A Kmer-based paired-end read (KPR) de novo assembler and genotyper to genotype major histocompatibility complex class I (MHC-I) alleles for the dog

Abstract

The major histocompatibility complex class I (MHC-I) genes are highly polymorphic among individuals. MHC-I genotyping is required for determining the antigen-binding specificity of each MHC-I molecule in an individual. Numerous tools have been developed for human MHC-I genotyping using deep sequencing data such as RNA-seq; however they do not work for the dog, due to very limited known canine alleles. To address this issue, we developed a Kmer-based paired-end read (KPR) de novo assembler and genotyper, which first assemble paired-end RNA-seq reads mapped to the MHC-I regions into contigs de novo and then genotype each contig. Our KPR tools are validated by Sanger sequencing, simulation and published genotype data. Applying our KPR tools on the published RNA-seq data of 158 tumor and 64 normal samples from 158 dogs, we have achieved a genotyping success rate of 86%, which includes 133 tumor and 57 normal samples from 142 dogs. We have identified 39 known alleles and 83 new alleles of high confidence in these dogs, yielding a more comprehensive MHC-I allele diversity landscape for the dog.

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“…Given the paucity of information regarding canine DLA‐I alleles, the workflow employed by HLA‐I genotyping tools 52–61 that relies upon a well curated database of known alleles, does not work for the dog. To address this deficiency, a new software tool has been developed for use in the dog that outperforms currently used approaches for typing new alleles 67 . Named the Kmer‐based paired‐end read (KPR) de novo assembler and genotyper, this tool assembles paired‐end RNA‐seq reads (fastq files) from MHC‐I regions into contigs, and then genotypes each assembled contig and estimates its expression level 67 .…”

“…To address this deficiency, a new software tool has been developed for use in the dog that outperforms currently used approaches for typing new alleles 67 . Named the Kmer‐based paired‐end read (KPR) de novo assembler and genotyper, this tool assembles paired‐end RNA‐seq reads (fastq files) from MHC‐I regions into contigs, and then genotypes each assembled contig and estimates its expression level 67 . It is written in Python (version 2.7), runs on the Unix/Linux platform and is freely available at Github at https://github.com/ZhaoS-Lab/KPR.git.…”