Unique Molecular Identifier-Based High-Resolution HLA Typing and Transcript Quantitation Using Long-Read Sequencing

Caleb Cornaby; Maureen C Montgomery; Chang Liu; Eric T Weimer

doi:10.3389/fgene.2022.901377

Unique Molecular Identifier-Based High-Resolution HLA Typing and Transcript Quantitation Using Long-Read Sequencing

Front Genet. 2022 Jun 13:13:901377. doi: 10.3389/fgene.2022.901377. eCollection 2022.

Authors

Caleb Cornaby¹, Maureen C Montgomery¹, Chang Liu², Eric T Weimer^{1

3}

Affiliations

¹ Molecular Immunology Laboratory, McLendon Clinical Laboratories, UNC Health, Chapel Hill, NC, United States.
² Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, School of Medicine, Washington University in St. Louis, St. Louis, MO, United States.
³ Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, United States.

Abstract

HLA typing provides essential results for stem cell and solid organ transplants, as well as providing diagnostic benefits for various rheumatology, gastroenterology, neurology, and infectious diseases. It is becoming increasingly clear that understanding the expression of patient HLA transcripts can provide additional benefits for many of these same patient groups. Our study cohort was evaluated using a long-read RNA sequencing methodology to provide rapid HLA genotyping results and normalized HLA transcript expression. Our assay used NGSEngine to determine the HLA genotyping result and normalized mRNA transcript expression using Athlon2. The assay demonstrated an excellent concordance rate of 99.7%. Similar to previous studies, for the class I loci, patients demonstrated significantly lower expression of HLA-C than HLA-A and -B (Mann-Whitney U, p value = 0.0065 and p value = 0.0154, respectively). In general, the expression of class II transcripts was lower than that of class I transcripts. This study demonstrates a rapid high-resolution HLA typing assay using RNA-Seq that can provide accurate HLA genotyping and HLA allele-specific transcript expression in 7-8 h, a timeline short enough to perform the assay for deceased donors.

Keywords: HLA; immunogenetics allele-specific expression, high-resolution HLA; long-read; nanopore; unique molecular identifier (UMI).