TY - JOUR
T1 - Accurate imputation of human leukocyte antigens with CookHLA
AU - Cook, Seungho
AU - Choi, Wanson
AU - Lim, Hyunjoon
AU - Luo, Yang
AU - Kim, Kunhee
AU - Jia, Xiaoming
AU - Raychaudhuri, Soumya
AU - Han, Buhm
N1 - Publisher Copyright:
© 2021, The Author(s).
PY - 2021/12
Y1 - 2021/12
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85101503286&partnerID=8YFLogxK
U2 - 10.1038/s41467-021-21541-5
DO - 10.1038/s41467-021-21541-5
M3 - Article
C2 - 33627654
AN - SCOPUS:85101503286
VL - 12
JO - Nature communications
JF - Nature communications
SN - 2041-1723
IS - 1
M1 - 1264
ER -