PMID- 25707395
OWN - NLM
STAT- MEDLINE
DCOM- 20160905
LR  - 20221207
IS  - 1473-1150 (Electronic)
IS  - 1470-269X (Print)
IS  - 1470-269X (Linking)
VI  - 15
IP  - 6
DP  - 2015 Dec
TI  - High-accuracy imputation for HLA class I and II genes based on high-resolution 
      SNP data of population-specific references.
PG  - 530-7
LID - 10.1038/tpj.2015.4 [doi]
AB  - Statistical imputation of classical human leukocyte antigen (HLA) alleles is 
      becoming an indispensable tool for fine-mappings of disease association signals 
      from case-control genome-wide association studies. However, most currently 
      available HLA imputation tools are based on European reference populations and 
      are not suitable for direct application to non-European populations. Among the 
      HLA imputation tools, The HIBAG R package is a flexible HLA imputation tool that 
      is equipped with a wide range of population-based classifiers; moreover, HIBAG R 
      enables individual researchers to build custom classifiers. Here, two data sets, 
      each comprising data from healthy Japanese individuals of difference sample 
      sizes, were used to build custom classifiers. HLA imputation accuracy in five HLA 
      classes (HLA-A, HLA-B, HLA-DRB1, HLA-DQB1 and HLA-DPB1) increased from the 
      82.5-98.8% obtained with the original HIBAG references to 95.2-99.5% with our 
      custom classifiers. A call threshold (CT) of 0.4 is recommended for our Japanese 
      classifiers; in contrast, HIBAG references recommend a CT of 0.5. Finally, our 
      classifiers could be used to identify the risk haplotypes for Japanese narcolepsy 
      with cataplexy, HLA-DRB1*15:01 and HLA-DQB1*06:02, with 100% and 99.7% accuracy, 
      respectively; therefore, these classifiers can be used to supplement the current 
      lack of HLA genotyping data in widely available genome-wide association study 
      data sets.
FAU - Khor, S-S
AU  - Khor SS
AD  - Department of Human Genetics, Graduate School of Medicine, The University of 
      Tokyo, Tokyo, Japan.
FAU - Yang, W
AU  - Yang W
AD  - StaGen Co., Ltd., Statistical Genetics Analysis Division, Tokyo, Japan.
FAU - Kawashima, M
AU  - Kawashima M
AD  - Department of Human Genetics, Graduate School of Medicine, The University of 
      Tokyo, Tokyo, Japan.
FAU - Kamitsuji, S
AU  - Kamitsuji S
AD  - StaGen Co., Ltd., Statistical Genetics Analysis Division, Tokyo, Japan.
FAU - Zheng, X
AU  - Zheng X
AD  - Department of Biostatistics, University of Washington, Seattle, WA, USA.
FAU - Nishida, N
AU  - Nishida N
AD  - Department of Human Genetics, Graduate School of Medicine, The University of 
      Tokyo, Tokyo, Japan.
AD  - The Research Center for Hepatitis and Immunology, National Center for Global 
      Health and Medicine, Ichikawa, Japan.
FAU - Sawai, H
AU  - Sawai H
AD  - Department of Human Genetics, Graduate School of Medicine, The University of 
      Tokyo, Tokyo, Japan.
FAU - Toyoda, H
AU  - Toyoda H
AD  - Department of Human Genetics, Graduate School of Medicine, The University of 
      Tokyo, Tokyo, Japan.
FAU - Miyagawa, T
AU  - Miyagawa T
AD  - Department of Human Genetics, Graduate School of Medicine, The University of 
      Tokyo, Tokyo, Japan.
FAU - Honda, M
AU  - Honda M
AD  - Sleep Disorders Project, Department of Psychiatry and Behavioral Sciences, Tokyo 
      Metropolitan Institute of Medical Science, Tokyo, Japan.
FAU - Kamatani, N
AU  - Kamatani N
AD  - StaGen Co., Ltd., Statistical Genetics Analysis Division, Tokyo, Japan.
FAU - Tokunaga, K
AU  - Tokunaga K
AD  - Department of Human Genetics, Graduate School of Medicine, The University of 
      Tokyo, Tokyo, Japan.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20150224
PL  - United States
TA  - Pharmacogenomics J
JT  - The pharmacogenomics journal
JID - 101083949
RN  - 0 (Histocompatibility Antigens Class I)
RN  - 0 (Histocompatibility Antigens Class II)
SB  - IM
MH  - Alleles
MH  - Asian People/genetics
MH  - Case-Control Studies
MH  - Gene Frequency/genetics
MH  - Genome-Wide Association Study/methods
MH  - Genotype
MH  - Histocompatibility Antigens Class I/*genetics
MH  - Histocompatibility Antigens Class II/*genetics
MH  - Humans
MH  - Linkage Disequilibrium/genetics
MH  - Polymorphism, Single Nucleotide/*genetics
MH  - White People/genetics
PMC - PMC4762906
EDAT- 2015/02/25 06:00
MHDA- 2016/09/07 06:00
PMCR- 2016/02/23
CRDT- 2015/02/25 06:00
PHST- 2014/08/15 00:00 [received]
PHST- 2014/10/23 00:00 [revised]
PHST- 2014/12/19 00:00 [accepted]
PHST- 2015/02/25 06:00 [entrez]
PHST- 2015/02/25 06:00 [pubmed]
PHST- 2016/09/07 06:00 [medline]
PHST- 2016/02/23 00:00 [pmc-release]
AID - tpj20154 [pii]
AID - 10.1038/tpj.2015.4 [doi]
PST - ppublish
SO  - Pharmacogenomics J. 2015 Dec;15(6):530-7. doi: 10.1038/tpj.2015.4. Epub 2015 Feb 
      24.