndrome of breast cancer, sarcomas, and other neoplasms. Science (New York, N.Y.) 250: 1233-1238.
8. Seal S, Thompson D, Renwick A, Elliott A, Kelly P, et al. (2006) Truncating mutations in the fanconi anemia J gene BRIP1 are low-penetrance breast cancer susceptibility alleles. Nature Genetics 38: 1239-1241.
9. Rahman N, Seal S, Thompson D, Kelly P, Renwick A, et al. (2007) PALB2, which encodes a BRCA2-interacting protein, is a breast cancer susceptibility gene. Nature Genetics 39: 165-167.
10. CHEK2 Breast Cancer Case-Control Consortium (2004) CHEK2*1100delC and susceptibility to breast cancer: A collaborative analysis involving 10,860 breast cancer cases and 9,065 controls from 10 studies. American Journal of Human Genetics 74: 1175-1182.
11. Shen J, Desai M, Agrawal M, Kennedy DO, Senie RT, et al. (2006) Polymorphisms in nucleotide excision repair genes and DNA repair capacity phenotype in sisters discordant for breast cancer. Cancer Epidemiology, Biomarkers & Prevention 15: 1614-1619.
12. Easton DF, Pooley KA, Dunning AM, Pharoah PD, Thompson D, et al. (2007) Genome-wide association study identifies novel breast cancer susceptibility loci. Nature 447: 1087-1093.
13. Pharoah PD, Antoniou AC, Easton DF, Ponder BA, (2008) Polygenes, risk prediction, and targeted prevention of breast cancer. The New England Journal of Medicine 358: 2796-2803.
14. Ahmed S, Thomas G, Ghoussaini M, Healey CS, Humphreys MK, et al. (2009) Newly discovered breast cancer susceptibility loci on 3p24 and 17q23.2. Nature Genetics 41: 585-590.
15. Cox A, Dunning AM, Garcia-Closas M, Balasubramanian S, Reed MW, et al. (2007) A common coding variant in CASP8 is associated with breast cancer risk. Nature Genetics 39: 352-358.
16. Ghoussaini M, Fletcher O, Michailidou K, Turnbull C, Schmidt MK, et al. (2012) Genome-wide association analysis identifies three new breast cancer susceptibility loci. Nature Genetics 44: 312-318.
17. Gold B, Kirchhoff T, Stefanov S, Lautenberger J, Viale A, et al. (2008) Genome-wide association study provides evidence for a breast cancer risk locus at 6q22.33. Proceedings of the National Academy of Sciences of the United States of America 105: 4340-4345.
18. Hunter DJ, Kraft P, Jacobs KB, Cox DG, Yeager M, et al. (2007) A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer. Nature Genetics 39: 870-874.
19. Sehrawat B, Sridharan M, Ghosh S, Robson P, Cass CE, et al. (2011) Potential novel candidate polymorphisms identified in genome-wide association study for breast cancer susceptibility. Human Genetics 130: 529-537.
20. Stacey SN, Manolescu A, Sulem P, Thorlacius S, Gudjonsson SA, et al. (2008) Common variants on chromosome 5p12 confer susceptibility to estrogen receptor-positive breast cancer. Nature Genetics 40: 703-706.
21. Thomas G, Jacobs KB, Kraft P, Yeager M, Wacholder S, et al. (2009) A multistage genome-wide association study in breast cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1). Nature Genetics 41: 579-584.
22. Moore J, (2003) The ubiquitous nature of epistasis in determining susceptibility to common human diseases. Human Heredity 56: 73-82.
23. Moore JH, (2005) A global view of epistasis. Nature Genetics 37: 13-14.
24. Lo S, Chernoff H, Cong L, Ding Y, Zheng T, (2008) Discovering interactions among BRCA1 and other candidate genes associated with sporadic breast cancer. Proceedings of the National Academy of Sciences of the United States of America 105: 12387-12392.
25. Onay VU, Briollais L, Knight JA, Shi E, Wang Y, et al. (2006) SNP-SNP interactions in breast cancer susceptibility. Bmc Cancer 6: 114.
