PMID- 23712092
OWN - NLM
STAT- MEDLINE
DCOM- 20141121
LR  - 20221207
IS  - 1473-1150 (Electronic)
IS  - 1470-269X (Print)
IS  - 1470-269X (Linking)
VI  - 14
IP  - 2
DP  - 2014 Apr
TI  - HIBAG--HLA genotype imputation with attribute bagging.
PG  - 192-200
LID - 10.1038/tpj.2013.18 [doi]
AB  - Genotyping of classical human leukocyte antigen (HLA) alleles is an essential 
      tool in the analysis of diseases and adverse drug reactions with associations 
      mapping to the major histocompatibility complex (MHC). However, deriving 
      high-resolution HLA types subsequent to whole-genome single-nucleotide 
      polymorphism (SNP) typing or sequencing is often cost prohibitive for large 
      samples. An alternative approach takes advantage of the extended haplotype 
      structure within the MHC to predict HLA alleles using dense SNP genotypes, such 
      as those available from genome-wide SNP panels. Current methods for HLA 
      imputation are difficult to apply or may require the user to have access to large 
      training data sets with SNP and HLA types. We propose HIBAG, HLA Imputation using 
      attribute BAGging, that makes predictions by averaging HLA-type posterior 
      probabilities over an ensemble of classifiers built on bootstrap samples. We 
      assess the performance of HIBAG using our study data (n=2668 subjects of European 
      ancestry) as a training set and HLA data from the British 1958 birth cohort study 
      (n approximately 1000 subjects) as independent validation samples. Prediction accuracies for 
      HLA-A, B, C, DRB1 and DQB1 range from 92.2% to 98.1% using a set of SNP markers 
      common to the Illumina 1M Duo, OmniQuad, OmniExpress, 660K and 550K platforms. 
      HIBAG performed well compared with the other two leading methods, HLA*IMP and 
      BEAGLE. This method is implemented in a freely available HIBAG R package that 
      includes pre-fit classifiers for European, Asian, Hispanic and African 
      ancestries, providing a readily available imputation approach without the need to 
      have access to large training data sets.
FAU - Zheng, X
AU  - Zheng X
AD  - Department of Biostatistics, University of Washington, Seattle, WA, USA.
FAU - Shen, J
AU  - Shen J
AD  - Quantitative Sciences, GlaxoSmithKline, Research Triangle Park, NC, USA.
FAU - Cox, C
AU  - Cox C
AD  - Quantitative Sciences, GlaxoSmithKline, Stevenage, UK.
FAU - Wakefield, J C
AU  - Wakefield JC
AD  - Department of Biostatistics, University of Washington, Seattle, WA, USA.
FAU - Ehm, M G
AU  - Ehm MG
AD  - Quantitative Sciences, GlaxoSmithKline, Research Triangle Park, NC, USA.
FAU - Nelson, M R
AU  - Nelson MR
AD  - Quantitative Sciences, GlaxoSmithKline, Research Triangle Park, NC, USA.
FAU - Weir, B S
AU  - Weir BS
AD  - Department of Biostatistics, University of Washington, Seattle, WA, USA.
LA  - eng
GR  - Wellcome Trust/United Kingdom
GR  - G1001799/MRC_/Medical Research Council/United Kingdom
GR  - R01 GM075091/GM/NIGMS NIH HHS/United States
GR  - GM 75091/GM/NIGMS NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
DEP - 20130528
PL  - United States
TA  - Pharmacogenomics J
JT  - The pharmacogenomics journal
JID - 101083949
RN  - 0 (HLA Antigens)
SB  - IM
MH  - Alleles
MH  - Asian People/genetics
MH  - Drug-Related Side Effects and Adverse Reactions/*genetics
MH  - Genome-Wide Association Study
MH  - Genotype
MH  - HLA Antigens/*genetics
MH  - Haplotypes
MH  - Humans
MH  - Major Histocompatibility Complex/*genetics
MH  - Polymorphism, Single Nucleotide
MH  - White People/genetics
PMC - PMC3772955
MID - NIHMS457572
EDAT- 2013/05/29 06:00
MHDA- 2014/12/15 06:00
CRDT- 2013/05/29 06:00
PHST- 2012/08/08 00:00 [received]
PHST- 2013/02/15 00:00 [revised]
PHST- 2013/03/18 00:00 [accepted]
PHST- 2013/05/29 06:00 [entrez]
PHST- 2013/05/29 06:00 [pubmed]
PHST- 2014/12/15 06:00 [medline]
AID - tpj201318 [pii]
AID - 10.1038/tpj.2013.18 [doi]
PST - ppublish
SO  - Pharmacogenomics J. 2014 Apr;14(2):192-200. doi: 10.1038/tpj.2013.18. Epub 2013 
      May 28.