Fast and accurate genotype imputation in genome-wide association studies through pre-phasing
نویسندگان
چکیده
منابع مشابه
A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies
Genotype imputation methods are now being widely used in the analysis of genome-wide association studies. Most imputation analyses to date have used the HapMap as a reference dataset, but new reference panels (such as controls genotyped on multiple SNP chips and densely typed samples from the 1,000 Genomes Project) will soon allow a broader range of SNPs to be imputed with higher accuracy, ther...
متن کاملdetermination of the impact of some factors on genotype imputation error rates for genome wide association studies in dairy cattle
in this study, effect of two genotype imputation strategies, relatedness between reference panel and test populations and minor allele frequency on imputation error rate were examined with using a stochastic simulated population. reference panel and test populations were composed of 1,000 and 500 individuals, respectively. individuals in the reference panel were genotyped with using a high and ...
متن کاملSimultaneous genotype calling and haplotype phasing improves genotype accuracy and reduces false-positive associations for genome-wide association studies.
We present a novel method for simultaneous genotype calling and haplotype-phase inference. Our method employs the computationally efficient BEAGLE haplotype-frequency model, which can be applied to large-scale studies with millions of markers and thousands of samples. We compare genotype calls made with our method to genotype calls made with the BIRDSEED, CHIAMO, GenCall, and ILLUMINUS genotype...
متن کاملImpact of missing genotype imputation on the power of Genome Wide Association Studies
Genome Wide Association Studies are often performed on datasets containing a relatively small number of genotypes. In those cases, statistical tests performed on subgroups of those genotypes lack power or may even not fulfill the requirements of minimal number of observations. In this work we present results of running a GWAS analysis including parametric and nonparametric analysis of variance ...
متن کاملFast pairwise IBD association testing in genome-wide association studies
MOTIVATION Recently, investigators have proposed state-of-the-art Identity-by-descent (IBD) mapping methods to detect IBD segments between purportedly unrelated individuals. The IBD information can then be used for association testing in genetic association studies. One approach for this IBD association testing strategy is to test for excessive IBD between pairs of cases ('pairwise method'). Ho...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Nature Genetics
سال: 2012
ISSN: 1061-4036,1546-1718
DOI: 10.1038/ng.2354