publication . Article . 2011

A powerful hybrid approach to select top single-nucleotide polymorphisms for genome-wide association study

Wang, Jian; Shete, Sanjay;
Open Access
  • Published: 01 Jan 2011 Journal: BMC Genetics, volume 12, page 3 (issn: 1471-2156, Copyright policy)
  • Publisher: Springer Science and Business Media LLC
Abstract
<p>Abstract</p> <p>Background</p> <p>Genome-wide association (GWA) study has recently become a powerful approach for detecting genetic variants for common diseases without prior knowledge of the variant's location or function. Generally, in GWA studies, the most significant single-nucleotide polymorphisms (SNPs) associated with top-ranked p values are selected in stage one, with follow-up in stage two. The value of selecting SNPs based on statistically significant p values is obvious. However, when minor allele frequencies (MAFs) are relatively low, less-significant p values can still correspond to higher odds ratios (ORs), which might be more useful for predict...
Subjects
free text keywords: Genetics(clinical), Genetics, Genetic variants, Allele frequency, Disease, Genome-wide association study, Bioinformatics, Single-nucleotide polymorphism, Minor allele frequency, Odds ratio, Biology, QH426-470, Research Article
Funded by
NIH| Genome Wide Association Study of Head and Neck Cancer
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01CA131324-04
  • Funding stream: NATIONAL CANCER INSTITUTE
29 references, page 1 of 2

Marchini, J, Donnelly, P, Cardon, LR. Genome-wide strategies for detecting multiple loci that influence complex diseases. Nat Genet. 2005; 37: 413-417 [OpenAIRE] [PubMed] [DOI]

Manolio, TA, Rodriguez, LL, Brooks, L, Abecasis, G, Ballinger, D, Daly, M, Donnelly, P, Faraone, SV, Frazer, K, Gabriel, S. New models of collaboration in genome-wide association studies: the Genetic Association Information Network. Nat Genet. 2007; 39: 1045-1051 [OpenAIRE] [PubMed] [DOI]

Pearson, TA, Manolio, TA. How to interpret a genome-wide association study. JAMA. 2008; 299: 1335-1344 [OpenAIRE] [PubMed] [DOI]

Manolio, TA, Brooks, LD, Collins, FS. A HapMap harvest of insights into the genetics of common disease. J Clin Invest. 2008; 118: 1590-1605 [OpenAIRE] [PubMed] [DOI]

Amos, CI, Wu, X, Broderick, P, Gorlov, IP, Gu, J, Eisen, T, Dong, Q, Zhang, Q, Gu, X, Vijayakrishnan, J. Genome-wide association scan of tag SNPs identifies a susceptibility locus for lung cancer at 15q25.1. Nat Genet. 2008; 40: 616-622 [OpenAIRE] [PubMed] [DOI]

Hung, RJ, McKay, JD, Gaborieau, V, Boffetta, P, Hashibe, M, Zaridze, D, Mukeria, A, Szeszenia-Dabrowska, N, Lissowska, J, Rudnai, P. A susceptibility locus for lung cancer maps to nicotinic acetylcholine receptor subunit genes on 15q25. Nature. 2008; 452: 633-637 [OpenAIRE] [PubMed] [DOI]

Thorgeirsson, TE, Geller, F, Sulem, P, Rafnar, T, Wiste, A, Magnusson, KP, Manolescu, A, Thorleifsson, G, Stefansson, H, Ingason, A. A variant associated with nicotine dependence, lung cancer and peripheral arterial disease. Nature. 2008; 452: 638-642 [OpenAIRE] [PubMed] [DOI]

Eeles, RA, Kote-Jarai, Z, Giles, GG, Olama, AA, Guy, M, Jugurnauth, SK, Mulholland, S, Leongamornlert, DA, Edwards, SM, Morrison, J. Multiple newly identified loci associated with prostate cancer susceptibility. Nat Genet. 2008; 40: 316-321 [OpenAIRE] [PubMed] [DOI]

Gudmundsson, J, Sulem, P, Manolescu, A, Amundadottir, LT, Gudbjartsson, D, Helgason, A, Rafnar, T, Bergthorsson, JT, Agnarsson, BA, Baker, A. Genome-wide association study identifies a second prostate cancer susceptibility variant at 8q24. Nat Genet. 2007; 39: 631-637 [OpenAIRE] [PubMed] [DOI]

Thomas, G, Jacobs, KB, Yeager, M, Kraft, P, Wacholder, S, Orr, N, Yu, K, Chatterjee, N, Welch, R, Hutchinson, A. Multiple loci identified in a genome-wide association study of prostate cancer. Nat Genet. 2008; 40: 310-315 [OpenAIRE] [PubMed] [DOI]

Yeager, M, Orr, N, Hayes, RB, Jacobs, KB, Kraft, P, Wacholder, S, Minichiello, MJ, Fearnhead, P, Yu, K, Chatterjee, N. Genome-wide association study of prostate cancer identifies a second risk locus at 8q24. Nat Genet. 2007; 39: 645-649 [OpenAIRE] [PubMed] [DOI]

Stacey, SN, Manolescu, A, Sulem, P, Thorlacius, S, Gudjonsson, SA, Jonsson, GF, Jakobsdottir, M, Bergthorsson, JT, Gudmundsson, J, Aben, KK. Common variants on chromosome 5p12 confer susceptibility to estrogen receptor-positive breast cancer. Nat Genet. 2008; 40: 703-706 [OpenAIRE] [PubMed] [DOI]

Hunter, DJ, Kraft, P, Jacobs, KB, Cox, DG, Yeager, M, Hankinson, SE, Wacholder, S, Wang, Z, Welch, R, Hutchinson, A. A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer. Nat Genet. 2007; 39: 870-874 [OpenAIRE] [PubMed] [DOI]

Easton, DF, Pooley, KA, Dunning, AM, Pharoah, PD, Thompson, D, Ballinger, DG, Struewing, JP, Morrison, J, Field, H, Luben, R. Genome-wide association study identifies novel breast cancer susceptibility loci. Nature. 2007; 447: 1087-1093 [OpenAIRE] [PubMed] [DOI]

Gold, B, Kirchhoff, T, Stefanov, S, Lautenberger, J, Viale, A, Garber, J, Friedman, E, Narod, S, Olshen, AB, Gregersen, P. Genome-wide association study provides evidence for a breast cancer risk locus at 6q22.33. Proc Natl Acad Sci USA. 2008; 105: 4340-4345 [OpenAIRE] [PubMed] [DOI]

29 references, page 1 of 2
Powered by OpenAIRE Research Graph
Any information missing or wrong?Report an Issue