Masood E: A consortium plans free SNP map of human genome. Nature. 1999, 398: 545-546. 10.1038/19126.
Article
CAS
PubMed
Google Scholar
Miki Y, Swensen J, Shattuck-Eidens D, Futreal PA, Harshman K, Tavigain S, Liu Q, Cochran C, Bennet LM, Ding W, et al: A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. Science. 1994, 266: 66-71. 10.1126/science.7545954.
Article
CAS
PubMed
Google Scholar
Wooster R, Bignell G, Lancaster J, Swift S, Seal S, Mangion J, Collins N, Gregory S, Gumbs C, Micklem G: Identification of the breast cancer susceptibility gene BRCA2. Nature. 1995, 21: 789-92. 10.1038/378789a0.
Article
Google Scholar
Tavtigian SV, Simard J, Rommens J, Couch F, Shattuck-Eidens D, Neuhausen S, Merajver S, Thorlacius S, Offit K, Stoppa-Lyonnet D, et al: The complete BRCA2 gene and mutations in chromosome 13q-linked kindreds. Nat Genet. 1996, 12: 333-7. 10.1038/ng0396-333.
Article
CAS
PubMed
Google Scholar
Mitrunen K, Hirvonen A: Molecular epidemiology of sporadic breast cancer. The role of polymorphic genes involved oestrogen biosynthesis and metabolism. Mutat Res. 2003, 544: 9-41. 10.1016/S1383-5742(03)00016-4.
Article
CAS
PubMed
Google Scholar
Goode EL, Ulrich CM, Potter JD: Polymorphisms in DNA repair genes and associations with cancer risk. Cancer Epidemiol Biomarkers Prev. 2002, 11: 1513-1530.
CAS
PubMed
Google Scholar
Kang D: Genetic polymorphisms and cancer susceptibility of breast cancer in Korean women. Biochem Mol Biol. 2003, 36: 28-34.
Article
CAS
Google Scholar
John EM, Hopper JL, Beck JC, Knight JA, Neuhausen SL, Senie RT, Ziogas A, Andrulis IL, Anton-Culver H, Boyd N, et al: The Breast Cancer Family Registry: an infrastructure for cooperative multinational, interdisciplinary and translational studies of the genetic epidemiology of breast cancer. Breast Cancer Res. 2004, 6: R375-389. 10.1186/bcr801.
Article
PubMed
PubMed Central
Google Scholar
Knight JA, Sutherland HJ, Glendon G, Boyd NF, Andrulis IL: Characteristics associated with participation at various stages at the Ontario site of the cooperative family registry for breast cancer studies. Ann Epidemiol. 2002, 12: 27-33. 10.1016/S1047-2797(01)00253-8.
Article
PubMed
Google Scholar
Brinton LA, Hoover R, Fraumeni JF: Interaction of familial and hormonal risk factors for breast cancer. J Natl Cancer Inst. 1982, 69: 817-822.
CAS
PubMed
Google Scholar
Egan KM, Stampfer MJ, Rosner BA, Trichopoulos D, Newcomb PA, Trentham-Dietz A, Longnecker MP, Mittendorf R, Greenberg ER, Willett WC: Risk factors for breast cancer in women with a breast cancer family history. Cancer Epidemiol Biomarkers Prev. 1998, 7: 359-364.
CAS
PubMed
Google Scholar
Marchbanks PA, McDonald JA, Wilson HG, Folger SG, Mandel MG, Daling JR, Bernstein L, Malone KE, Ursin G, Strom BL, et al: Oral contraceptives and the risk of breast cancer. N Engl J Med. 2002, 346: 2025-2032. 10.1056/NEJMoa013202.
Article
CAS
PubMed
Google Scholar
Au WW, Salama SA, Sierra-Torres CH: Functional characterization of polymorphisms in DNA repair genes using cytogenetic challenge assays. Environ Health Perspect. 2003, 111: 1843-1850.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hemminki K, Xu G, Angelini S, Snellman E, Jansen CT, Lambert B, Hou SM: XPD exon 10 and 23 polymorphisms and DNA repair in human skin in situ. Carcinogenesis. 2001, 22: 1185-1188. 10.1093/carcin/22.8.1185.
Article
CAS
PubMed
Google Scholar
Spitz MR, Wu X, Wang Y, Wang LE, Shete S, Amos CI, Guo Z, Lei L, Mohrenweiser H, Wei Q: Modulation of nucleotide excision repair capacity by XPD polymorphisms in lung cancer patients. Cancer Res. 2001, 61: 1354-1357.
