PMID- 33627654
OWN - NLM
STAT- MEDLINE
DCOM- 20210303
LR  - 20240331
IS  - 2041-1723 (Electronic)
IS  - 2041-1723 (Linking)
VI  - 12
IP  - 1
DP  - 2021 Feb 24
TI  - Accurate imputation of human leukocyte antigens with CookHLA.
PG  - 1264
LID - 10.1038/s41467-021-21541-5 [doi]
LID - 1264
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.
FAU - Cook, Seungho
AU  - Cook S
AUID- ORCID: 0000-0003-4334-7840
AD  - Department of Biomedical Sciences, BK21 Plus Biomedical Science Project, Seoul 
      National University College of Medicine, Seoul, South Korea.
AD  - Department of Convergence Medicine, University of Ulsan College of Medicine & 
      Asan Institute for Life Sciences, Asan Medical Center, Seoul, South Korea.
FAU - Choi, Wanson
AU  - Choi W
AD  - Department of Biomedical Sciences, BK21 Plus Biomedical Science Project, Seoul 
      National University College of Medicine, Seoul, South Korea.
FAU - Lim, Hyunjoon
AU  - Lim H
AUID- ORCID: 0000-0002-7550-1825
AD  - Interdisciplinary Program for Bioengineering, Seoul National University, Seoul, 
      South Korea.
FAU - Luo, Yang
AU  - Luo Y
AUID- ORCID: 0000-0001-7385-6166
AD  - Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical 
      School, Boston, MA, USA.
AD  - Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, 
      Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
AD  - Division of Genetics, Department of Medicine, Brigham and Women's Hospital and 
      Harvard Medical School, Boston, MA, USA.
AD  - Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 
      Cambridge, MA, USA.
FAU - Kim, Kunhee
AU  - Kim K
AD  - Department of Biomedical Sciences, BK21 Plus Biomedical Science Project, Seoul 
      National University College of Medicine, Seoul, South Korea.
AD  - Department of Convergence Medicine, University of Ulsan College of Medicine & 
      Asan Institute for Life Sciences, Asan Medical Center, Seoul, South Korea.
FAU - Jia, Xiaoming
AU  - Jia X
AD  - Department of Neurology, University of California San Francisco, San Francisco, 
      CA, USA.
FAU - Raychaudhuri, Soumya
AU  - Raychaudhuri S
AUID- ORCID: 0000-0002-1901-8265
AD  - Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical 
      School, Boston, MA, USA.
AD  - Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, 
      Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
AD  - Division of Genetics, Department of Medicine, Brigham and Women's Hospital and 
      Harvard Medical School, Boston, MA, USA.
AD  - Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 
      Cambridge, MA, USA.
AD  - Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
AD  - Centre for Genetics and Genomics Versus Arthritis, Manchester Academic Health 
      Science Centre, University of Manchester, Manchester, UK.
FAU - Han, Buhm
AU  - Han B
AUID- ORCID: 0000-0002-2266-5164
AD  - Department of Biomedical Sciences, BK21 Plus Biomedical Science Project, Seoul 
      National University College of Medicine, Seoul, South Korea. buhm.han@snu.ac.kr.
AD  - Department of Convergence Medicine, University of Ulsan College of Medicine & 
      Asan Institute for Life Sciences, Asan Medical Center, Seoul, South Korea. 
      buhm.han@snu.ac.kr.
AD  - Interdisciplinary Program for Bioengineering, Seoul National University, Seoul, 
      South Korea. buhm.han@snu.ac.kr.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20210224
PL  - England
TA  - Nat Commun
JT  - Nature communications
JID - 101528555
RN  - 0 (HLA Antigens)
SB  - IM
MH  - Alleles
MH  - Asian People
MH  - Diabetes Mellitus, Type 1/genetics
MH  - Genome, Human/genetics
MH  - Genome-Wide Association Study
MH  - Genotype
MH  - HLA Antigens/genetics/*metabolism
MH  - Humans
MH  - Models, Theoretical
MH  - Phenotype
MH  - Polymorphism, Single Nucleotide/genetics
PMC - PMC7904773
COIS- B.H. is the CTO of Genealogy, Inc. The remaining authors declare no competing 
      interests.
EDAT- 2021/02/26 06:00
MHDA- 2021/03/04 06:00
PMCR- 2021/02/24
CRDT- 2021/02/25 05:36
PHST- 2020/05/21 00:00 [received]
PHST- 2021/02/01 00:00 [accepted]
PHST- 2021/02/25 05:36 [entrez]
PHST- 2021/02/26 06:00 [pubmed]
PHST- 2021/03/04 06:00 [medline]
PHST- 2021/02/24 00:00 [pmc-release]
AID - 10.1038/s41467-021-21541-5 [pii]
AID - 21541 [pii]
AID - 10.1038/s41467-021-21541-5 [doi]
PST - epublish
SO  - Nat Commun. 2021 Feb 24;12(1):1264. doi: 10.1038/s41467-021-21541-5.