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 HLA genes in the IHWG reference B-lymphoblastoid cell lines (B-LCLs) was one of the major goals for the 17th International HLA and Immunogenetics Workshop (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 HLA genes. To address this, we conducted a single-blind study where select panels of B-LCL genomic DNA samples were distributed to multiple laboratories for HLA genotyping 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 HLA genotypes. 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 genes was 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 HLA genotypes with the HLA genotypes catalogued in the IPD-IMGT/HLA Database 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 HLA genotypes for some samples listed in the IPD-IMGT/HLA Database Cell Repository. Our approach of multiple-laboratory NGS HLA typing of the B-LCLs has provided accurate genotyping data. The data generated by the tremendous collaborative efforts of the 17th IHIW participants is useful for updating the current cell and sequence databases and will be a valuable resource for future studies.

HLA class II immunopeptidomics reveals that co‐inherited HLA‐allotypes within an extended haplotype can improve proteome coverage for immunosurveillance

“…The differential pairing of the 03:01 beta chain gives rise to four DQ7 haplotypes referred to as DQ7.3, DQ7.4, DQ7.5, and DQ7.6. The C1R cells used in this study were shown to express DQA1*0505 paired with HLA DQB1*0301 (HLA DQ7.5) through a combination of DNA tissue typing and proteomic analysis of the expressed alpha chain which is consistent with literature [57]. HLA DQ7.5 is common in South‐eastern European and Eastern Mediterranean populations and the extended haplotype of HLA DR11‐DQ7.5 has been linked to protection against T1D diabetes [58] and susceptibility to Juvenile idiopathic arthritis, a heterogeneous group of chronic inflammatory joint diseases of childhood [56, 59].…”

Next-Generation Sequencing Identifies Extended HLA Class I and II Haplotypes Associated With Early-Onset and Late-Onset Myasthenia Gravis in Italian, Norwegian, and Swedish Populations

“…Next-generation sequencing (NGS) is an attractive option for variant characterization of HLA genes due to its comparatively low cost, high-accuracy and unbiased variant discovery. NGS of extended HLA gene segments has been applied successfully in population-based and trait-association studies to identify allelic variants in non-coding regions, and to achieve mostly unambiguous HLA genotyping (28)(29)(30)(31). In this study, we report the analyses of HLA alleles and haplotypes, defined using high-resolution NGS, associated with susceptibility and protection to EOMG and LOMG in Italian, Norwegian, and Swedish cohorts.…”

Recombinant HA-based vaccine outperforms split and subunit vaccines in elicitation of influenza-specific CD4 T cells and CD4 T cell-dependent antibody responses in humans

“…Elicitation of CD4 T cells by influenza vaccines requires host HLA class II molecules to bind and present peptides derived from the H1, H3 and HA-B proteins. HLA is highly variable in humans 26 , 27 and thus each subject likely presents a distinct constellation of vaccine HA-derived peptides. Therefore, without any knowledge of the HLA class II molecules expressed, it is not possible to predict the potential of any subject to respond to the influenza-derived epitopes.…”