Howlader NNA, Krapcho M, Neyman N, Aminou R, Waldron W, Altekruse SF, Kosary CL, Ruhl J, Tatalovich Z, Cho H, Mariotto A, Eisner MP, Lewis DR, Chen HS, Feuer EJ, Cronin KA, Edwards BK: SEER Cancer Statistics Review 1975–2008. 2011, National Cancer Institute, Bethesda, MD, USA
Google Scholar
Siegel R, Naishadham D, Jemal A: Cancer statistics, 2012. CA Cancer J Clin. 2012, 62 (1): 10-29. 10.3322/caac.20138.
Article
PubMed
Google Scholar
Bove B, Dunbrack RL, Godwin AK: BRCA1, BRCA2, and Hereditary Breast Cancer. Breast Cancer: Prognosis, Treatment and Prevention. Edited by: Pasqualini JR. 2002, Marcel Dekker Inc, New York, NY, USA, 555-624.
Google Scholar
Miki Y, Swensen J, Shattuck-Eidens D, Futreal PA, Harshman K, Tavtigian S, Liu Q, Cochran C, Bennett LM, Ding W, et al: A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. Science. 1994, 266 (5182): 66-71. 10.1126/science.7545954.
Article
CAS
PubMed
Google Scholar
Wooster R, Neuhausen SL, Mangion J, Quirk Y, Ford D, Collins N, Nguyen K, Seal S, Tran T, Averill D, et al: Localization of a breast cancer susceptibility gene, BRCA2, to chromosome 13q12-13. Science. 1994, 265 (5181): 2088-2090. 10.1126/science.8091231.
Article
CAS
PubMed
Google Scholar
King MC, Marks JH, Mandell JB: Breast and ovarian cancer risks due to inherited mutations in BRCA1 and BRCA2. Science. 2003, 302 (5645): 643-646. 10.1126/science.1088759.
Article
CAS
PubMed
Google Scholar
Walsh T, Casadei S, Coats KH, Swisher E, Stray SM, Higgins J, Roach KC, Mandell J, Lee MK, Ciernikova S, et al: Spectrum of mutations in BRCA1, BRCA2, CHEK2, and TP53 in families at high risk of breast cancer. Jama. 2006, 295 (12): 1379-1388. 10.1001/jama.295.12.1379.
Article
CAS
PubMed
Google Scholar
Li J, Yen C, Liaw D, Podsypanina K, Bose S, Wang SI, Puc J, Miliaresis C, Rodgers L, McCombie R, et al: PTEN, a putative protein tyrosine phosphatase gene mutated in human brain, breast, and prostate cancer. Science. 1997, 275 (5308): 1943-1947. 10.1126/science.275.5308.1943.
Article
CAS
PubMed
Google Scholar
Thompson D, Duedal S, Kirner J, McGuffog L, Last J, Reiman A, Byrd P, Taylor M, Easton DF: Cancer risks and mortality in heterozygous ATM mutation carriers. J Natl Cancer Inst. 2005, 97 (11): 813-822. 10.1093/jnci/dji141.
Article
CAS
PubMed
Google Scholar
Meijers-Heijboer H, van den Ouweland A, Klijn J, Wasielewski M, de Snoo A, Oldenburg R, Hollestelle A, Houben M, Crepin E, van Veghel-Plandsoen M, et al: Low-penetrance susceptibility to breast cancer due to CHEK2(*)1100delC in noncarriers of BRCA1 or BRCA2 mutations. Nat Genet. 2002, 31 (1): 55-59. 10.1038/ng879.
Article
CAS
PubMed
Google Scholar
Seal S, Thompson D, Renwick A, Elliott A, Kelly P, Barfoot R, Chagtai T, Jayatilake H, Ahmed M, Spanova K, et al: Truncating mutations in the Fanconi anemia J gene BRIP1 are low-penetrance breast cancer susceptibility alleles. Nat Genet. 2006, 38 (11): 1239-1241. 10.1038/ng1902.