CAS
PubMed
Google Scholar
Qiao Y, Spitz MR, Shen H, Guo Z, Shete S, Hedayati M, Grossman L, Mohrenweiser H, Wei Q: Modulation of repair of ultraviolet damage in the host-cell reactivation assay by polymorphic XPC and XPD/ERCC2 genotypes. Carcinogenesis. 2002, 23: 295-299. 10.1093/carcin/23.2.295.
Article
CAS
PubMed
Google Scholar
Yamada K, Chen Z, Rozen R, Matthews RG: Effects of common polymorphisms on the properties of recombinant human methylenetetrahydrofolate reductase. Proc Natl Acad Sci USA. 2001, 98: 14853-14858. 10.1073/pnas.261469998.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lotta T, Vidgren J, Tilgmann C, Ulmanen I, Melen K, Julkunen I, Taskinen J: Kinetics of human soluble and membrane-bound catechol O-methyltransferase: a revised mechanism and description of the thermolabile variant of the enzyme. Biochemistry. 1995, 34: 4202-4210. 10.1021/bi00013a008.
Article
CAS
PubMed
Google Scholar
Lachman HM, Papolos DF, Saito T, Yu YM, Szumlanski CL, Weinshilboum RM: Human catechol-O-methyltransferase pharmacogenetics: description of a functional polymorphism and its potential application to neuropsychiatric disorders. Pharmacogenetics. 1996, 6: 243-250. 10.1097/00008571-199606000-00007.
Article
CAS
PubMed
Google Scholar
Sundberg K, Johansson AS, Stenberg G, Widersten M, Seidel A, Mannervik B, Jernstrom B: Differences in the catalytic efficiencies of allelic variants of glutathione transferase P1-1 towards carcinogenic diol epoxides of polycyclic aromatic hydrocarbons. Carcinogenesis. 1998, 19: 433-436. 10.1093/carcin/19.3.433.
Article
CAS
PubMed
Google Scholar
Zimniak P, Nanduri B, Pikula S, Bandorowicz-Pikula J, Singhal SS, Srivastava SK, Awasthi S, Awasthi YC: Naturally occurring human glutathione S-transferase GSTP1-1 isoforms with isoleucine and valine in position 104 differ in enzymic properties. Eur J Biochem. 1994, 224: 893-899. 10.1111/j.1432-1033.1994.00893.x.
Article
CAS
PubMed
Google Scholar
Betticher DC, Thatcher N, Altermatt HJ, Hoban P, Ryder WD, Heighway J: Alternate splicing produces a novel cyclin D1 transcript. Oncogene. 1995, 11: 1005-1011.
CAS
PubMed
Google Scholar
Diehl JA, Sherr CJ: A dominant-negative cyclin D1 mutant prevents nuclear import of cyclin-dependent kinase 4 (CDK4) and its phosphorylation by CDK-activating kinase. Mol Cell Biol. 1997, 17: 7362-7374.
Article
CAS
PubMed
PubMed Central
Google Scholar
Alt JR, Cleveland JL, Hannink M, Diehl JA: Phosphorylation-dependent regulation of cyclin D1 nuclear export and cyclin D1-dependent cellular transformation. Genes Dev. 2000, 14: 3102-3114. 10.1101/gad.854900.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lu F, Gladden AB, Diehl JA: An alternatively spliced cyclin D1 isoform, cyclin D1b, is a nuclear oncogene. Cancer Res. 2003, 63: 7056-7061.
CAS
PubMed
Google Scholar
Rutter JL, Mitchell TI, Buttice G, Meyers J, Gusella JF, Ozelius LJ, Brinckerhoff CE: A single nucleotide polymorphism in the matrix metalloproteinase-1 promoter creates an Ets binding site and augments transcription. Cancer Res. 1998, 58: 5321-5325.
CAS
PubMed
Google Scholar
Tower GB, Coon CI, Brinckerhoff CE: The 2G single nucleotide polymorphism (SNP) in the MMP-1 promoter contributes to high levels of MMP-1 transcription in MCF-7/ADR breast cancer cells. Breast Cancer Res Treat. 2003, 82: 75-82. 10.1023/B:BREA.0000003948.14026.7c.
Article
CAS
PubMed
Google Scholar
Turner DM, Williams DM, Sankaran D, Lazarus M, Sinnott PJ, Hutchinson IV: An investigation of polymorphism in the interleukin-10 gene promoter. Eur J Immunogenet. 1997, 24: 1-8.
