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HLA*IMP specifications


Unique identifier OMICS_19620
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, Perl
License GNU General Public License version 3.0
Computer skills Medium
Version 1.3.2
Stability Stable
Maintained Yes




No version available


  • person_outline Alexander Dilthey

Publications for HLA*IMP

HLA*IMP citations


Hidden genomic MHC disparity between HLA matched sibling pairs in hematopoietic stem cell transplantation

Sci Rep
PMCID: 5876349
PMID: 29599509
DOI: 10.1038/s41598-018-23682-y

[…] r quality controls, 5137 SNPs were included in the study.The alleles of the classical HLA-A, -B, -C, -DRB1, -DQA1, -DQB1 and -DPB1 genes were imputed at four-digit resolution level using the software HLA*IMP:02 (The Oxford HLA Imputation Framework, UK). Missing data threshold was set to 0.20. SNPs were aligned and genotypes phased against HapMap (CEU) reference panel (hapmap3_r27_b36_fwd.consensus […]


Bayesian analysis of genetic association across tree structured routine healthcare data in the UK Biobank

Nat Genet
PMCID: 5580804
PMID: 28759005
DOI: 10.1038/ng.3926

[…] kbiobank.ac.uk/scientists-3/genetic-data). We imputed 356 classical HLA alleles for the HLA-A, -B, -C, -DRB5, -DRB4, -DRB3, -DRB1, -DQB1, -DQA1, -DPB1 and -DPA1 loci at four digit resolution with the HLA*IMP:02 algorithm, using data from a multi-population reference panel. The imputation panel contained 2,263 SNPs in the MHC region (GRCh37 coordinates chr6:29500000-33500000) which overlapped UK Bi […]


Transancestral mapping and genetic load in systemic lupus erythematosus

Nat Commun
PMCID: 5520018
PMID: 28714469
DOI: 10.1038/ncomms16021

[…] RB1 were imputed using the program HIBAG. HIBAG uses an ensemble classifier and bagging technique to arrive at an average posterior probability. Unlike alternative imputation software such as BEAGLE, HLA*IMP and SNP2HLA, HIBAG did not require training data for any of our three cohorts, as it provides multiple ancestry reference panels (European, African, Hispanic and Asian). This, combined with it […]


Maternal and neonatal vitamin D status, genotype and childhood celiac disease

PLoS One
PMCID: 5501391
PMID: 28686601
DOI: 10.1371/journal.pone.0179080

[…] at Oslo University Hospital performed single nucleotide polymorphism (SNP) genotyping using a Custom GoldenGate assay (Illumina, San Diego, CA, US) per manufacturer’s protocol. We used 66 tagSNPs and HLA*IMP:02 to impute the main human leukocyte antigen (HLA) class II haplotypes conferring a high risk for celiac disease.[] The imputed HLA genotype was confirmed using classical HLA genotyping with […]


The MHC locus and genetic susceptibility to autoimmune and infectious diseases

Genome Biol
PMCID: 5406920
PMID: 28449694
DOI: 10.1186/s13059-017-1207-1

[…] ne, glycine and serine) are protective.Several tools allowing imputation of classic HLA alleles at four-digit resolution are now available for MHC imputation analysis; the most common are SNP2HLA [], HLA*IMP:01 [], and an improved HLA*IMP:02 []. HLA*IMP:02 outperforms HLA*IMP:01 on heterogeneous European populations and it increases the power and accuracy in cross-European GWAS []. Missing data ar […]


Genetic and environmental risk factors for rheumatoid arthritis in a UK African ancestry population: the GENRA case–control study

PMCID: 5638023
PMID: 28407095
DOI: 10.1093/rheumatology/kex048

[…] lso has limitations. First, the absence of HLA allele genotyping prevented imputation internal validation; however, posterior-probability scores suggested common HLA variants were accurately imputed: HLA*IMP:02 has documented accuracy at imputing HLA alleles [], and the SE prevalence in GENRA (24%) was similar to that observed in Cameroonian RA cases (30%) []. Second, as RA patients retrospectivel […]

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HLA*IMP institution(s)
Department of Statistics, University of Oxford, Oxford, UK; Wellcome Trust Centre for Human Genetics, Oxford, UK; Murdoch Childrens Research Institute, Royal Children’s Hospital, Parkville, VIC, Australia; Quantitative Sciences, GlaxoSmithKline, Research Triangle Park, NC, USA; Quantitative Sciences, GlaxoSmithKline, Stevenage, UK
HLA*IMP funding source(s)
Supported by Studienstiftung des deutschen Volkes, EPSRC, The Leverhulme Trust, HFSP, The Wellcome Trust, and GlaxoSmithKline. We also acknowledge funding from the Wellcome Trust core grant.

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