Article
CAS
PubMed
Google Scholar
Xia B, Sheng Q, Nakanishi K, Ohashi A, Wu J, Christ N, Liu X, Jasin M, Couch FJ, Livingston DM: Control of BRCA2 cellular and clinical functions by a nuclear partner, PALB2. Mol Cell. 2006, 22 (6): 719-729. 10.1016/j.molcel.2006.05.022.
Article
CAS
PubMed
Google Scholar
Steffen J, Nowakowska D, Niwinska A, Czapczak D, Kluska A, Piatkowska M, Wisniewska A, Paszko Z: Germline mutations 657del5 of the NBS1 gene contribute significantly to the incidence of breast cancer in Central Poland. Int J Cancer. 2006, 119 (2): 472-475. 10.1002/ijc.21853.
Article
CAS
PubMed
Google Scholar
Heikkinen K, Rapakko K, Karppinen SM, Erkko H, Knuutila S, Lundan T, Mannermaa A, Borresen-Dale AL, Borg A, Barkardottir RB, et al: RAD50 and NBS1 are breast cancer susceptibility genes associated with genomic instability. Carcinogenesis. 2006, 27 (8): 1593-1599.
Article
PubMed Central
CAS
PubMed
Google Scholar
Van't Veer LJ, Paik S, Hayes DF, Van't Veer LJ, Paik S, Hayes DF: Gene expression profiling of breast cancer: a new tumor marker. J Clin Oncol. 2005, 23 (8): 1631-1635. 10.1200/JCO.2005.12.005.
Article
PubMed
Google Scholar
Chen X, Truong TT, Weaver J, Bove BA, Cattie K, Armstrong BA, Daly MB, Godwin AK: Intronic alterations in BRCA1 and BRCA2: effect on mRNA splicing fidelity and expression. Hum Mutat. 2006, 27 (5): 427-435. 10.1002/humu.20319.
Article
CAS
PubMed
Google Scholar
Chen X, Weaver J, Bove BA, Vanderveer LA, Weil SC, Miron A, Daly MB, Godwin AK: Allelic imbalance in BRCA1 and BRCA2 gene expression is associated with an increased breast cancer risk. Hum Mol Genet. 2008, 17 (9): 1336-1348. 10.1093/hmg/ddn022.
Article
CAS
PubMed
Google Scholar
Buckland PR: Allele-specific gene expression differences in humans. Hum Mol Genet. 2004, 13 Spec No 2: R255-R260.
Article
PubMed
Google Scholar
Song MY, Kim HE, Kim S, Choi IH, Lee JK: SNP-based large-scale identification of allele-specific gene expression in human B cells. Gene. 2012, 493 (2): 211-218. 10.1016/j.gene.2011.11.058.
Article
CAS
PubMed
Google Scholar
Ge B, Pokholok DK, Kwan T, Grundberg E, Morcos L, Verlaan DJ, Le J, Koka V, Lam KC, Gagne V, et al: Global patterns of cis variation in human cells revealed by high-density allelic expression analysis. Nat Genet. 2009, 41 (11): 1216-1222. 10.1038/ng.473.
Article
CAS
PubMed
Google Scholar
Gunderson KL: Whole-genome genotyping on bead arrays. Methods Mol Biol. 2009, 529: 197-213. 10.1007/978-1-59745-538-1_13.
Article
CAS
PubMed
Google Scholar
Bjornsson HT, Albert TJ, Ladd-Acosta CM, Green RD, Rongione MA, Middle CM, Irizarry RA, Broman KW, Feinberg AP: SNP-specific array-based allele-specific expression analysis. Genome Res. 2008, 18 (5): 771-779. 10.1101/gr.073254.107.
Article
PubMed Central
CAS
PubMed
Google Scholar
Serre D, Gurd S, Ge B, Sladek R, Sinnett D, Harmsen E, Bibikova M, Chudin E, Barker DL, Dickinson T, et al: Differential allelic expression in the human genome: a robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression. PLoS Genet. 2008, 4 (2): e1000006-10.1371/journal.pgen.1000006.
Article
PubMed Central
PubMed
Google Scholar
Tchatchou S, Riedel A, Lyer S, Schmutzhard J, Strobel-Freidekind O, Gronert-Sum S, Mietag C, D'Amato M, Schlehe B, Hemminki K, et al: Identification of a DMBT1 polymorphism associated with increased breast cancer risk and decreased promoter activity. Hum Mutat. 2010, 31 (1): 60-66. 10.1002/humu.21134.
