Improve availability of publicly available, renewable, and well-characterized genomic DNA reference materials to support molecular HLA typing assay development, validation and verification, quality control, and proficiency testing.
The Centers for Disease Control and Prevention’s (CDC) Genetic Testing Reference Materials Coordination Program (GeT-RM) together with three clinical laboratories and the Coriell Cell Repositories characterized genomic DNA from 108 cell lines for HLA-A, B, C, DRB1, DRB3, DRB4, DRB5, DQA1, DQB1, DPA1, and DPB1. DNA was isolated by the Coriell Cell Repositories and distributed to the 3 laboratories. Methodologies used were: PCR-SSO-LABType® SSO (One Lambda, Canoga Park, CA), SSP – Olerup SSP® (Stockholm, Sweden), SBT-AlleleSEQR® HLA-SBT (Abbott Molecular, Des Plaines, IL) and NGS – HoloType HLA™ kits (Omixon Inc., Budapest, Hungary). Each of the 11 genes was tested by 2 or 3 methods. Consensus genotype was the NGS result, which provided the highest level of resolution, and was consistent with the results obtained by the parallel testing using other methods.
HLA typing results using SBT, SSP, SSO and NGS were 99.95 % concordant. Of the 1905 alleles typed, only one discrepancy was observed. The discrepant result was found to be due to an error in SBT/SSO typing. Five unique novel alleles with differences in exonic regions were identified and three were submitted to the WHO Nomenclature Committee. Ambiguities persisted in 50/1905 allele calls, most due to alternative cis/trans combinations of exons 2 and 3 of DPB1 (n = 21 pairs: 42 alleles) and 8 caused by polymorphisms in a non-covered region (exon1) of the DRB1and DPB1 genes. Thirty HLA-A, 54-B, 30-C, 36-DRB1, 4-DRB3, 4-DRB4, 3-DRB5, 19-DQA1, 17-DQB1, 10-DPA1 and 29-DPB1 alleles are represented in the panel. These alleles cover a high percentage of HLA specificities present in five ancestry groups in the USA population.
These genomic DNA samples are publicly available from the National Institutes of General Medical Science (NIGMS) Repository at the Coriell Cell Repositories.
M. Bettinotti: 3. Speaker’s Bureau; Company/Organization; One Lambda Thermo Fisher. D. Ferriola: 7. Other (Identify); Company/Organization; Licensing proceeds of the HLA-NGS protocol by CHOP to Omixon. J.L. Duke: 7. Other (Identify); Company/Organization; receiving proceeds from the licensing of the HLA-NGS protocol by CHOP to Omixon. D. Monos: 4. Scientific/Medical Advisor; Company/Organization; Omixon. 7. Other (Identify); Company/Organization; receiving proceeds from the licensing of the HLA-NGS protocol by CHOP to Omixon.