International journal of immunogenetics · 2026
Long-Read Next-Generation Sequencing Technologies Can Address Some Limitations of Short-Read Technologies in HLA Typing.
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Lion Julien, Perriere Marianne, Desoutter Judith, Guillaume Nicolas
Аннотация
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.
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.