Reduced PCR-generated errors from a hybrid capture-based NGS assay for HLA typing.

Next generation sequencing (NGS) assays are state of the art for HLA genotyping. To sequence on an Illumina sequencer, the DNA of interest must be enriched, fragmented, and bookended with known oligonucleotide sequences, a process known as library construction. Many HLA genotyping assays enrich the target loci by long-range PCR (LR-PCR), prior to fragmentation. This PCR step has been reported to introduce errors in the DNA to be sequenced, including inaccurate replication of repeated sequences, and the in vitro recombination of alleles encoded on separate chromosomes. An alternative library construction method involves fragmentation of genomic DNA, followed by hybrid-capture (HC) enrichment of target HLA loci. This HC-based method involves PCR, but with far fewer cycles. Consequently, the HC method had significantly fewer PCR-induced errors, including more faithful replication of repeated sequences, and the near elimination of recombinant sequences. These improvements likely produce more accurate NGS sequencing data of HLA loci.

New HLA alleles discovered by next generation sequencing in routine histocompatibility lab work in a medium-volume laboratory.

The immunogenetics research and clinical communities are undergoing a revolution in the way that Human Leukocyte Antigens (HLA) alleles are typed, thanks to the introduction and increasing acceptance of next-generation sequencing into laboratory practice. With the ability to sequence all exons of each allele, instead of the previously routine typing of exons 2 and 3 of class I and exon 2 of class II, the sequencing of previously unsequenced areas of HLA alleles is causing a host of new alleles to be discovered through the course of routine laboratory testing. In the first 4 months of routine next generation sequencing, we have identified 10 novel alleles that have been discovered through laboratory testing for all facets of HLA typing, i.e. solid organ transplantation, hematopoietic stem cell transplantation, disease association typing and pharmacogenomics testing. The advent of NGS HLA typing in routine clinical practice, and the concomitant routine typing of exons outside the norm, opens the window for rapid discovery of new HLA alleles and a potential for overwhelming the current HLA nomenclature naming conventions.