一种基于Kmer的双端读取组装器和基因分型器，用于犬类MHC I类基因分型。
A Kmer-based paired-end read assembler and genotyper for canine MHC class I genotyping.
作者信息
Feng Yuan, Hess Paul R, Tompkins Stephen M, Hildebrand William H, Zhao Shaying
机构信息
Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
Department of Clinical Sciences, North Carolina State University, College of Veterinary Medicine, Raleigh, NC 27607, USA.
出版信息
iScience. 2023 Jan 16;26(2):105996. doi: 10.1016/j.isci.2023.105996. eCollection 2023 Feb 17.
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.
主要组织相容性复合体I类（MHC-I）基因具有高度多态性。确定个体T细胞库可用的肽表位需要进行MHC-I基因分型。由于已知的犬类等位基因非常有限，目前的基因分型软件工具对犬类不起作用。为了解决这个问题，我们开发了一种基于Kmer的双端读段（KPR）组装器和基因分型器，它将来自MHC-I区域的双端RNA测序读段组装成重叠群，然后对每个重叠群进行基因分型并估计其表达水平。在分型新等位基因方面，KPR工具优于其他所检测的流行软件。我们使用KPR工具成功地对一个已发表数据集中的152只狗进行了基因分型。该研究发现了33个推定的新等位基因，在4个犬种中找到了优势等位基因，并构建了152只狗之间的等位基因多样性和表达图谱。我们的软件满足了生物医学研究中的一项重大需求。
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