A Kmer-based Paired-end Read Assembler and Genotyper for Canine MHC Class I Genotyping

Overview

Journal iScience

Publisher Cell Press

Date 2023 Feb 17

PMID 36798440

Authors

Yuan Feng

Paul R Hess

Stephen M Tompkins

William H Hildebrand

Shaying Zhao

Affiliations

Soon will be listed here.

Abstract

The major histocompatibility complex class I (MHC-I) genes are highly polymorphic. MHC-I genotyping is required for determining the peptide epitopes available to an individual's T-cell repertoire. Current genotyping software tools do not work for the dog, due to very limited known canine alleles. To address this, we developed a Kmer-based paired-end read (KPR) assembler and genotyper, which assemble paired-end RNA-seq reads from MHC-I regions into contigs, and then genotype each contig and estimate its expression level. KPR tools outperform other popular software examined in typing new alleles. We used KPR tools to successfully genotype152 dogs from a published dataset. The study discovers 33 putative new alleles, finds dominant alleles in 4 dog breeds, and builds allele diversity and expression landscapes among the 152 dogs. Our software meets a significant need in biomedical research.

Citing Articles

Human basal-like breast cancer is represented by one of the two mammary tumor subtypes in dogs.

Watson J, Wang T, Ho K, Feng Y, Dobbin K, Zhao S bioRxiv. 2023; .

PMID: 37034591 PMC: 10081165. DOI: 10.1101/2023.03.02.530622.

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