Common and well-documented HLA alleles: 2012 update to the CWD catalogue

We have updated the catalogue of common and well-documented (CWD) human leukocyte antigen (HLA) alleles to reflect current understanding of the prevalence of specific allele sequences. The original CWD catalogue designated 721 alleles at the HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, and -DPB1 loci in IMGT (IMmunoGeneTics)/HLA Database release 2.15.0 as being CWD. The updated CWD catalogue designates 1122 alleles at the HLA-A, -B, -C, -DRB1, -DRB3/4/5, -DQA1, -DQB1, -DPA1 and -DPB1 loci as being CWD, and represents 14.3% of the HLA alleles in IMGT/HLA Database release 3.9.0. In particular, we identified 415 of these alleles as being 'common' (having known frequencies) and 707 as being 'well-documented' on the basis of ~140,000 sequence-based typing observations and available HLA haplotype data. Using these allele prevalence data, we have also assigned CWD status to specific G and P designations. We identified 147/151 G groups and 290/415 P groups as being CWD. The CWD catalogue will be updated on a regular basis moving forward, and will incorporate changes to the IMGT/HLA Database as well as empirical data from the histocompatibility and immunogenetics community. This version 2.0.0 of the CWD catalogue is available online at cwd.immunogenomics.org, and will be integrated into the Allele Frequencies Net Database, the IMGT/HLA Database and National Marrow Donor Program's bioinformatics web pages.

Haplotype associations of 90 rare alleles from the National Marrow Donor Program

The National Marrow Donor Program maintains an HLA database of over 4.1 million US adult volunteers, 43,000 cord blood units, and 111,000 patients from which we identified 1,999,424 samples having allele-level HLA-A, HLA-B, or HLA-DRB1 results. We analyzed 811 rare alleles reported at a frequency of less than 1 in 50,000 in this study pool and found strong predicted haplotype associations for 90 of them. The data set includes the number of times the allele was seen, the predicted haplotypes, and the racial or ethnic groups in which it was identified. This information can be helpful in designing search strategies for patients with rare alleles requiring hematopoietic stem cell therapy.