PMID- 24698974
OWN - NLM
STAT- MEDLINE
DCOM- 20160322
LR  - 20221207
IS  - 1460-2083 (Electronic)
IS  - 0964-6906 (Linking)
VI  - 23
IP  - 16
DP  - 2014 Aug 15
TI  - Predicting HLA alleles from high-resolution SNP data in three Southeast Asian 
      populations.
PG  - 4443-51
LID - 10.1093/hmg/ddu149 [doi]
AB  - The major histocompatibility complex (MHC) containing the classical human 
      leukocyte antigen (HLA) Class I and Class II genes is among the most polymorphic 
      and diverse regions in the human genome. Despite the clinical importance of 
      identifying the HLA types, very few databases jointly characterize densely 
      genotyped single nucleotide polymorphisms (SNPs) and HLA alleles in the same 
      samples. To date, the HapMap presents the only public resource that provides a 
      SNP reference panel for predicting HLA alleles, constructed with four collections 
      of individuals of north-western European, northern Han Chinese, cosmopolitan 
      Japanese and Yoruba Nigerian ancestry. Owing to complex patterns of linkage 
      disequilibrium in this region, it is unclear whether the HapMap reference panels 
      can be appropriately utilized for other populations. Here, we describe a public 
      resource for the Singapore Genome Variation Project with: (i) dense genotyping 
      across  approximately  9000 SNPs in the MHC; (ii) four-digit HLA typing for eight Class I and 
      Class II loci, in 96 southern Han Chinese, 89 Southeast Asian Malays and 83 Tamil 
      Indians. This resource provides population estimates of the frequencies of HLA 
      alleles at these eight loci in the three population groups, particularly for 
      HLA-DPA1 and HLA-DPB1 that were not assayed in HapMap. Comparing between 
      population-specific reference panels and a cosmopolitan panel created from all 
      four HapMap populations, we demonstrate that more accurate imputation is obtained 
      with population-specific panels than with the cosmopolitan panel, especially for 
      the Malays and Indians but even when imputing between northern and southern Han 
      Chinese. As with SNP imputation, common HLA alleles were imputed with greater 
      accuracy than low-frequency variants.
CI  - (c) The Author 2014. Published by Oxford University Press. All rights reserved. For 
      Permissions, please email: journals.permissions@oup.com.
FAU - Pillai, Nisha Esakimuthu
AU  - Pillai NE
AD  - Saw Swee Hock School of Public Health.
FAU - Okada, Yukinori
AU  - Okada Y
AD  - Division of Rheumatology, Immunology, and Allergy, Division of Genetics, Brigham 
      and Women's Hospital, Harvard Medical School, Boston, MA, USA, Program in Medical 
      and Population Genetics, Broad Institute, Cambridge, MA, USA.
FAU - Saw, Woei-Yuh
AU  - Saw WY
AD  - Saw Swee Hock School of Public Health.
FAU - Ong, Rick Twee-Hee
AU  - Ong RT
AD  - Saw Swee Hock School of Public Health.
FAU - Wang, Xu
AU  - Wang X
AD  - Saw Swee Hock School of Public Health.
FAU - Tantoso, Erwin
AU  - Tantoso E
AD  - Saw Swee Hock School of Public Health.
FAU - Xu, Wenting
AU  - Xu W
AD  - Saw Swee Hock School of Public Health.
FAU - Peterson, Trevor A
AU  - Peterson TA
AD  - Department of Medical Microbiology, University of Manitoba, 730 William Avenue, 
      Winnipeg, Manitoba R3E 0Z2, Canada, National Microbiology Laboratory, Winnipeg, 
      Manitoba, Canada.
FAU - Bielawny, Thomas
AU  - Bielawny T
AD  - Department of Medical Microbiology, University of Manitoba, 730 William Avenue, 
      Winnipeg, Manitoba R3E 0Z2, Canada, National Microbiology Laboratory, Winnipeg, 
      Manitoba, Canada.
FAU - Ali, Mohammad
AU  - Ali M
AD  - Life Sciences Institute.
FAU - Tay, Koon-Yong
AU  - Tay KY
AD  - Life Sciences Institute.
FAU - Poh, Wan-Ting
AU  - Poh WT
AD  - Saw Swee Hock School of Public Health.