Article
CAS
PubMed
Google Scholar
Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E: The role of site accessibility in microRNA target recognition. Nat Genet. 2007, 39 (10): 1278-1284. 10.1038/ng2135.
Article
CAS
PubMed
Google Scholar
Daelemans C, Ritchie ME, Smits G, Abu-Amero S, Sudbery IM, Forrest MS, Campino S, Clark TG, Stanier P, Kwiatkowski D, et al: High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta. BMC Genet. 2010, 11: 25-
Article
PubMed Central
PubMed
Google Scholar
Moran VA: Perera RJ. 2012, Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs. Nucleic Acids Res, Khalil AM
Google Scholar
Wapinski O, Chang HY: Long noncoding RNAs and human disease. Trends Cell Biol. 2011, 21 (6): 354-361. 10.1016/j.tcb.2011.04.001.
Article
CAS
PubMed
Google Scholar
Gunderson KL, Steemers FJ, Ren H, Ng P, Zhou L, Tsan C, Chang W, Bullis D, Musmacker J, King C, et al: Whole-genome genotyping. Methods Enzymol. 2006, 410: 359-376.
Article
CAS
PubMed
Google Scholar
Mavaddat N, Antoniou AC, Easton DF, Garcia-Closas M: Genetic susceptibility to breast cancer. Mol Oncol. 2010, 4 (3): 174-191. 10.1016/j.molonc.2010.04.011.
Article
CAS
PubMed
Google Scholar
Easton DF, Pooley KA, Dunning AM, Pharoah PD, Thompson D, Ballinger DG, Struewing JP, Morrison J, Field H, Luben R, et al: Genome-wide association study identifies novel breast cancer susceptibility loci. Nature. 2007, 447 (7148): 1087-1093. 10.1038/nature05887.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hunter DJ, Kraft P, Jacobs KB, Cox DG, Yeager M, Hankinson SE, Wacholder S, Wang Z, Welch R, Hutchinson A, 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. 10.1038/ng2075.
Article
PubMed Central
CAS
PubMed
Google Scholar
Stacey SN, Manolescu A, Sulem P, Rafnar T, Gudmundsson J, Gudjonsson SA, Masson G, Jakobsdottir M, Thorlacius S, Helgason A, et al: Common variants on chromosomes 2q35 and 16q12 confer susceptibility to estrogen receptor-positive breast cancer. Nat Genet. 2007, 39 (7): 865-869. 10.1038/ng2064.
Article
CAS
PubMed
Google Scholar
Ghoussaini M, Fletcher O, Michailidou K, Turnbull C, Schmidt MK, Dicks E, Dennis J, Wang Q, Humphreys MK, Luccarini C, et al: Genome-wide association analysis identifies three new breast cancer susceptibility loci. Nat Genet. 2012, 44 (3): 312-318. 10.1038/ng.1049.
Article
PubMed Central
CAS
PubMed
Google Scholar
McCarthy MI, Hirschhorn JN: Genome-wide association studies: potential next steps on a genetic journey. Hum Mol Genet. 2008, 17 (R2): R156-R165. 10.1093/hmg/ddn289.
Article
PubMed Central
CAS
PubMed
Google Scholar
Easton DF, Eeles RA: Genome-wide association studies in cancer. Hum Mol Genet. 2008, 17 (R2): R109-R115. 10.1093/hmg/ddn287.
Article
CAS
PubMed
Google Scholar
Spencer C, Hechter E, Vukcevic D, Donnelly P: Quantifying the underestimation of relative risks from genome-wide association studies. PLoS Genet. 2011, 7 (3): e1001337-10.1371/journal.pgen.1001337.
Article
PubMed Central
CAS
PubMed
Google Scholar
Meyer KB, Maia AT, O'Reilly M, Teschendorff AE, Chin SF, Caldas C, Ponder BA: Allele-specific up-regulation of FGFR2 increases susceptibility to breast cancer. PLoS Biol. 2008, 6 (5): e108-10.1371/journal.pbio.0060108.
