SNP2HLA statistics

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SNP2HLA specifications


Unique identifier OMICS_17675
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data SNP dataset and reference dataset.
Input format bed/bim/fam PLINK format and .bgl.phased/.markers Beagle formatbed/bim/fam PLINK format and .bgl.phased/.markers Beagle format
Operating system Unix/Linux
Computer skills Advanced
Version 1.0.3
Stability Stable
Maintained Yes



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Publication for SNP2HLA

SNP2HLA in publications

PMCID: 5955905
PMID: 29769526
DOI: 10.1038/s41467-018-04332-3

[…] was conducted using the genotypes from that variant as an additional covariate in a logistic regression implemented in epacts., we imputed classical hla alleles using the method implemented in the snp2hla v 1.0 package, which uses beagle v 3.0.4 as the imputation machine and the t1dgc reference panel. up to 424 hla alleles were imputed of which 190 had a maf > 1% in the following hla genes: […]

PMCID: 5929530
PMID: 29715290
DOI: 10.1371/journal.pone.0188911

[…] humanexome array contains a set of 2,459 snps that tag variation across the hla. we used these snps to impute snps, amino acids, and hla alleles across the region. imputation was performed using snp2hla,[] using the type 1 diabetes genetics consortium (t1dgc) reference panel of 5,225 unrelated individuals. this resulted in imputed data relating to 728 hla amino acids, 180 hla alleles, […]

PMCID: 5890276
PMID: 29632299
DOI: 10.1038/s41467-018-03178-z

[…] of cis,. association plots were generated using vispig., classical hla alleles were imputed, both common and rare (a, b, c, dqa1, dqb1, drb1) and coding variants across the hla region using snp2hla. the imputation was based on a reference panel from the t1dgc consisting of genotype data from 5225 individuals of european descent with genotyping data of 8961 common snps and indel […]

PMCID: 5876265
PMID: 29404672
DOI: 10.1007/s00125-018-4555-9

[…] snps in the mhc region were imputed using genotyped snps from illumina 1m beadarrays in dcct and illumina humancoreexome beadarrays in the joslin 50-year medalist, cacti, wesdr and edc studies; and snp2hla ( the type 1 diabetes genetic consortium (t1dgc) dataset (5196 unrelated individuals, including 4323 european participants: 182 participants […]

PMCID: 5806895
PMID: 29381699
DOI: 10.1371/journal.pgen.1007172

[…] using plink v1.07 []., targeted imputation was performed for hla haplotypes within the major histocompatibility complex using 9,785 high quality snps within the region; for this we utilised snp2hla software (version 1.0.3) and the default caucasian reference panel []. association tests for this targeted analysis were performed through the pipeline described above. similarly, 1,202 […]

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SNP2HLA institution(s)
Harvard-MIT (Massachusetts Institute of Technology) Division of Health Sciences and Technology, Boston, MA, USA; Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Division of Rheumatology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA; School of Medicine, University of Virginia, Charlottesville, VA, USA; Partners HealthCare Center for Personalized Genetic Medicine, Boston, MA, USA; Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK; Department of Epidemiology, University Medical Center Utrecht, Utrecht, Netherlands; Department of Medical Genetics, University Medical Center Utrecht, Utrecht, Netherlands
SNP2HLA funding source(s)
Supported by the Howard Hughes Medical Institute (Research Fellowship for Medical Students), the Bill and Melinda Gates Foundation (Collaboration for AIDS Vaccine Discovery sub-award), the National Institutes of Health (K08AR055688 and 1R01AR062886-01).

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