FAU - Tan, Linda Wei-Lin
AU  - Tan LW
AD  - Saw Swee Hock School of Public Health.
FAU - Koo, Seok-Hwee
AU  - Koo SH
AD  - Department of Pharmacology, National University of Singapore, Singapore 117597, 
      Singapore.
FAU - Lim, Wei-Yen
AU  - Lim WY
AD  - Saw Swee Hock School of Public Health.
FAU - Soong, Richie
AU  - Soong R
AD  - Cancer Science Institute of Singapore, National University of Singapore, 
      Singapore 117599, Singapore.
FAU - Wenk, Markus
AU  - Wenk M
AD  - Department of Biochemistry, National University of Singapore, Singapore 117596, 
      Singapore, Department of Biological Sciences, National University of Singapore, 
      Singapore 117543, Singapore.
FAU - Raychaudhuri, Soumya
AU  - Raychaudhuri S
AD  - Division of Rheumatology, Immunology, and Allergy, Division of Genetics, Brigham 
      and Women's Hospital, Harvard Medical School, Boston, MA, USA, Program in Medical 
      and Population Genetics, Broad Institute, Cambridge, MA, USA, Centre for Human 
      Genetic Research, Massachusetts General Hospital, Boston, MA 02114-2790, USA.
FAU - Little, Peter
AU  - Little P
AD  - Life Sciences Institute.
FAU - Plummer, Francis A
AU  - Plummer FA
AD  - Department of Medical Microbiology, University of Manitoba, 730 William Avenue, 
      Winnipeg, Manitoba R3E 0Z2, Canada, National Microbiology Laboratory, Winnipeg, 
      Manitoba, Canada.
FAU - Lee, Edmund J D
AU  - Lee EJ
AD  - Department of Pharmacology, National University of Singapore, Singapore 117597, 
      Singapore.
FAU - Chia, Kee-Seng
AU  - Chia KS
AD  - Saw Swee Hock School of Public Health.
FAU - Luo, Ma
AU  - Luo M
AD  - Department of Medical Microbiology, University of Manitoba, 730 William Avenue, 
      Winnipeg, Manitoba R3E 0Z2, Canada, National Microbiology Laboratory, Winnipeg, 
      Manitoba, Canada.
FAU - De Bakker, Paul I W
AU  - De Bakker PI
AD  - Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA, 
      Centre for Human Genetic Research, Massachusetts General Hospital, Boston, MA 
      02114-2790, USA.
FAU - Teo, Yik-Ying
AU  - Teo YY
AD  - Saw Swee Hock School of Public Health, Life Sciences Institute, Department of 
      Statistics and Applied Probability, National University of Singapore, Singapore, 
      Singapore, NUS Graduate School for Integrative Science and Engineering, National 
      University of Singapore, Singapore 117456, Singapore and Agency for Science, 
      Technology and Research, Genome Institute of Singapore, Singapore 138672, 
      Singapore statyy@nus.edu.sg.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20140403
PL  - England
TA  - Hum Mol Genet
JT  - Human molecular genetics
JID - 9208958
RN  - 0 (HLA Antigens)
RN  - 0 (HLA-DP alpha-Chains)
RN  - 0 (HLA-DP beta-Chains)
RN  - 0 (HLA-DPA1 antigen)
RN  - 0 (HLA-DPB1 antigen)
SB  - IM
MH  - *Alleles
MH  - Asian People/genetics/statistics & numerical data
MH  - Genetic Loci
MH  - HLA Antigens/*genetics
MH  - HLA-DP alpha-Chains/*genetics
MH  - HLA-DP beta-Chains/*genetics
MH  - Humans
MH  - Major Histocompatibility Complex/genetics
MH  - *Polymorphism, Single Nucleotide
EDAT- 2014/04/05 06:00
MHDA- 2016/03/24 06:00
CRDT- 2014/04/05 06:00
PHST- 2014/04/05 06:00 [entrez]
PHST- 2014/04/05 06:00 [pubmed]
PHST- 2016/03/24 06:00 [medline]
AID - ddu149 [pii]
AID - 10.1093/hmg/ddu149 [doi]
PST - ppublish
SO  - Hum Mol Genet. 2014 Aug 15;23(16):4443-51. doi: 10.1093/hmg/ddu149. Epub 2014 Apr 
      3.