Allele-specific quantification of human leukocyte antigen transcript isoforms by nanopore sequencing

Area of Science:

• Immunogenetics
• Molecular Biology
• Genomics

Background:

• Human Leukocyte Antigen (HLA) diversity is crucial for immune response.
• The role of alternative splicing in HLA diversity remains largely uncharacterized.
• Accurate quantification of allele-specific HLA transcripts is needed.

Purpose of the Study:

• To determine if long-read sequencing can accurately quantify allele-specific HLA transcripts.
• To investigate the contribution of alternative splicing to HLA diversity.

Main Methods:

• Peripheral blood lymphocytes from 12 donors were sequenced using nanopore long-read sequencing.
• HLA reads were aligned to donor-specific reference sequences.
• Allele-specific exon utilization and transcript isoforms were quantified.

Main Results:

• Splice variants were rare in most HLA class I and class II genes.
• Several HLA-C alleles exhibited exon 5 splicing out in up to 15% of reads.
• HLA-DQB1 showed a significant loss of exon 5, even with an intact splice acceptor site.

Conclusions:

• A bioinformatic workflow was developed for quantifying allele-specific HLA transcript isoforms.
• Further research is needed to explore HLA transcript repertoires in various cell types and populations.