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

ABSTRACT:

Introduction

While tens of thousands of HLA alleles have been identified by DNA sequencing, the contribution of alternative splicing to HLA diversity is not well characterized. In this study, we sought to determine if long-read sequencing could be used to accurately quantify allele-specific HLA transcripts in primary human lymphocytes.

Methods

cDNA libraries were prepared from peripheral blood lymphocytes from 12 donors and sequenced by nanopore long-read sequencing. HLA reads were aligned to donor-specific reference sequences based on the known type of each donor. Allele-specific exon utilization was calculated as the proportion of reads aligning to each allele containing known exons, and transcript isoforms were quantified based on patterns of exon utilization within indiv

SUBMITTER: Hughes AEO 

PROVIDER: S-EPMC10471969 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature