Accurate imputation of human leukocyte antigens with CookHLA

Seungho Cook, Wanson Choi, Hyunjoon Lim, Yang Luo, Kunhee Kim, Xiaoming Jia, Soumya Raychaudhuri, Buhm Han

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


The recent development of imputation methods enabled the prediction of human leukocyte antigen (HLA) alleles from intergenic SNP data, allowing studies to fine-map HLA for immune phenotypes. Here we report an accurate HLA imputation method, CookHLA, which has superior imputation accuracy compared to previous methods. CookHLA differs from other approaches in that it locally embeds prediction markers into highly polymorphic exons to account for exonic variability, and in that it adaptively learns the genetic map within MHC from the data to facilitate imputation. Our benchmarking with real datasets shows that our method achieves high imputation accuracy in a wide range of scenarios, including situations where the reference panel is small or ethnically unmatched.

Original languageEnglish
Article number1264
JournalNature Communications
Issue number1
StatePublished - Dec 2021


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