Article
CAS
PubMed
Google Scholar
Suarez A, Castro P, Alonso R, Mozo L, Gutierrez C: Interindividual variations in constitutive interleukin-10 messenger RNA and protein levels and their association with genetic polymorphisms. Transplantation. 2003, 75: 711-717. 10.1097/01.TP.0000055216.19866.9A.
Article
CAS
PubMed
Google Scholar
Reuss E, Fimmers R, Kruger A, Becker C, Rittner C, Hohler T: Differential regulation of interleukin-10 production by genetic and environmental factors – a twin study. Genes Immun. 2002, 3: 407-413. 10.1038/sj.gene.6363920.
Article
CAS
PubMed
Google Scholar
Kibel AS, Suarez BK, Belani J, Oh J, Webster R, Brophy-Ebbers M, Guo C, Catalona WJ, Picus J, Goodfellow PJ: CDKN1A and CDKN1B polymorphisms and risk of advanced prostate carcinoma. Cancer Res. 2003, 63: 2033-2036.
CAS
PubMed
Google Scholar
Yengi L, Inskip A, Gilford J, Alldersea J, Bailey L, Smith A, Lear JT, Heagerty AH, Bowers B, Hand P, et al: Polymorphism at the glutathione S-transferase locus GSTM3: interactions with cytochrome P450 and glutathione S-transferase genotypes as risk factors for multiple cutaneous basal cell carcinoma. Cancer Res. 1996, 56: 1974-1977.
CAS
PubMed
Google Scholar
Uglialoro AM, Turbay D, Pesavento PA, Delgado JC, McKenzie FE, Gribben JG, Hartl D, Yunis EJ, Goldfeld AE: Identification of three new single nucleotide polymorphisms in the human tumor necrosis factor-alpha gene promoter. Tissue Antigens. 1998, 52: 359-367.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bayley JP, de Rooij H, van den Elsen PJ, Huizinga TW, Verweij CL: Functional analysis of linker-scan mutants spanning the -376, -308, -244, and -238 polymorphic sites of the TNF-alpha promoter. Cytokine. 2001, 14: 316-323. 10.1006/cyto.2001.0902.
Article
CAS
PubMed
Google Scholar
Wilson AG, Symons JA, McDowell TL, McDevitt HO, Duff GW: Effects of a polymorphism in the human tumor necrosis factor alpha promoter on transcriptional activation. Proc Natl Acad Sci USA. 1997, 94: 3195-3199. 10.1073/pnas.94.7.3195.
Article
CAS
PubMed
PubMed Central
Google Scholar
Baseggio L, Bartholin L, Chantome A, Charlot C, Rimokh R, Salles G: Allele-specific binding to the -308 single nucleotide polymorphism site in the tumour necrosis factor-alpha promoter. Eur J Immunogenet. 2004, 31: 15-19. 10.1111/j.1365-2370.2004.00440.x.
Article
CAS
PubMed
Google Scholar
Nedelcheva Kristensen V, Haraldsen EK, Anderson KB, Lonning PE, Erikstein B, Karesen R, Gabrielsen OS, Borresen-Dale AL: CYP17 and breast cancer risk: the polymorphism in the 5' flanking area of the gene does not influence binding to Sp-1. Cancer Res. 1999, 59: 2825-2828.
CAS
PubMed
Google Scholar
Feigelson HS, Shames LS, Pike MC, Coetzee GA, Stanczyk FZ, Henderson BE: Cytochrome P450c17alpha gene (CYP17) polymorphism is associated with serum estrogen and progesterone concentrations. Cancer Res. 1998, 58: 585-587.
CAS
PubMed
Google Scholar
Graves PE, Kabesch M, Halonen M, Holberg CJ, Baldini M, Fritzsch C, Weiland SK, Erickson RP, von Mutius E, Martinez FD: A cluster of seven tightly linked polymorphisms in the IL-13 gene is associated with total serum IgE levels in three populations of white children. J Allergy Clin Immunol. 2000, 105: 506-513. 10.1067/mai.2000.104940.
Article
CAS
PubMed
Google Scholar
Livak KJ: Allelic discrimination using fluorogenic probes and the 5' nuclease assay. Genet Anal. 1999, 14: 143-149.
Article
CAS
PubMed
Google Scholar
Onay V, Briollais L, Knight JA, Shi E, Wang Y, Wells S, Li H, Rajendram I, Andrulis IL, Ozcelik H: SNP-SNP interactions in breast cancer susceptibility. BMC Cancer. 2006, 6: 114-10.1186/1471-2407-6-114.
