Long-Read Next-Generation Sequencing Technologies Can Address Some Limitations of Short-Read Technologies in HLA Typing.

Abstract

Introduction: Accurate HLA allele identification is essential to ensure graft-recipient compatibility. Advances in next-generation sequencing (NGS), such as those provided by Illumina and Oxford Nanopore Technologies, have improved resolution of HLA-typing.

Methods and results: Here, a novel HLA-C*12 allele with a silent mutation (G to A) was identified in a bone marrow donor homozygous for HLA-C*12. The allele was initially linked to HLA-C*12:03:01 by short-read NGS, but further investigation by long-read sequencing revealed the mutation to be associated with HLA-C*12:02:02. Phasing limitations of short-read NGS made accurate allele assignment difficult, but precise differentiation became possible with longer reads. The origin of the mutation was subsequently confirmed by sequencing parental samples.

Conclusion: This case highlights the ability of long-read sequencing to resolve cis-trans ambiguities and improve allele phasing, and to enhance accuracy for new HLA allele identification.