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Perspective

Reducing GWAS Complexity

, , , , , , , & show all
Pages 22-24 | Received 19 Aug 2015, Accepted 12 Nov 2015, Published online: 15 Jan 2016

References

  • Han Y, Hazelett DJ, Wiklund F, Schumacher FR, Stram DO, Berndt SI, Wang Z, Rand KA, Hoover RN, Machiela MJ, et al. Integration of Multiethnic Fine-mapping and Genomic Annotation to Prioritize Candidate Functional SNPs at Prostate Cancer Susceptibility Regions. Hum Mol Genet 2015; 24(19):5603–18.
  • Amin Al Olama A, Dadaev T, Hazelett DJ, Li Q, Leongamornlert D, Saunders EJ, Stephens S, Cieza-Borrella C, Whitmore I, Benlloch Garcia S, et al. Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans. Hum Mol Genet 2015; 24(19):5589–602.
  • Coetzee SG, Rhie SK, Berman BP, Coetzee GA, Noushmehr H. FunciSNP: an R/bioconductor tool integrating functional non-coding data sets with genetic association studies to identify candidate regulatory SNPs. Nucleic Acids Res 2012; 40:e139; PMID:22684628; http://dx.doi.org/10.1093/nar/gks542
  • Boyle AP, Hong EL, Hariharan M, Cheng Y, Schaub MA, Kasowski M, Karczewski KJ, Park J, Hitz BC, Weng S, et al. Annotation of functional variation in personal genomes using RegulomeDB. Genome Res 2012; 22:1790–7; PMID:22955989; http://dx.doi.org/10.1101/gr.137323.112
  • Ward LD, Kellis M. HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Res 2012; 40:D930–4; PMID:22064851; http://dx.doi.org/10.1093/nar/gkr917
  • Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 2010; 38:e164; PMID:20601685; http://dx.doi.org/10.1093/nar/gkq603
  • Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. Integrative genomics viewer. Nat Biotechnol 2011; 29:24–6; PMID:21221095; http://dx.doi.org/10.1038/nbt.1754
  • Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, et al. Integrative annotation of variants from 1092 humans: application to cancer genomics. Science 2013; 342:1235587; PMID:24092746; http://dx.doi.org/10.1126/science.1235587
  • Coetzee SG, Coetzee GA, Hazelett DJ. motifbreakR: an R/Bioconductor package for predicting variant effects at transcription factor binding sites. Bioinformaticts 2015; 31:3847-9; PMID:26272984; http://dx.doi.org/10.1093/bioinformatics/btv470
  • Hazelett DJ, Rhie SK, Gaddis M, Yan C, Lakeland DL, Coetzee SG, Ellipse G-ONc, Practical C, Henderson BE, Noushmehr H, et al. Comprehensive functional annotation of 77 prostate cancer risk loci. PLoS Genet 2014; 10:e1004102; PMID:24497837; http://dx.doi.org/10.1371/journal.pgen.1004102
  • Rhie SK, Coetzee SG, Noushmehr H, Yan C, Kim JM, Haiman CA, Coetzee GA. Comprehensive functional annotation of seventy-one breast cancer risk Loci. PLoS ONE 2013; 8:e63925; PMID:23717510; http://dx.doi.org/10.1371/journal.pone.0063925
  • Wakefield J. A Bayesian measure of the probability of false discovery in genetic epidemiology studies. Am J Hum Genet 2007; 81:208–27; PMID:17668372; http://dx.doi.org/10.1086/519024
  • Wakefield J. Bayes factors for genome-wide association studies: comparison with P-values. Genet Epidemiol 2009; 33:79–86; PMID:18642345; http://dx.doi.org/10.1002/gepi.20359
  • Wallace C, Cutler AJ, Pontikos N, Pekalski ML, Burren OS, Cooper JD, Garcia AR, Ferreira RC, Guo H, Walker NM, et al. Dissection of a Complex Disease Susceptibility Region Using a Bayesian Stochastic Search Approach to Fine Mapping. PLoS Genet 2015; 11:e1005272; PMID:26106896; http://dx.doi.org/10.1371/journal.pgen.1005272
  • Hormozdiari F, Kostem E, Kang EY, Pasaniuc B, Eskin E. Identifying causal variants at loci with multiple signals of association. Genetics 2014; 198:497–508; PMID:25104515; http://dx.doi.org/10.1534/genetics.114.167908
  • Chen W, Larrabee BR, Ovsyannikova IG, Kennedy RB, Haralambieva IH, Poland GA, Schaid DJ. Fine Mapping Causal Variants with an Approximate Bayesian Method Using Marginal Test Statistics. Genetics 2015; 200:719–36; PMID:25948564; http://dx.doi.org/10.1534/genetics.115.176107
  • Kichaev G, Yang WY, Lindstrom S, Hormozdiari F, Eskin E, Price AL, Kraft P, Pasaniuc B. Integrating functional data to prioritize causal variants in statistical fine-mapping studies. PLoS Genet 2014; 10:e1004722; PMID:25357204; http://dx.doi.org/10.1371/journal.pgen.1004722
  • Quintana MA, Conti DV. Integrative variable selection via Bayesian model uncertainty. Statistics in medicine 2013; 32:4938–53; PMID:23824835; http://dx.doi.org/10.1002/sim.5888
  • Coetzee SG, Shen HC, Hazelett DJ, Lawrenson K, Kuchenbaecker K, Tyrer J, Rhie SK, Levanon K, Karst A, Drapkin R, et al. Cell-type-specific enrichment of risk-associated regulatory elements at ovarian cancer susceptibility loci. Hum Mol Genet 2015; 24:3595–607; PMID:25804953

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