Article
PubMed
PubMed Central
Google Scholar
McCullagh P, Nelder JA: Generalized Linear Models. 1989, London: Chapman and Hall
Book
Google Scholar
Akaike H: Information theory as an extension of the maximum likelihood principle. Second International Symposium on Information theory: 1973; Budapest. Edited by: Petrov BN, Csaki F. 1973, Budapest: Akademiai Kiado, 267-281.
Google Scholar
Hosmer DW, Lemeshow S: Applied Logistic Regression. 1989, New York: John Wiley and Sons
Google Scholar
Morgan JN, Sonquist JA: Problems in the analysis of survey data and a proposal. J Am Stat Assoc. 1965, 58: 415-34. 10.2307/2283276.
Article
Google Scholar
Breiman L, Friedman JH, Olshen RA, Stone CJ: Classification and Regression Trees. 1984, Belmont CA: Wadsworth International Group
Google Scholar
Clark LA, Pregibon D: Tree-based models. Statistical Models in S. Edited by: Chambers JM, Hastie TJ. 1992, Pacific Grove, California: Wadsworth and Brooks/Cole Advanced Books and Software, 377-419.
Google Scholar
Ritchie MD, Hahn LW, Roodi N, Bailey LR, Dupont WD, Parl FF, Moore JH: Multifactor-dimensionality reduction reveals high-order interactions among estrogen metabolism genes in sporadic breast cancer. Am J Hum Genet. 2001, 69: 138-147. 10.1086/321276.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ritchie MD, Hahn LW, Moore JH: Power of multifactor dimensionality reduction for detecting gene-gene interactions in the presence of genotyping error, missing data, phenocopy, and genetic heterogeneity. Genet Epidemiol. 2003, 24: 150-157. 10.1002/gepi.10218.
Article
PubMed
Google Scholar
Hahn LW, Ritchie MD, Moore JH: Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactions. Bioinformatics. 2003, 19: 376-382. 10.1093/bioinformatics/btf869.
Article
CAS
PubMed
Google Scholar
Moore JH, Gilbert JC, Tsai C-T, Chiang FT, Holden W, Barney N, White BC: A flexible computational framework for detecting, characterizing, and interpreting statistical patterns of epistasis in genetic studies of human disease susceptibility. J Theoret Biol. 2006, 241: 252-261. 10.1016/j.jtbi.2005.11.036.
Article
Google Scholar
Ihaka R, Gentleman R: R: A Language for Data Analysis and Graphics. Journal of Computational and Graphical Statistics. 1996, 5: 299-314. 10.2307/1390807.
Google Scholar
Benjamini Y, Hochberg Y: Controlling the false discovery rate: A practical and powerful approach to multiple testing. J Roy Stat Soc B. 1995, 57: 289-300.
Google Scholar
Li W, Reich J: A complete enumeration and classification of two-locus disease locus. Hum Hered. 2000, 50: 334-349. 10.1159/000022939.
Article
CAS
PubMed
Google Scholar
Hastie T, Tibshirani R, Friedman J: The Elements of Statistical Learning: Data Mining, Inference, and Prediction. 2001, Springer, Bickel P, Diggle P, Fienberg S, Gather U, Olkin I, Zeger S (Series Editors): Springer Series in Statistics, 1
Book
Google Scholar
Peduzzi P, Concato J, Kemper E, Holford TR, Feinstein AR: A simulation study of the number of events per variable in logistic regression analysis. J Clin Epidemiol. 1996, 49: 1373-1379. 10.1016/S0895-4356(96)00236-3.
Article
CAS
PubMed
Google Scholar
Kooperberg C, Ruczinski I, LeBlanc M, Hsu L: Sequence analysis using logic regression. Genet Epidemiol. 2001, 21: 626-631.
Google Scholar
Friedman JH: Multivariate adaptive regression splines. Ann Stat. 1991, 19: 1-66.
Article
Google Scholar
Friedman JH, Meulman JJ: Multiple additive regression trees with applications in epidemiology. Stat Med. 2003, 22: 1365-1381. 10.1002/sim.1501.
Article
PubMed
Google Scholar
Foulkes AS, DeGruttola V, Hertogs K: Combining genotype groups and recursive partitioning: An application to HIV-1 genetics data. JRSS C. 2004, 53: 311-323.
Google Scholar
Breiman L: Random forests. Machine Learn. 2001, 45: 5-32. 10.1023/A:1010933404324.
Article
Google Scholar
Marchini J, Donnelly P, Cardon LR: Genome-wide strategies for detecting multiple loci that influence complex diseases. Nat Genet. 2005, 37: 413-417. 10.1038/ng1537.
