PMID- 25398076
OWN - NLM
STAT- MEDLINE
DCOM- 20151230
LR  - 20221207
IS  - 1932-6203 (Electronic)
IS  - 1932-6203 (Linking)
VI  - 9
IP  - 11
DP  - 2014
TI  - Construction and application of a Korean reference panel for imputing classical 
      alleles and amino acids of human leukocyte antigen genes.
PG  - e112546
LID - 10.1371/journal.pone.0112546 [doi]
LID - e112546
AB  - Genetic variations of human leukocyte antigen (HLA) genes within the major 
      histocompatibility complex (MHC) locus are strongly associated with disease 
      susceptibility and prognosis for many diseases, including many autoimmune 
      diseases. In this study, we developed a Korean HLA reference panel for imputing 
      classical alleles and amino acid residues of several HLA genes. An HLA reference 
      panel has potential for use in identifying and fine-mapping disease associations 
      with the MHC locus in East Asian populations, including Koreans. A total of 413 
      unrelated Korean subjects were analyzed for single nucleotide polymorphisms 
      (SNPs) at the MHC locus and six HLA genes, including HLA-A, -B, -C, -DRB1, -DPB1, 
      and -DQB1. The HLA reference panel was constructed by phasing the 5,858 MHC SNPs, 
      233 classical HLA alleles, and 1,387 amino acid residue markers from 1,025 amino 
      acid positions as binary variables. The imputation accuracy of the HLA reference 
      panel was assessed by measuring concordance rates between imputed and genotyped 
      alleles of the HLA genes from a subset of the study subjects and East Asian 
      HapMap individuals. Average concordance rates were 95.6% and 91.1% at 2-digit and 
      4-digit allele resolutions, respectively. The imputation accuracy was minimally 
      affected by SNP density of a test dataset for imputation. In conclusion, the 
      Korean HLA reference panel we developed was highly suitable for imputing HLA 
      alleles and amino acids from MHC SNPs in East Asians, including Koreans.
FAU - Kim, Kwangwoo
AU  - Kim K
AD  - Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, 
      Seoul, Republic of Korea; Division of Rheumatology, Immunology and Allergy, 
      Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, 
      United States of America; Division of Genetics, Brigham and Women's Hospital, 
      Harvard Medical School, Boston, Massachusetts, United States of America; Program 
      in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, 
      United States of America.
FAU - Bang, So-Young
AU  - Bang SY
AD  - Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, 
      Seoul, Republic of Korea.
FAU - Lee, Hye-Soon
AU  - Lee HS
AD  - Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, 
      Seoul, Republic of Korea.
FAU - Bae, Sang-Cheol
AU  - Bae SC
AD  - Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, 
      Seoul, Republic of Korea.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20141114
PL  - United States
TA  - PLoS One
JT  - PloS one
JID - 101285081
RN  - 0 (HLA Antigens)
SB  - IM
MH  - *Alleles
MH  - Amino Acid Sequence
MH  - Asian People/*genetics
MH  - *Gene Library
MH  - *Genetic Variation
MH  - HLA Antigens/*genetics
MH  - Humans
MH  - Molecular Sequence Data
MH  - Polymorphism, Single Nucleotide
MH  - Republic of Korea
PMC - PMC4232350
COIS- Competing Interests: The authors have declared that no competing interests exist.
EDAT- 2014/11/15 06:00
MHDA- 2015/12/31 06:00
PMCR- 2014/11/14
CRDT- 2014/11/15 06:00
PHST- 2014/06/25 00:00 [received]
PHST- 2014/09/26 00:00 [accepted]
PHST- 2014/11/15 06:00 [entrez]
PHST- 2014/11/15 06:00 [pubmed]
PHST- 2015/12/31 06:00 [medline]
PHST- 2014/11/14 00:00 [pmc-release]
AID - PONE-D-14-28436 [pii]
AID - 10.1371/journal.pone.0112546 [doi]
PST - epublish
SO  - PLoS One. 2014 Nov 14;9(11):e112546. doi: 10.1371/journal.pone.0112546. 
      eCollection 2014.