Improved accuracy of clinical HLA genotyping by next-generation DNA sequencing affects unrelated donor search results for hematopoietic stem cell transplantation

Matching of human leukocyte antigen (HLA) genes is critically important in hematopoietic stem cell transplantation (HSCT). HLA genes are highly polymorphic and HLA matching has historically been limited by technologies that are unable to unambiguously determine HLA genotypes. Next generation DNA sequencing (NGS) overcomes these limitations by enabling near full-gene sequences with phase determination for heterozygous alleles. Here we examine the efficacy and utility of HLA-NGS in the clinical setting. In a 54-sample validation study and 955 patient samples subsequently tested using HLA-NGS, we observed significant improvement in the ability to unambiguously identify HLA genotypes in both the validation (97.3%) and clinical (97.4%) sample cohorts compared to previous standard-of care HLA genotyping methods. We modeled the clinical impact of this improved diagnostic ability by comparing National Marrow Donor Program (NMDP) search results for 56 patients using HLA-NGS genotypes and simulated standard-of-care HLA genotypes. Surprisingly, we observed significant differences in 7.1% of NMDP searches, with improved unambiguous HLA genotyping correlating with improved prediction of finding well-matched and partially-matched unrelated HSCT donors. These data demonstrate that HLA-NGS can provide highly accurate and unambiguous HLA genotyping that facilitates donor selection for allogeneic HSCT.