PMID- 21385049
OWN - NLM
STAT- MEDLINE
DCOM- 20110622
LR  - 20191210
IS  - 1557-8666 (Electronic)
IS  - 1066-5277 (Linking)
VI  - 18
IP  - 3
DP  - 2011 Mar
TI  - HLA type inference via haplotypes identical by descent.
PG  - 483-93
LID - 10.1089/cmb.2010.0258 [doi]
AB  - The human leukocyte antigen (HLA) genes play a major role in adaptive immune 
      response and are used to differentiate self antigens from non-self ones. HLA 
      genes are hypervariable with nearly every locus harboring over a dozen alleles. 
      This variation plays an important role in susceptibility to multiple autoimmune 
      diseases and needs to be matched on for organ transplantation. Unfortunately, HLA 
      typing by serological methods is time consuming and expensive compared to 
      high-throughput single nucleotide polymorphism (SNP) data. We present a new 
      computational method to infer per-locus HLA types using shared segments identical 
      by descent (IBD), inferred from SNP genotype data. IBD information is modeled as 
      graph where shared haplotypes are explored among clusters of individuals with 
      known and unknown HLA types to identify the latter. We analyze performance of the 
      method in a previously typed subset of the HapMap population, achieving accuracy 
      of 96% in HLA-A, 94% in HLA-B, 95% in HLA-C, 77% in HLA-DR1, 93% in HLA-DQA1, and 
      90% in HLA-DQB1 genes. We compare our method to a tag SNP-based approach, and 
      demonstrate higher sensitivity and specificity. Our method demonstrates the power 
      of using shared haplotype segments for large-scale imputation at the HLA locus.
FAU - Setty, Manu N
AU  - Setty MN
AD  - Computational Biology Program, Memorial Sloan-Kettering Cancer Center, New York, 
      New York, USA.
FAU - Gusev, Alexander
AU  - Gusev A
FAU - Pe'er, Itsik
AU  - Pe'er I
LA  - eng
PT  - Evaluation Study
PT  - Journal Article
PL  - United States
TA  - J Comput Biol
JT  - Journal of computational biology : a journal of computational molecular cell 
      biology
JID - 9433358
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 alpha-Chains)
RN  - 0 (HLA-DQA1 antigen)
RN  - 0 (HLA-DR1 Antigen)
SB  - IM
MH  - Algorithms
MH  - Genomics/*methods
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 alpha-Chains
MH  - HLA-DR1 Antigen/genetics
MH  - *Haplotypes
MH  - Humans
MH  - Polymorphism, Single Nucleotide
MH  - Sensitivity and Specificity
EDAT- 2011/03/10 06:00
MHDA- 2011/06/23 06:00
CRDT- 2011/03/10 06:00
PHST- 2011/03/10 06:00 [entrez]
PHST- 2011/03/10 06:00 [pubmed]
PHST- 2011/06/23 06:00 [medline]
AID - 10.1089/cmb.2010.0258 [doi]
PST - ppublish
SO  - J Comput Biol. 2011 Mar;18(3):483-93. doi: 10.1089/cmb.2010.0258.