Simultaneous Genotype Calling and Haplotype Phasing Improves Genotype Accuracy and Reduces False-Positive Associations for Genome-wide Association Studies

DOI: 10.1016/J.AJHG.2009.11.004

关键词: Allele 、 Genotype 、 Genome-wide association study 、 Haplotype 、 Bipolar disorder 、 Concordance 、 Biology 、 Genetic association 、 Genotyping 、 Genetics

摘要: We present a novel method for simultaneous genotype calling and haplotype-phase inference. Our employs the computationally efficient BEAGLE haplotype-frequency model, which can be applied to large-scale studies with millions of markers thousands of samples. compare calls made our BIRDSEED, CHIAMO, GenCall, ILLUMINUS genotype-calling methods, using data from Illumina 550K Affymetrix 500K arrays. show that has higher genotype-call accuracy yields fewer uncalled genotypes than competing methods. perform single-marker analysis Wellcome Trust Case Control Consortium bipolar disorder type 2 diabetes studies. For disorder, in original study yield 25 apparent false-positive association at p < 10−7 significance level, whereas no associated this threshold. Conversely, replicated diabetes, there is good concordance between used by method. Results haplotypic method's indicate highly effective eliminating genotyping artifacts cause associations genome-wide new methods are implemented BEAGLECALL software packages.

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Simultaneous Genotype Calling and Haplotype Phasing Improves Genotype Accuracy and Reduces False-Positive Associations for Genome-wide Association Studies

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Simultaneous Genotype Calling and Haplotype Phasing Improves Genotype Accuracy and Reduces False-Positive Associations for Genome-wide Association Studies

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