Article
PubMed Central
PubMed
Google Scholar
Pomerantz MM, Ahmadiyeh N, Jia L, Herman P, Verzi MP, Doddapaneni H, Beckwith CA, Chan JA, Hills A, Davis M, et al: The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer. Nat Genet. 2009, 41 (8): 882-884. 10.1038/ng.403.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lei H, Hemminki K, Johansson R, Altieri A, Enquist K, Henriksson R, Lenner P, Forsti A: Single nucleotide polymorphisms in the DMBT1 promoter and the progression of breast cancer. Int J Cancer. 2007, 120 (2): 447-449. 10.1002/ijc.22182.
Article
CAS
PubMed
Google Scholar
Blackburn AC, Hill LZ, Roberts AL, Wang J, Aud D, Jung J, Nikolcheva T, Allard J, Peltz G, Otis CN, et al: Genetic mapping in mice identifies DMBT1 as a candidate modifier of mammary tumors and breast cancer risk. Am J Pathol. 2007, 170 (6): 2030-2041. 10.2353/ajpath.2007.060512.
Article
PubMed Central
CAS
PubMed
Google Scholar
Braidotti P, Nuciforo PG, Mollenhauer J, Poustka A, Pellegrini C, Moro A, Bulfamante G, Coggi G, Bosari S, Pietra GG: DMBT1 expression is down-regulated in breast cancer. BMC cancer. 2004, 4: 46-10.1186/1471-2407-4-46.
Article
PubMed Central
CAS
PubMed
Google Scholar
Mollenhauer J, Helmke B, Medina D, Bergmann G, Gassler N, Muller H, Lyer S, Diedrichs L, Renner M, Wittig R, et al: Carcinogen inducibility in vivo and down-regulation of DMBT1 during breast carcinogenesis. Genes, Chromosomes & Cancer. 2004, 39 (3): 185-194. 10.1002/gcc.10309.
Article
CAS
Google Scholar
Tycko B: Mapping allele-specific DNA methylation: a new tool for maximizing information from GWAS. Am J Hum Genet. 2010, 86 (2): 109-112. 10.1016/j.ajhg.2010.01.021.
Article
PubMed Central
CAS
PubMed
Google Scholar
Futreal PA, Coin L, Marshall M, Down T, Hubbard T, Wooster R, Rahman N, Stratton MR: A census of human cancer genes. Nat Rev Cancer. 2004, 4 (3): 177-183. 10.1038/nrc1299.
Article
PubMed Central
CAS
PubMed
Google Scholar
Klee EW, Hoppman-Chaney NL, Ferber MJ: Expanding DNA diagnostic panel testing: is more better?. Expert Rev Mol Diagn. 2011, 11 (7): 703-709. 10.1586/erm.11.58.
Article
CAS
PubMed
Google Scholar
Godwin AK, Vanderveer L, Schultz DC, Lynch HT, Altomare DA, Buetow KH, Daly M, Getts LA, Masny A, Rosenblum N, et al: A common region of deletion on chromosome 17q in both sporadic and familial epithelial ovarian tumors distal to BRCA1. Am J Hum Genet. 1994, 55 (4): 666-677.
PubMed Central
CAS
PubMed
Google Scholar
Chomczynski P, Sacchi N: Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem. 1987, 162 (1): 156-159.
Article
CAS
PubMed
Google Scholar
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA: Circos: an information aesthetic for comparative genomics. Genome Res. 2009, 19 (9): 1639-1645. 10.1101/gr.092759.109.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wagner JR, Ge B, Pokholok D, Gunderson KL, Pastinen T, Blanchette M: Computational analysis of whole-genome differential allelic expression data in human. PLoS Comput Biol. 2010, 6 (7): e1000849-10.1371/journal.pcbi.1000849.
Article
PubMed Central
PubMed
Google Scholar
Benjamini Y, Hochberg Y: Controlling the False Discovery Rate: A practical and powerful approach to multiple testing. J R Stat Soc. 1995, 57: 289-300.
Google Scholar
Team RDC: R: A language and environment for statistical computing. 2005, In. Edited by Computing RFfS, Vienna
Google Scholar