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Open Access Highly Accessed Software

ProbABEL package for genome-wide association analysis of imputed data

Yurii S Aulchenko12*, Maksim V Struchalin1 and Cornelia M van Duijn1

Author Affiliations

1 Department of Epidemiology, Erasmus MC, Postbus 2040, 3000 CA Rotterdam, The Netherlands

2 Institute of Cytology and Genetics SD RAS, Novosibirsk, 630090, Russia

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BMC Bioinformatics 2010, 11:134  doi:10.1186/1471-2105-11-134

Published: 16 March 2010

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.