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# Pre-built Pan-Asian reference panel for SNP2HLA
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# Author: Yukinori Okada (yokada.brc@tmd.ac.jp, yokada@broadinstitute.org)
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# USAGE: ./SNP2HLA.csh DATA (.bed/.bim/.fam) ../Pan-Asian/Pan-Asian_REF (.bgl.phased/.markers) OUTPUT plink {optional: max_memory[mb] window_size}
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Thank you for downloading SNP2HLA.
This is a pre-built reference panel based on the data of pan-Asian subjects (including Han Chinese, Southeast Asian Malay, Tamil Indian ancestries, and Japanese).
Total 530 individuals are included that are all classical typed for HLA-A, B, C, DRB1, DQA1, DQB1, DPB1, DPA1 4-digit alleles.
This reference panel will be a useful resource for imputing HLA alleles for Asian population data.
For other populations, it may be necessary to type HLA alleles for a subset of the cohort and use MakeReference software to build the population specific reference panel.

Details of the reference panel are described at;

1. Pillai NE et al. (2014) Predicting HLA alleles from high-resolution SNP data in three Southeast Asian populations. Hum Mol Genet, doi:10.1093/hmg/ddu149.
2. Okada Y et al. (2014) Risk for ACPA-positive rheumatoid arthritis is driven by shared HLA amino acid polymorphisms in Asian and European populations. Hum Mol Genet, In Press.