Article
CAS
PubMed
Google Scholar
Satagopan JM, Verbel DA, Venkatraman ES, Offit KE, Begg CB: Two-stage designs for gene-disease association studies. Biometrics. 2002, 58: 163-170. 10.1111/j.0006-341X.2002.00163.x.
Article
PubMed
Google Scholar
Satagopan JM, Elston RC: Optimal two-stage genotyping in population-based association studies. Genet Epidemiol. 2003, 25: 149-157. 10.1002/gepi.10260.
Article
PubMed
Google Scholar
Van Steen K, McQueen MB, Herbert A, Raby B, Lyon H, DeMeo DL, Murphy A, Su J, Datta S, Rosenow C, et al: Genomic screening and replication using the same dataset in family-based association testing. Nat Genet. 2005, 37: 683-691. 10.1038/ng1582.
Article
CAS
PubMed
Google Scholar
Skol AD, Scott LJ, Abecasis GR, Boehnke M: Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies. Nat Genet. 2006, 38: 209-213. 10.1038/ng1706.
Article
CAS
PubMed
Google Scholar
Lunetta KL, Hayward LB, Segal J, van Eerdewegh P: Screening large-scale association study data: exploiting interactions using random forests. BMC Genetics. 2004, 5: 32-10.1186/1471-2156-5-32.
Article
PubMed
PubMed Central
Google Scholar
Bureau A, Dupuis J, Falls K, Lunetta KL, Hayward B, Keith TP, van Eerdewegh P: Identifying SNPs predictive of phenotype using random forests. Genet Epidemiol. 2005, 28: 171-182. 10.1002/gepi.20041.
Article
PubMed
Google Scholar
Moore JH, White BC: Exploiting expert knowledge in genetic programming for genome-wide genetic analysis. Lecture Notes in Computer Science. Edited by: Runarsson TP, Beyer H-G, Burke E, Merelo-Guervos JJ, Whitely LD, Yao X. 2006, New York: Springer, 4193: 969-977.
Google Scholar
Moore JH, White BC: Genome-wide genetic analysis using genetic programming: the critical need for expert knowledge. Genetic Programming Theory and Practice IV. Berlin: Springer.
Moore JH: Genome-wide analysis of epistasis using multifactor dimensionality reduction: feature selection and construction in the domain of human genetics. Knowledge Discovery and Data Mining: Challenges and Realities with Real World Data. Edited by: Zhu X, Davidson I. IGI, Hershey, PA, USA.
Moore JH, White BC: Tuning ReliefF for genome-wide genetic analysis. Lecture Notes in Computer Science. Edited by: Marchiori E, Moore JH, Rajapakse JC. 2007, New York: Springer, 4447: 166-175.
Google Scholar
Franke L, van Bakel H, Fokkens L, de Jong ED, Egmont-Petersen M, Wijmenga C: Reconstruction of a functional human gene network with an application for prioritizing positional candidate genes. Am J Hum Genet. 2006, 78: 1011-1125. 10.1086/504300.
Article
CAS
PubMed
PubMed Central
Google Scholar
Westfall PH, Young S: P value adjustments for multiple tests in multivariate binomial models. J Am Stat Assoc. 1989, 84: 780-786. 10.2307/2289666.
Google Scholar
Holm S: A simple sequentially rejective multiple test procedure. Scand J Stat. 1979, 6: 65-70.
Google Scholar
Wacholder S, Chanock S, Garcia-Closas M, El Ghormli L, Rothman N: Assessing the probability that a positive report is false: an approach for molecular epidemiology studies. J Natl Cancer Inst. 2004, 96: 434-442.
Article
PubMed
Google Scholar
Segrè D, DeLuna A, Church GM, Kishony R: Modular epistasis in yeast metabolism. Nat Genet. 2005, 37: 77-83.
PubMed
Google Scholar
Moore JH, Williams SM: Traversing the conceptual divide between biological and statistical epistasis: systems biology and a more modern synthesis. BioEssays. 2005, 27: 637-646. 10.1002/bies.20236.
Article
CAS
PubMed
Google Scholar
Thornton-Wells TA, Moore JH, Haines JL: Genetics, statistics and human disease: analytical retooling for complexity. Trends Genet. 2004, 20: 640-647. 10.1016/j.tig.2004.09.007.
Article
CAS
PubMed
Google Scholar
Moore JH: A global view of epistasis. Nat Genet. 2005, 37: 13-14. 10.1038/ng0105-13.
Article
CAS
PubMed
Google Scholar