ProbABEL package for genome-wide association analysis of imputed data. 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 in zbMATH (referenced in 6 articles )
Showing results 1 to 6 of 6.
- Frank, Alvaro; Fabregat-Traver, Diego; Bientinesi, Paolo: Large-scale linear regression: development of high-performance routines (2016)
- Patel, Vivak: Kalman-based stochastic gradient method with stop condition and insensitivity to conditioning (2016)
- Fabregat-Traver, Diego; Aulchenko, Yurii S.; Bientinesi, Paolo: Solving sequences of generalized least-squares problems on multi-threaded architectures (2014)
- Fabregat-Traver, Diego; Bientinesi, Paolo: Computing petaflops over terabytes of data: the case of genome-wide association studies (2014)
- Acar, Elif F.; Sun, Lei: A generalized Kruskal-Wallis test incorporating group uncertainty with application to genetic association studies (2013)
- Aulchenko, Yurii S.; Struchalin, Maksim V.; Van Duijn, Cornelia M.: Probabel package for genome-wide association analysis of imputed data (2010) ioport