title: 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.
authors: School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
authors: Yumei
authors: Y
authors: Yang
authors: School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
authors: Qishan
authors: Q
authors: Wang
authors: School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
authors: Qiang
authors: Q
authors: Chen
authors: School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
authors: Rongrong
authors: R
authors: Liao
authors: School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
authors: Xiangzhe
authors: X
authors: Zhang
authors: National Animal Husbandry Services, Beijing, China.
authors: Hongjie
authors: H
authors: Yang
authors: National Animal Husbandry Services, Beijing, China.
authors: Youmin
authors: Y
authors: Zheng
authors: Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America; Department of Crop and Soil Science, Washington State University, Pullman, Washington, United States of America.
authors: Zhiwu
authors: Z
authors: Zhang
authors: School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, China.
authors: Yuchun
authors: Y
authors: Pan
mesh_terms: D000818:Animals; D006239:Haplotypes; D011110:Polymorphism, Genetic; D012680:Sensitivity and Specificity; D012984:Software; D013552:Swine