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Comment
. 2013 Dec;31(12):1095-7.
doi: 10.1038/nbt.2757.

Mining the ultimate phenome repository

Nigam H Shah  1
Affiliations
Comment

Mining the ultimate phenome repository

Nigam H Shah. Nat Biotechnol. 2013 Dec.

Abstract

Combining genotyping and the data locked in medical records yields a large number of known genotype-phenotype associations.

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Figures

Figure 1
Figure 1
Approaches for deriving associations between genetic variants and disease phenotypes. Rows represent individual genetic variants (usually SNPs); columns represent individual phenotypes. (a) A GWAS tests one phenotype for association with many genetic variants, whereas previous PheWAS have tested associations of a genetic variant with many phenotypes. (b) In an expanded PheWAS, Denny et al. test many genetic variants against many phenotypes extracted from electronic medical records to validate PheWAS and to make new discoveries. Note that not all phenotypes can be reliably extracted from electronic medical record data.
See this image and copyright information in PMC

Comment on

  • Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data.
    Denny JC, Bastarache L, Ritchie MD, Carroll RJ, Zink R, Mosley JD, Field JR, Pulley JM, Ramirez AH, Bowton E, Basford MA, Carrell DS, Peissig PL, Kho AN, Pacheco JA, Rasmussen LV, Crosslin DR, Crane PK, Pathak J, Bielinski SJ, Pendergrass SA, Xu H, Hindorff LA, Li R, Manolio TA, Chute CG, Chisholm RL, Larson EB, Jarvik GP, Brilliant MH, McCarty CA, Kullo IJ, Haines JL, Crawford DC, Masys DR, Roden DM. Denny JC, et al. Nat Biotechnol. 2013 Dec;31(12):1102-10. doi: 10.1038/nbt.2749. Nat Biotechnol. 2013. PMID: 24270849 Free PMC article.

References

    1. Denny JC, et al. Bioinformatics. 2010;26:1205–1210. - PMC - PubMed
    1. Denny JC, et al. Nat. Biotechnol. 2013;31:1102–1104. - PubMed
    1. Denny JC, et al. Am. J. Hum. Genet. 2011;89:529–542. - PMC - PubMed
    1. Hebbring SJ, et al. Genes Immun. 2013;14:187–191. - PMC - PubMed
    1. Liao KP, et al. Arthritis Rheum. 2013;65:571–581. - PMC - PubMed

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