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



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  • person_outline Alexander Dilthey <>

Publications for HLA*IMP

HLA*IMP in publications

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

[…] 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 […]

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

[…] 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 […]

PMCID: 5520018
PMID: 28714469
DOI: 10.1038/ncomms16021

[…] 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 […]

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

[…] 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 […]

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

[…] 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 […]

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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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