26. Sapkota Y, Robson P, Lai R, Cass CE, Mackey JR, et al. (2012) A two-stage association study identifies methyl-CpG-binding domain protein 2 gene polymorphisms as candidates for breast cancer susceptibility. European Journal of Human Genetics 20: 682-689.
27. Smith TR, Levine EA, Freimanis RI, Akman SA, Allen GO, et al. (2008) Polygenic model of DNA repair genetic polymorphisms in human breast cancer risk. Carcinogenesis 29: 2132-2138.
28. Conde J, Silva SN, Azevedo AP, Teixeira V, Pina JE, et al. (2009) Association of common variants in mismatch repair genes and breast cancer susceptibility: A multigene study. Bmc Cancer 9: 344-2407-9-344.
29. Boersma BJ, Howe TM, Goodman JE, Yfantis HG, Lee DH, et al. (2006) Association of breast cancer outcome with status of p53 and MDM2 SNP309. Journal of the National Cancer Institute 98: 911-919.
30. Gochhait S, Bukhari SIA, Bairwa N, Vadhera S, Darvishi K, et al. (2007) Implication of BRCA2-26G>A 5′ untranslated region polymorphism in susceptibility to sporadic breast cancer and its modulation by p53 codon 72 arg >pro polymorphism. Breast Cancer Research 9: R71.
31. Rajaraman P, Bhatti P, Doody MM, Simon SL, Weinstock RM, et al. (2008) Nucleotide excision repair polymorphisms may modify ionizing radiation-related breast cancer risk in US radiologic technologists. International Journal of Cancer 123: 2713-2716.
32. Mitra AK, Singh N, Singh A, Garg VK, Agarwal A, et al. (2008) Association of polymorphisms in base excision repair genes with the risk of breast cancer: A case-control study in north indian women. Oncology Research 17: 127-135.
33. Economopoulos KP, Sergentanis TN, (2010) XRCC3 Thr241Met polymorphism and breast cancer risk: A meta-analysis. Breast Cancer Research and Treatment 121: 439-443.
34. Leng S, Bernauer A, Stidley CA, Picchi MA, Sheng X, et al. (2008) Association between common genetic variation in cockayne syndrome A and B genes and nucleotide excision repair capacity among smokers. Cancer Epidemiology Biomarkers & Prevention 17: 2062-2069.
35. Roberts MR, Shields PG, Ambrosone CB, Nie J, Marian C, et al. (2011) Single-nucleotide polymorphisms in DNA repair genes and association with breast cancer risk in the web study. Carcinogenesis 32: 1223-1230.
36. Rao NM, Pai SA, Shinde SR, Ghosh SN, (1998) Reduced DNA repair capacity in breast cancer patients and unaffected individuals from breast cancer families. Cancer Genetics and Cytogenetics 102: 65-73.
37. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, et al. (2007) PLINK: A tool set for whole-genome association and population-based linkage analyses. American Journal of Human Genetics 81: 559-575.
38. Benjamini Y, Hochberg Y, (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series B (Methodological) 57: 289-300.
39. Dinu I, Mahasirimongkol S, Liu Q, Yanai H, Eldin NS, et al. (2012) SNP-SNP interactions discovered by logic regression explain crohn's disease genetics. Plos One 7: e43035.
40. Feng Q, Balasubramanian A, Hawes SE, Toure P, Sow PS, et al. (2005) Detection of hypermethylated genes in women with and without cervical neoplasia. Journal of the National Cancer Institute 97: 273-282.
41. Kooperberg C, Ruczinski I (2012) LogicReg: Logic regression. R package version 1.5.3. Available: http://CRAN.R-project.org/package=LogicReg. Accessed 2013 January 10.
42. R Core Team. (2012) R: A language and environment for statistical computing. R foundation for statistical computing, vienna, austria. ISBN 3-900051-07-0, URL http://www.R-project.org/. Accessed 2013 January 10.
43. Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, et al. (2010) The GeneMANIA prediction server: Biological network integration for gene prioritization and predicting gene function. Nucleic Acids Research 38: W214-20.
44. Wood RD, Mitchell M, Sgouros J, Lindahl T, (2001) Human DNA repair genes. Science (New York, N.Y.) 291: 1284-1289.