Direct HLA Genetic Comparisons Identify Highly Matched Unrelated Donor-Recipient Pairs with Improved Transplantation Outcome

Abstract

HLA matching by allele-level genotyping is largely based on genetic similarity between a few exons that encode the antigen recognition domain (ARD) of the HLA protein. Next-generation sequencing (NGS) can identify HLA genetic polymorphisms in non-ARD-encoding exons, introns, and untranslated regions, but the impact of these polymorphisms on hematopoietic cell transplantation (HCT) outcome is unclear. We performed NGS-based sequencing of 11 HLA loci on a well-characterized retrospective cohort of 166 unrelated donor-recipient HCT pairs. Genetic differences between HCT pairs were identified and visualized using a novel bioinformatics approach that directly compares phased full-length HLA sequences. Our approach was able to correctly classify HCT pairs without known HLA allele-level mismatches and also to identify a subset of HLA allele-matched HCT pairs with very few to no genetic differences in the sequenced HLA regions. This highly HLA genetically matched unrelated HCT group shows improved overall survival and reduced acute graft-versus-host disease compared with HCT pairs with HLA allele-level mismatches. These results suggest that direct genetic matching of HLA loci may offer an additional means of HCT donor selection beyond traditional HLA allele comparisons and suggests that genetic similarity as defined by HLA sequencing may have a novel role in unrelated HCT donor selection. Finally, our approach can enable larger cohort studies with adequate power to detect differences in other HCT outcomes based on genetic similarity within the HLA loci.

Evaluation of the AllType kit for HLA typing using the Ion Torrent S5 XL platform

“…Determining the sequence of HLA proteins expressed by a recipient or donor by exon typing without ambiguity in the second field is considered sufficient for current clinical practice . However, our understanding of the impact of polymorphisms in coding positions out of the peptide‐binding groove, in non‐coding regions on HLA expression, disease susceptibility, and transplantation outcomes is continuing to evolve, and new perspectives in terms of NGS applications are emerging . Moreover, nucleotide substitutions, insertions, and deletions in the enhancer–promoter, intron, and 3′‐UTR regions can result in null alleles requiring identification in clinical settings …”

“…7 However, our understanding of the impact of polymorphisms in coding positions out of the peptide-binding groove, in non-coding regions on HLA expression, disease susceptibility, and transplantation outcomes is continuing to evolve, and new perspectives in terms of NGS applications are emerging. [9][10][11][12] Moreover, nucleotide substitutions, insertions, and deletions in the enhancer-promoter, intron, and 3 0 -UTR regions can result in null alleles requiring identification in clinical settings. 13 NGS methods are based principally on the following steps: immobilization of the DNA sample onto a solid support, cyclic sequencing reactions at the clonal level using automated fluidic devices, and detection of millions of simultaneous molecular events.…”

HLA diversity in the Russian population assessed by next generation sequencing

“…в соответствии с современной номенклатурой HLA -на уровне 4-го поля, например, А*01:01:01:01 [16]. Подбор донора и реципиента при алло-ТГСК с аллельным разрешением, позволяющим выявлять генетические полиморфизмы вне экзонов, кодирующих пептидсвязывающие домены HLA-молекул, повышает выживаемость больных после алло-ТГСК [17,25]. Предполагают, что полиморфизмы в некодирующих областях HLA-генов являются маркерами HLA-гаплотипов [17,25].…”

A reply to Hurley et al. regarding Recipients Receiving Better HLA-Matched Hematopoietic Cell Transplantation Grafts, Uncovered by a Novel HLA Typing Method, Have Superior Survival: A Retrospective Study

“…Finally, it should be noted that previously published data on major histocompatibility complex haplotype matching, coupled with the accepted reduced risk of complications in related donor transplantation, suggest that greater compatibility of the HLA region is associated with better outcome. We also point out that since the acceptance and publication of our article, 2 independent studies (a published manuscript [1] and a presented abstract [2]) have also demonstrated the beneficial effect of matching for additional regions of the HLA gene on unrelated donor HCT outcome, suggesting these observations are not unique, and that there is much still to learn about the impact of genetic variation outside of the ARD on HCT outcome.…”