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A new genotype imputation method with tolerance to high missing rate and rare variants.

ABSTRACT: We report a novel algorithm, iBLUP, to impute missing genotypes by simultaneously and comprehensively using identity by descent and linkage disequilibrium information. The simulation studies showed that the algorithm exhibited drastically tolerance to high missing rate, especially for rare variants than other common imputation methods, e.g. BEAGLE and fastPHASE. At a missing rate of 70%, the accuracy of BEAGLE and fastPHASE dropped to 0.82 and 0.74 respectively while iBLUP retained an accuracy of 0.95. For minor allele, the accuracy of BEAGLE and fastPHASE decreased to -0.1 and 0.03, while iBLUP still had an accuracy of 0.61.We implemented the algorithm in a publicly available software package also named iBLUP. The application of iBLUP for processing real sequencing data in an outbred pig population was demonstrated.

SUBMITTER: Yang Y

PROVIDER: S-EPMC4074155 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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A new genotype imputation method with tolerance to high missing rate and rare variants.

Yang Yumei Y Wang Qishan Q Chen Qiang Q Liao Rongrong R Zhang Xiangzhe X Yang Hongjie H Zheng Youmin Y Zhang Zhiwu Z Pan Yuchun Y

PloS one 20140627 6

We report a novel algorithm, iBLUP, to impute missing genotypes by simultaneously and comprehensively using identity by descent and linkage disequilibrium information. The simulation studies showed that the algorithm exhibited drastically tolerance to high missing rate, especially for rare variants than other common imputation methods, e.g. BEAGLE and fastPHASE. At a missing rate of 70%, the accuracy of BEAGLE and fastPHASE dropped to 0.82 and 0.74 respectively while iBLUP retained an accuracy o ...[more]

PMID: 24972110

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