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HLA imputation
HLA-TAPAS imputes classical HLA alleles, amino acids, and SNPs in the MHC region from GWAS genotyping array data. There are five types of HLA markers: (1) binary marker for classical HLA alleles; (2) binary marker for the presence/absence of a specific amino acid residue; (3) HLA intragenic SNPs, and (4) binary markers for insertion/deletions, as described in the typical output below. The goal is to minimize prior assumption on which types of variations will be causal and test all types of variations simultaneously in an unbiased fashion. However, the users are always free to restrict analyses to specific marker subsets.
For binary encodings, T = Present, A = Absent.
| Type | Format | Example |
|---|---|---|
| Classical HLA alleles | HLA_[GENE]*[ALLELE] | HLA_A*01:02 (two-field allele); HLA_A*02 (one-field allele) |
| HLA amino acids | AA_[GENE]_[AMINO ACID POSITION]_[GENOMIC POSITION]_[EXON#]_[RESIDUE] | AA_B_97_31324201_exon3_V (amino acid position 97 in HLA-B, genomic position 31324201 (GRCh37) in exon 3, residue = V (Val) ); AA_B_97_31324201_exon3_VW (amino acid position 97 in HLA-B, genomic position 31324201 (GRCh37) in exon 3, residue = V (Val) or W (Trp)) ; AA_A_60_29910711_exon2_X (amino acid position 60 in HLA-A, genomic position 29910711 (GRCh37) in exon 2, undefined residue (based on the IMTG/HLA reference with "N" in the sequence)); AA_A_60_29910711_exon2_x (amino acid position 60 in HLA-A, genomic position 29910711 (GRCh37) in exon 2, insertion/deletion); AA_A_60_29910711_exon2_. (amino acid position 60 in HLA-A, genomic position 29910711 (GRCh37) in exon 2, unmapped (based on the IMTG/HLA reference with "*" in the sequence)) |
| HLA intragenic SNPs | SNPS_[GENE]_[GENE POSITION]_[GENOMIC POSITION]_[EXON/INTRON] | SNPS_C_2666_31237183_intron6 (SNP at position 2666 of the gene body, genomic position 31237183 in intron 6) |
| Insertions/deletions | INDEL_[TYPE]_[GENE]_[POSITION] | INDEL_AA_C_300x301_31237792 Indel between amino acids 300 and 301 in HLA-C, at genomic position 31237792) |
Our multi-ethnic HLA reference panel is now available on the michigan imputation server! This panel consists of >21,000 individuals of five global populations, greatly improving upon existing HLA panels.
The European only T1DGC reference panel (N=5,225) can be obtained by contacting the NIDDK Central Repository