PMID- 21254215
OWN - NLM
STAT- MEDLINE
DCOM- 20110427
LR  - 20211020
IS  - 1098-2272 (Electronic)
IS  - 0741-0395 (Print)
IS  - 0741-0395 (Linking)
VI  - 35
IP  - 2
DP  - 2011 Feb
TI  - Predicting multiallelic genes using unphased and flanking single nucleotide 
      polymorphisms.
PG  - 85-92
LID - 10.1002/gepi.20549 [doi]
AB  - Recent advances in genotyping technologies have enabled genomewide association 
      studies (GWAS) of many complex traits including autoimmune disease, infectious 
      disease, cancer and heart disease. To facilitate interpretations and establish 
      biological basis, it could be advantageous to identify alleles of functional 
      genes, beyond just single nucleotide polymorphisms (SNPs) within or nearby genes. 
      Leslie et al. ([2008] Am J Hum Genet 82:48-56) have proposed an 
      Identity-by-Decent method (IBD-based) for predicting human leukocyte antigen 
      (HLA) alleles (multiallelic and highly polymorphic) with SNP data, and 
      predictions have achieved a satisfactory accuracy on the order of 97%. Building 
      upon their success, we introduce a complementary method for predicting highly 
      polymorphic alleles using unphased SNP data as the training data set. Due to its 
      generality and flexibility, the new method is readily applicable to large 
      population studies. Applying it to HLA genes in a cohort of 630 healthy 
      individuals as a training set, we constructed predictive models for HLA-A, B, C, 
      DRB1 and DQB1. Then, we performed a validation study with another cohort of 630 
      healthy individuals, and the predictive models achieved predictive accuracies for 
      HLA alleles defined at intermediate or high resolution ranging as high as (100%, 
      97%) for HLA-A, (98%, 96%) for B, (98%, 98%) for C, (97%, 96%) for DRB1 and (98%, 
      95%) for DQB1, respectively. These preliminary results suggest the feasibility of 
      predicting other polymorphic genetic alleles, since HLA loci are almost certainly 
      among most polymorphic genes.
CI  - (c) 2011 Wiley-Liss, Inc.
FAU - Li, Shuying S
AU  - Li SS
AD  - Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 
      Seattle, Washington 98109-1024, USA.
FAU - Wang, Hongwei
AU  - Wang H
FAU - Smith, Anajane
AU  - Smith A
FAU - Zhang, Bo
AU  - Zhang B
FAU - Zhang, Xinyi Cindy
AU  - Zhang XC
FAU - Schoch, Gary
AU  - Schoch G
FAU - Geraghty, Daniel
AU  - Geraghty D
FAU - Hansen, John A
AU  - Hansen JA
FAU - Zhao, Lue Ping
AU  - Zhao LP
LA  - eng
GR  - R01 CA106320/CA/NCI NIH HHS/United States
GR  - R01 MH084621-03/MH/NIMH NIH HHS/United States
GR  - R01 CA119225-03/CA/NCI NIH HHS/United States
GR  - R01CA106320/CA/NCI NIH HHS/United States
GR  - R01CA119225/CA/NCI NIH HHS/United States
GR  - R01 CA119225/CA/NCI NIH HHS/United States
GR  - R01 MH084621/MH/NIMH NIH HHS/United States
GR  - R01MH084621/MH/NIMH NIH HHS/United States
GR  - R01 HL087690/HL/NHLBI NIH HHS/United States
GR  - R01 CA106320-07/CA/NCI NIH HHS/United States
GR  - R01 HL087690-03/HL/NHLBI NIH HHS/United States
GR  - R01HL087690/HL/NHLBI NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
DEP - 20101231
PL  - United States
TA  - Genet Epidemiol
JT  - Genetic epidemiology
JID - 8411723
RN  - 0 (HLA Antigens)
RN  - 0 (HLA-A Antigens)
RN  - 0 (HLA-B Antigens)
RN  - 0 (HLA-C Antigens)
RN  - 0 (HLA-DQ Antigens)
RN  - 0 (HLA-DQ beta-Chains)
RN  - 0 (HLA-DQbeta antigen)
RN  - 0 (HLA-DR Antigens)
SB  - IM
MH  - *Alleles
MH  - Cohort Studies
MH  - Genetic Techniques
MH  - Genetics, Population
MH  - HLA Antigens/*genetics
MH  - HLA-A Antigens/genetics
MH  - HLA-B Antigens/genetics
MH  - HLA-C Antigens/genetics
MH  - HLA-DQ Antigens/genetics
MH  - HLA-DQ beta-Chains
MH  - HLA-DR Antigens/genetics
MH  - Haplotypes
MH  - Humans
MH  - Molecular Epidemiology
MH  - Polymorphism, Genetic
MH  - *Polymorphism, Single Nucleotide
MH  - Reproducibility of Results
PMC - PMC3057054
MID - NIHMS265768
EDAT- 2011/01/22 06:00
MHDA- 2011/04/28 06:00
PMCR- 2012/02/01
CRDT- 2011/01/22 06:00
PHST- 2010/07/23 00:00 [received]
PHST- 2010/10/11 00:00 [accepted]
PHST- 2011/01/22 06:00 [entrez]
PHST- 2011/01/22 06:00 [pubmed]
PHST- 2011/04/28 06:00 [medline]
PHST- 2012/02/01 00:00 [pmc-release]
AID - 10.1002/gepi.20549 [doi]
PST - ppublish
SO  - Genet Epidemiol. 2011 Feb;35(2):85-92. doi: 10.1002/gepi.20549. Epub 2010 Dec 31.