Files and links (2)
CC BY V4.0, Open Access
Journal article
A new genotype imputation method with tolerance to high missing rate and rare variants
PloS one, Vol.9(6), pp.e101025-e101025
2014
Handle:
https://hdl.handle.net/2376/106814
PMCID: PMC4074155
PMID: 24972110
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.
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Details
- Title
- A new genotype imputation method with tolerance to high missing rate and rare variants
- Creators
- Yumei Yang - School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, ChinaQishan Wang - School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, ChinaQiang Chen - School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, ChinaRongrong Liao - School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, ChinaXiangzhe Zhang - School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, ChinaHongjie Yang - National Animal Husbandry Services, Beijing, ChinaYoumin Zheng - National Animal Husbandry Services, Beijing, ChinaZhiwu Zhang - 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 AmericaYuchun Pan - School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, China
- Publication Details
- PloS one, Vol.9(6), pp.e101025-e101025
- Academic Unit
- Department of Crop and Soil Sciences
- Publisher
- United States
- Identifiers
- 99900546710901842
- Language
- English
- Resource Type
- Journal article