PMID- 22761960
OWN - NLM
STAT- MEDLINE
DCOM- 20130104
LR  - 20221207
IS  - 1932-6203 (Electronic)
IS  - 1932-6203 (Linking)
VI  - 7
IP  - 6
DP  - 2012
TI  - Prediction of HLA class II alleles using SNPs in an African population.
PG  - e40206
LID - 10.1371/journal.pone.0040206 [doi]
LID - e40206
AB  - BACKGROUND: Despite the importance of the human leukocyte antigen (HLA) gene 
      locus in research and clinical practice, direct HLA typing is laborious and 
      expensive. Furthermore, the analysis requires specialized software and expertise 
      which are unavailable in most developing country settings. Recently, in silico 
      methods have been developed for predicting HLA alleles using single nucleotide 
      polymorphisms (SNPs). However, the utility of these methods in African 
      populations has not been systematically evaluated. METHODOLOGY/PRINCIPAL 
      FINDINGS: In the present study, we investigate prediction of HLA class II 
      (HLA-DRB1 and HLA-DQB1) alleles using SNPs in the Wolaita population, southern 
      Ethiopia. The subjects comprised 297 Ethiopians with genome-wide SNP data, of 
      whom 188 had also been HLA typed and were used for training and testing the 
      model. The 109 subjects with SNP data alone were used for empirical prediction 
      using the multi-allelic gene prediction method. We evaluated accuracy of the 
      prediction, agreement between predicted and HLA typed alleles, and discriminative 
      ability of the prediction probability supplied by the model. We found that the 
      model predicted intermediate (two-digit) resolution for HLA-DRB1 and HLA-DQB1 
      alleles at accuracy levels of 96% and 87%, respectively. All measures of 
      performance showed high accuracy and reliability for prediction. The distribution 
      of the majority of HLA alleles in the study was similar to that previously 
      reported for the Oromo and Amhara ethnic groups from Ethiopia. 
      CONCLUSIONS/SIGNIFICANCE: We demonstrate that HLA class II alleles can be 
      predicted from SNP genotype data with a high level of accuracy at intermediate 
      (two-digit) resolution in an African population. This finding offers new 
      opportunities for HLA studies of disease epidemiology and population genetics in 
      developing countries.
FAU - Tekola Ayele, Fasil
AU  - Tekola Ayele F
AD  - Center for Research on Genomics and Global Health, National Human Genome Research 
      Institute, National Institutes of Health, Bethesda, Maryland, United States of 
      America. ayeleft@mail.nih.gov
FAU - Hailu, Elena
AU  - Hailu E
FAU - Finan, Chris
AU  - Finan C
FAU - Aseffa, Abraham
AU  - Aseffa A
FAU - Davey, Gail
AU  - Davey G
FAU - Newport, Melanie J
AU  - Newport MJ
FAU - Rotimi, Charles N
AU  - Rotimi CN
FAU - Adeyemo, Adebowale
AU  - Adeyemo A
LA  - eng
GR  - Wellcome Trust/United Kingdom
GR  - P20 MD006899/MD/NIMHD NIH HHS/United States
GR  - 079791/WT_/Wellcome Trust/United Kingdom
GR  - ImNIH/Intramural NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Intramural
PT  - Research Support, Non-U.S. Gov't
DEP - 20120628
PL  - United States
TA  - PLoS One
JT  - PloS one
JID - 101285081
RN  - 0 (Histocompatibility Antigens Class II)
SB  - IM
EIN - PLoS One. 2012;7(7): doi/10.1371/annotation/3529a6a2-4ba2-47dc-929e-399d441b0afa. 
      Ayele, Fasil Tekola [corrected ti Tekora Ayele, Fasil].
MH  - *Alleles
MH  - Black People/*genetics
MH  - Histocompatibility Antigens Class II/*genetics
MH  - Humans
MH  - *Polymorphism, Single Nucleotide
PMC - PMC3386230
COIS- Competing Interests: The authors have declared that no competing interests exist.
EDAT- 2012/07/05 06:00
MHDA- 2013/01/05 06:00
PMCR- 2012/06/28
CRDT- 2012/07/05 06:00
PHST- 2012/02/17 00:00 [received]
PHST- 2012/06/04 00:00 [accepted]
PHST- 2012/07/05 06:00 [entrez]
PHST- 2012/07/05 06:00 [pubmed]
PHST- 2013/01/05 06:00 [medline]
PHST- 2012/06/28 00:00 [pmc-release]
AID - PONE-D-12-04709 [pii]
AID - 10.1371/journal.pone.0040206 [doi]
PST - ppublish
SO  - PLoS One. 2012;7(6):e40206. doi: 10.1371/journal.pone.0040206. Epub 2012 Jun 28.