T1DGC HLA Reference Panel for Imputation with SNP2HLA

The [T1DGC Immunochip/HLA Reference Panel](http://www.ncbi.nlm.nih.gov/pubmed/23762245) (described in Jia et al., PLoS ONE 2013; Jun 6;8(6):e64683) enables accurate imputation of classical HLA types starting from SNP genotype data. Exploiting long-range linkage disequilibrium between HLA loci and SNP markers across the major histocompatibility complex (MHC) region, a computational strategy, called SNP2HLA, has been developed to impute classical alleles and amino acid polymorphisms at class I (HLA-A, -B, -C) and class II (-DPA1, -DPB1, -DQA1, -DQB1, and -DRB1) loci. A European ancestry reference panel was constructed based on data collected by the Type 1 Diabetes Genetics Consortium (T1DGC, 5,225 individuals). For validation, HLA alleles were imputed in the British 1958 Birth Cohort (N = 918) with gold-standard four-digit HLA types and SNPs genotyped using the Affymetrix GeneChip 500K and Illumina ImmunoChip microarrays. Using the T1DGC reference panel, the average accuracy at four-digit resolution is 96.7% using the high-density Illumina Immunochip. For amino acid polymorphisms within HLA genes, accuracy was 99.3% using the Illumina ImmunoChip. A link to the SNP2HLA software via the Broad institute is located below. The T1DGC reference panel can be accessed by submitting a request from this page.

* [The SNP2HLA software package](http://www.broadinstitute.org/mpg/snp2hla/)
* [T1DGC main study](/studies/t1dgc/)

<b>Note: The panel may only be used for research in the areas of diabetes, autoimmune diseases and diabetes complications.</b>