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. 2010 Mar 16:11:134.
doi: 10.1186/1471-2105-11-134.

ProbABEL package for genome-wide association analysis of imputed data

Yurii S Aulchenko  1 , Maksim V Struchalin, Cornelia M van Duijn
Affiliations

ProbABEL package for genome-wide association analysis of imputed data

Yurii S Aulchenko et al. BMC Bioinformatics. .

Abstract

Background: Over the last few years, genome-wide association (GWA) studies became a tool of choice for the identification of loci associated with complex traits. Currently, imputed single nucleotide polymorphisms (SNP) data are frequently used in GWA analyzes. Correct analysis of imputed data calls for the implementation of specific methods which take genotype imputation uncertainty into account.

Results: We developed the ProbABEL software package for the analysis of genome-wide imputed SNP data and quantitative, binary, and time-till-event outcomes under linear, logistic, and Cox proportional hazards models, respectively. For quantitative traits, the package also implements a fast two-step mixed model-based score test for association in samples with differential relationships, facilitating analysis in family-based studies, studies performed in human genetically isolated populations and outbred animal populations.

Conclusions: ProbABEL package provides fast efficient way to analyze imputed data in genome-wide context and will facilitate future identification of complex trait loci.

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References

    1. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA. 2009;106(23):9362–9367. doi: 10.1073/pnas.0903103106. - DOI - PMC - PubMed
    1. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;81(3):559–575. doi: 10.1086/519795. - DOI - PMC - PubMed
    1. Aulchenko YS, Ripke S, Isaacs A, van Duijn CM. GenABEL: an R library for genome-wide association analysis. Bioinformatics. 2007;23(10):1294–1296. doi: 10.1093/bioinformatics/btm108. - DOI - PubMed
    1. Marchini J, Howie B, Myers S, McVean G, Donnelly P. A new multipoint method for genome-wide association studies by imputation of genotypes. Nat Genet. 2007;39(7):906–913. doi: 10.1038/ng2088. - DOI - PubMed
    1. Clayton D, Leung HT. An R package for analysis of whole-genome association studies. Hum Hered. 2007;64:45–51. doi: 10.1159/000101422. - DOI - PubMed

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