Evaluating new candidate SNPs as low penetrance risk factors in sporadic breast cancer: A two-stage Spanish case-control study

Gynecologic Oncology

Volumn 112, Issue 1, 2009, Pages 210-214

  Vega, Ana ^a   Salas, Antonio ^b   Milne, Roger L ^c   Carracedo, Begoña ^a   Ribas, Gloria ^c   Ruibal, Álvaro ^d   de León, Antonio Cabrera ^e   González Hernández, Ana ^f   Benítez, Javier ^c   Carracedo, Ángel ^a,b  

^a CENTRO DE INVESTIGACIÓN BIOMÉDICA EN RED DE ENFERMEDADES RARAS CIBERER   (Spain)

^b Facultad de Medicina   (Spain)

^c Centro Nacional de Investigaciones Oncológicas   (Spain)

^d Instituto de Salud Carlos III   (Spain)

^e UNIVERSIDAD DE LA LAGUNA   (Spain)

^f HOSPITAL UNIVERSITARIO NUESTRA SEÑORA DE CANDELARIA   (Spain)

Author keywords

Association study; Breast cancer; Candidate genes; Case control; Gene gene interaction; SNPs

Indexed keywords

GENOMIC DNA;

ADULT; AGED; ARTICLE; BREAST CANCER; CANCER RISK; CASE CONTROL STUDY; CHI SQUARE TEST; CONTROLLED STUDY; DNA ISOLATION; FEMALE; GENE INTERACTION; GENETIC ASSOCIATION; GENETIC RISK; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENOTYPE; HIGH THROUGHPUT SCREENING; HISPANIC; HUMAN; HUMAN CELL; HUS1 GENE; MULTIFACTORIAL INHERITANCE; PENETRANCE; PRIORITY JOURNAL; RISK ASSESSMENT; SINGLE NUCLEOTIDE POLYMORPHISM; TUMOR GENE;

ADULT; AGED; AGED, 80 AND OVER; ALLELES; BREAST NEOPLASMS; CELL CYCLE PROTEINS; FEMALE; GENETIC PREDISPOSITION TO DISEASE; GENOTYPE; HAPLOTYPES; HUMANS; MIDDLE AGED; PENETRANCE; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 57649099402     PISSN: 00908258     EISSN: 10956859     Source Type: Journal    
DOI: 10.1016/j.ygyno.2008.09.012     Document Type: Article

References (40)

