PMID- 32042094
OWN - NLM
STAT- MEDLINE
DCOM- 20210707
LR  - 20220420
IS  - 1473-1150 (Electronic)
IS  - 1470-269X (Linking)
VI  - 20
IP  - 5
DP  - 2020 Oct
TI  - A high-resolution HLA imputation system for the Taiwanese population: a study of 
      the Taiwan Biobank.
PG  - 695-704
LID - 10.1038/s41397-020-0156-3 [doi]
AB  - An imputation algorithm for human leukocyte antigen (HLA) is helpful for 
      exploring novel disease associations. However, population-specific HLA imputation 
      references are essential for achieving high imputation accuracy. In this study, a 
      subset of 1012 individuals from the Taiwan Biobank (TWB) who underwent both 
      whole-genome SNP array and NGS-based HLA typing were used to establish Taiwanese 
      HLA imputation references. The HIBAG package was used to generate the imputation 
      references for eight HLA loci at a two- and three-field resolution. Internal 
      validation was carried out to evaluate the call threshold and accuracy for each 
      HLA gene. HLA class II genes found to be associated with rheumatoid arthritis 
      (RA) were validated in this study by the imputed HLA alleles. Our Taiwanese 
      population-specific references achieved average HLA imputation accuracies of 
      98.11% for two-field and 98.08% for three-field resolution. The frequency 
      distribution of imputed HLA alleles among 23,972 TWB subjects were comparable 
      with PCR-based HLA alleles in general Taiwanese reported in the allele frequency 
      net database. We replicated four common HLA alleles (HLA-DRB1*03:01, DRB1*04:05, 
      DQA1*03:03, and DQB1*04:01) significantly associated with RA. The 
      population-specific references provide an informative tool to investigate the 
      associations of HLA variants and human diseases in large-scale population-based 
      studies.
FAU - Huang, Yu-Han
AU  - Huang YH
AD  - Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan.
FAU - Khor, Seik-Soon
AU  - Khor SS
AUID- ORCID: 0000-0002-6809-4731
AD  - Department of Human Genetics, Graduate School of Medicine, the University of 
      Tokyo, Toyo, Japan.
FAU - Zheng, Xiuwen
AU  - Zheng X
AUID- ORCID: 0000-0002-1390-0708
AD  - Department of Biostatistics, University of Washington, Seattle, WA, USA.
FAU - Chen, Hsuan-Yu
AU  - Chen HY
AD  - Institute of Statistical Science, Academia Sinica, Taipei, Taiwan.
FAU - Chang, Ya-Hsuan
AU  - Chang YH
AD  - Institute of Statistical Science, Academia Sinica, Taipei, Taiwan.
FAU - Chu, Hou-Wei
AU  - Chu HW
AD  - Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
FAU - Wu, Pei-Ei
AU  - Wu PE
AD  - Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
FAU - Lin, Yu-Ju
AU  - Lin YJ
AD  - Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan.
FAU - Liao, Shu-Fen
AU  - Liao SF
AD  - Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan.
AD  - Institute of Statistical Science, Academia Sinica, Taipei, Taiwan.
FAU - Shen, Chen-Yang
AU  - Shen CY
AD  - Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
FAU - Tokunaga, Katsushi
AU  - Tokunaga K
AD  - Department of Human Genetics, Graduate School of Medicine, the University of 
      Tokyo, Toyo, Japan. tokunaga@m.u-tokyo.ac.jp.
FAU - Lee, Mei-Hsuan
AU  - Lee MH
AD  - Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan. 
      meihlee@ntu.edu.tw.
CN  - HLA & KIR imputation network (HKimp.net)
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PT  - Validation Study
DEP - 20200211
PL  - United States
TA  - Pharmacogenomics J
JT  - The pharmacogenomics journal
JID - 101083949
RN  - 0 (HLA Antigens)
RN  - 0 (HLA-DQ alpha-Chains)
RN  - 0 (HLA-DQ beta-Chains)
RN  - 0 (HLA-DQA1 antigen)
RN  - 0 (HLA-DQB1 antigen)
RN  - 0 (HLA-DRB1 Chains)
RN  - 0 (HLA-DRB1*03:01 antigen)
RN  - 0 (HLA-DRB1*04:05 antigen)
SB  - IM
MH  - Arthritis, Rheumatoid/diagnosis/*genetics/immunology
MH  - Databases, Genetic
MH  - *Genetics, Population
MH  - Genotype
MH  - HLA Antigens/*genetics
MH  - HLA-DQ alpha-Chains/genetics
MH  - HLA-DQ beta-Chains/genetics
MH  - HLA-DRB1 Chains/genetics
MH  - High-Throughput Nucleotide Sequencing
MH  - Humans
MH  - Phenotype
MH  - *Polymorphism, Single Nucleotide
MH  - Reproducibility of Results
MH  - Taiwan
MH  - Whole Genome Sequencing
EDAT- 2020/02/12 06:00
MHDA- 2021/07/08 06:00
CRDT- 2020/02/12 06:00
PHST- 2019/04/12 00:00 [received]
PHST- 2020/01/27 00:00 [accepted]
PHST- 2020/01/22 00:00 [revised]
PHST- 2020/02/12 06:00 [pubmed]
PHST- 2021/07/08 06:00 [medline]
PHST- 2020/02/12 06:00 [entrez]
AID - 10.1038/s41397-020-0156-3 [pii]
AID - 10.1038/s41397-020-0156-3 [doi]
PST - ppublish
SO  - Pharmacogenomics J. 2020 Oct;20(5):695-704. doi: 10.1038/s41397-020-0156-3. Epub 
      2020 Feb 11.