Next-generation HLA typing of 382 International Histocompatibility Working Group reference B-Lymphoblastoid cell lines: report from the 17th International HLA and Immunogenetics Workshop

Abstract Extended molecular characterization of HLAgenes in the IHWG reference B-lymphoblastoid cell lines (B-LCLs) was one of the major goals for the 17 th International HLAand ImmunogeneticsWorkshop (IHIW). Although reference B-LCLs have been examined extensively in previous workshops complete high-resolution typing was not completed for all the classical class I and class II HLAgenes. To address this, we conducted a single-blind study where select panels of B-LCL genomic DNA samples were distributed to multiple laboratories for HLAgenotyping by next-generation sequencing methods. Identical cell panels comprised of 24 and 346 samples were distributed and typed by at least four laboratories in order to derive accurate consensus HLAgenotypes. Overall concordance rates calculated at both 2- and 4-field allele-level resolutions ranged from 90.4% to 100%. Concordance for the class I genes ranged from 91.7 to 100%, whereas concordance for class II geneswas variable; the lowest observed at HLA-DRB3(84.2%). At the maximum allele-resolution 78 B-LCLs were defined as homozygous for all 11 loci. We identified 11 novel exon polymorphisms in the entire cell panel. A comparison of the B-LCLs NGS HLAgenotypes with the HLAgenotypes catalogued in the IPD-IMGT/ HLADatabase Cell Repository, revealed an overall allele match at 68.4%. Typing discrepancies between the two datasets were mostly due to the lower-resolution historical typing methods resulting in incomplete HLAgenotypes for some samples listed in the IPD-IMGT/ HLADatabase Cell Repository. Our approach of multiple-laboratory NGS HLAtyping of the B-LCLs has provided accurate genotyping data. The data generated by the tremendous collaborative efforts of the 17 th IHIW participants is useful for updating the current cell and sequence databasesand will be a valuable resource for future studies.