Our server offers imputation from the following reference panels:
HRC (Version r1.1 2016)
The HRC panel consists of 64,940 haplotypes of predominantly European ancestry.
|Number of Samples||32,470|
|Website||http://www.haplotype-reference-consortium.org; HRC r1.1 Release Note|
1000 Genomes Phase 3 (Version 5)
Phase 3 of the 1000 Genomes Project consists of 5,008 haplotypes from 26 populations across the world.
|Number of Samples||2,504|
Genome Asia Pilot - GAsP
|Number of Samples||1,654|
Genome Asia v2 - GAsP
|Number of Samples||6,461|
Four-digit Multi-ethnic HLA v1 (2021)
The multi-ethnic HLA panel consists of 36,586 haplotypes of five global populations. We have released the panel at both two-field (four-digit) and G-group resolution.
|Number of Samples||18,293|
|Sites (chr6)||56,310 (1,781 HLA alleles; 4,513 HLA amino acids; 10,924 SNPs within HLA; 39,092 scaffold SNPs)|
Please cite this manuscript if you would like to include imputed results from the panel in your work:
Luo, Y., Kanai, M., Choi, W., Li, X., Yamamoto, K., Ogawa, K., Gutierrez-Arcelus, M., Gregersen, P. K., Stuart, P. E., Elder, J. T., Fellay, J., Carrington, M., Haas, D. W., Guo, X., Palmer, N. D., Chen, Y.-D. I., Rotter, J. I., Taylor, K. D., Rich, S., … Raychaudhuri, S. (2020). A high-resolution HLA reference panel capturing global population diversity enables multi-ethnic fine-mapping in HIV host response. https://doi.org/10.1101/2020.07.16.20155606
Four-digit Multi-ethnic HLA v2 (2022)
|Number of Samples||20,349|
|Sites (chr6)||22,733 (570 HLA alleles; 3,449 HLA amino acids; 4,023 SNPs within HLA; 14,691 scaffold SNPs)|
Multi-ethnic HLA v2 Details
- We added Japanese samples with HLA alleles called with deep target sequencing (n = 723; Hirata et al. Nat Genet. 2019).
- Add Estonian biobank samples with IRB approval (n = 2,233; Mitt et al. Eur J Hum Genet. 2017).
- We used gold-standard HLA allele calls (instead of inferred calls from whole genome sequencing) when possible.
- We updated and recalled HLA alleles using HLA-LA (Dilthey et al. Bioinformatics. 2019) in Jackson Heart Study (n = 3,026).
- We updated and recalled HLA alleles using HLA-LA in Estonian Biobank (n = 2,233).
- We added population-specific SNP variants which are common in one population but rare in the other populations when they are in 1KG and pass QC, by cross-cohort SNP imputation within the reference panel.
- We removed all SNP variants that are not included in the commonly-used genotyping arrays.
- We optimized
--topThresholdparameters in minimac4. Optimized parameters are now used for all HLA panels.
- We output 2-digit and 4-digit-resolution HLA alleles. We do not output higher resolution HLA alleles in this version.
CAAPA - African American Panel
Whole genome sequences were available on 883 individuals from 19 case-control studies of asthma included in the Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) and were used to summarize the genomic contributions to individuals of African ancestry.
|Number of Samples||883|
|Website||http://www.caapa-project.org/. Further details can also be found here|
HRC (Version r1 2015)
This HRC panel consists of 64,976 haplotypes of predominantly European ancestry.
|Number of Samples||32,488|
|Website||http://www.haplotype-reference-consortium.org; HRC r1 Release Note|
1000 Genomes Phase 1 (Version 3)
|Number of Samples||1,092|
|Number of Samples||60|