1. Thompson D., and Easton D. The genetic epidemiology of breast cancer genes. J. Mammary. Gland. Biol. Neoplasia. 9 (2004) 221-236
2. Antoniou A.C., Pharoah P.D., McMullan G., Day N.E., Stratton M.R., Peto J., et al. A comprehensive model for familial breast cancer incorporating BRCA1, BRCA2 and other genes. Br. J. Cancer 86 (2002) 76-83
3. Altshuler D., Brooks L.D., Chakravarti A., Collins F.S., Daly M.J., and Donnelly P. A haplotype map of the human genome. Nature 437 (2005) 1299-1320
4. Dunning A.M., Healey C.S., Pharoah P.D., Teare M.D., Ponder B.A., and Easton D.F. A systematic review of genetic polymorphisms and breast cancer risk. Cancer Epidemiol. Biomarkers Prev. 8 (1999) 843-854
5. Lee K.M., Choi J.Y., Park S.K., Chung H.W., Ahn B., Yoo K.Y., et al. Genetic polymorphisms of ataxia telangiectasia mutated and breast cancer risk. Cancer Epidemiol. Biomarkers. Prev. 14 (2005) 821-825
6. Angele S., Romestaing P., Moullan N., Vuillaume M., Chapot B., Friesen M., et al. ATM haplotypes and cellular response to DNA damage: association with breast cancer risk and clinical radiosensitivity. Cancer Res. 63 (2003) 8717-8725
7. Szabo C.I., Schutte M., Broeks A., Houwing-Duistermaat J.J., Thorstenson Y.R., Durocher F., et al. Are ATM mutations 7271T→G and IVS10-6T→G really high-risk breast cancer-susceptibility alleles?. Cancer Res. 64 (2004) 840-843
8. Lindeman G.J., Hiew M., Visvader J.E., Leary J., Field M., Gaff C.L., et al. Frequency of the ATM IVS10-6T→G variant in Australian multiple-case breast cancer families. Breast Cancer Res. 6 (2004) R401-407
9. Bernstein L., Teal C.R., Joslyn S., and Wilson J. Ethnicity-related variation in breast cancer risk factors. Cancer 97 (2003) 222-229
10. Maguire P., Holmberg K., Kost-Alimova M., Imreh S., Skoog L., and Lindblom A. CGH analysis of familial non-BRCA1/BRCA2 breast tumors and mutation screening of a candidate locus on chromosome 17q11.2-12. Int. J. Mol. Med. 16 (2005) 135-141
11. Gold B., Kalush F., Bergeron J., Scott K., Mitra N., Wilson K., et al. Estrogen receptor genotypes and haplotypes associated with breast cancer risk. Cancer. Res. 64 (2004) 8891-8900
12. Wedren S., Lovmar L., Humphreys K., Magnusson C., Melhus H., Syvanen A.C., et al. Oestrogen receptor alpha gene haplotype and postmenopausal breast cancer risk: a case control study. Breast. Cancer. Res. 6 (2004) R437-449
13. Tamimi R.M., Hankinson S.E., Spiegelman D., Kraft P., Colditz G.A., and Hunter D.J. Common ataxia telangiectasia mutated haplotypes and risk of breast cancer: a nested case-control study. Breast Cancer Res. 6 (2004) R416-422
14. Cox D.G., Kraft P., Hankinson S.E., and Hunter D.J. Haplotype analysis of common variants in the BRCA1 gene and risk of sporadic breast cancer. Breast Cancer Res. 7 (2005) R171-175
15. Benusiglio P.R., Lesueur F., Luccarini C., Conroy D.M., Shah M., Easton D.F., et al. Common ERBB2 polymorphisms and risk of breast cancer in a white British population: a case-control study. Breast Cancer Res. 7 (2005) R204-209
16. Lesueur F., Pharoah P.D., Laing S., Ahmed S., Jordan C., Smith P.L., et al. Allelic association of the human homologue of the mouse modifier Ptprj with breast cancer. Hum. Mol. Genet. 14 (2005) 2349-2356
17. Barroso E., Milne R.L., Fernández L.P., Zamora P., Arias J.I., Benitez J., et al. FANCD2 associated with sporadic breast cancer risk. Carcinogenesis 27 (2006) 1930-1937
18. Milne R.L., Ribas G., González-Neira A., Fagerholm R., Salas A., González E., et al. ERCC4 associated with breast cancer risk. A two-stage case-control study using high-throughput genotyping. Cancer Res. 66 (2006) 9420-9427
19. Kammerer S., Roth R.B., Reneland R., Marnellos G., Hoyal C.R., Markward N.J., et al. Large-scale association study identifies ICAM gene region as breast and prostate cancer susceptibility locus. Cancer Res. 64 (2004) 8906-8910
20. Kammerer S., Roth R.B., Hoyal C.R., Reneland R., Marnellos G., Kiechle M., et al. Association of the NuMA region on chromosome 11q13 with breast cancer susceptibility. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 2004-2009
21. Hoyal C.R., Kammerer S., Roth R.B., Reneland R., Marnellos G., Kiechle M., et al. Genetic polymorphisms in DPF3 associated with risk of breast cancer and lymph node metastases. J. Carcinog. 4 (2005) 13
22. Stacey S.N., Manolescu A., Sulem P., Thorlacius S., Gudjonsson S.A., Jonsson G.F., et al. Common variants on chromosome 5p12 confer susceptibility to estrogen receptor-positive breast cancer. Nat Genet 40 (2008) 703-706
23. Stacey S.N., Manolescu A., Sulem P., Rafnar T., Gudmundsson J., Gudjonsson S.A., et al. Common variants on chromosomes 2q35 and 16q12 confer susceptibility to estrogen receptor-positive breast cancer. Nat Genet 39 (2007) 865-869
24. Hunter D.J., Kraft P., Jacobs K.B., Cox D.G., Yeager M., Hankinson S.E., et al. A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer. Nat Genet 39 (2007) 870-874
25. Easton D.F., Pooley K.A., Dunning A.M., Pharoah P.D., Thompson D., Ballinger D.G., et al. Genome-wide association study identifies novel breast cancer susceptibility loci. Nature 447 (2007) 1087-1093
26. Nyholt D.R. A simple correction for multiple testing for single-nucleotide polymorphisms in linkage disequilibrium with each other. Am. J. Hum. Genet. 74 (2004) 765-769
27. Nyholt D.R. Evaluation of Nyholt's procedure for multiple testing correction - author's reply. Hum. Hered. 60 (2005) 61-62
28. Li J., and Ji L. Adjusting multiple testing in multilocus analyses using the eigenvalues of a correlation matrix. Heredity 95 (2005) 221-227
29. Benjamini Y., and Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B 57 (1995) 289-300
30. Barrett J.C., Fry B., Maller J., and Daly M.J. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21 (2005) 263-265
31. Dudbridge F. Pedigree disequilibrium tests for multilocus haplotypes. Genet. Epidemiol. 25 (2003) 115-121
32. Vega A., Salas A., Phillips C., Sobrino B., Carracedo B., Ruiz-Ponte C., et al. Large-scale single nucleotide polymorphism analysis of candidates for low-penetrance breast cancer genes. Breast Cancer Res. 7 Suppl. 22 (2005) S22-22
33. Ritchie M.D., Hahn L.W., and Moore J.H. Power of multifactor dimensionality reduction for detecting gene-gene interactions in the presence of genotyping error, missing data, phenocopy, and genetic heterogeneity. Genet. Epidemiol. 24 (2003) 150-157
34. Ritchie M.D., Hahn L.W., Roodi N., Bailey L.R., Dupont W.D., Parl F.F., et al. Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer. Am. J. Hum. Genet. 69 (2001) 138-147
35. Hahn L.W., Ritchie M.D., and Moore J.H. Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactions. Bioinformatics 19 (2003) 376-382
36. Pritchard J.K., Stephens M., and Donnelly P. Inference of population structure using multilocus genotype data. Genetics 155 (2000) 945-959
37. Ribas G., Gonzalez-Neira A., Salas A., Milne R.L., Vega A., Carracedo B., et al. Evaluating HapMap SNP data transferability in a large-scale genotyping project involving 175 cancer-associated genes. Hum. Genet. 118 (2006) 669-679
38. Zimmerman E.S., Chen J., Andersen J.L., Ardon O., Dehart J.L., Blackett J., et al. Human immunodeficiency virus type 1 Vpr-mediated G2 arrest requires Rad17 and Hus1 and induces nuclear BRCA1 and gamma-H2AX focus formation. Mol. Cell. Biol. 24 (2004) 9286-9294
39. Huang J., Yuan H., Lu C., Liu X., Cao X., and Wan M. Jab1 mediates protein degradation of the Rad9-Rad1-Hus1 checkpoint complex. J. Mol. Biol. 371 (2007) 514-527
40. Ioannidis J.P., Ntzani E.E., and Trikalinos T.A. 'Racial' differences in genetic effects for complex diseases. Nat. Genet. 36 (2004) 1312-1318