Efficient analysis of mouse genome sequences reveal many nonsense variants

Significance Mouse genome sequences have been generated of tens of inbred strains. We here describe a user-friendly bioinformatics tool for revealing the sequence variations in protein-coding genes in one or more inbred strains and predicting which proteins are significantly different compared with those of the reference genome of C57BL/6J inbred mice. The analysis of truncated proteins in the strain SPRET/Ei, as an example, results in a user-friendly PDF file. This information is essential for interpreting biological data obtained using a given inbred strain, and confirms that inbred lines are a rich source of variant alleles of protein-coding genes, including knockout alleles. Genetic polymorphisms in coding genes play an important role when using mouse inbred strains as research models. They have been shown to influence research results, explain phenotypical differences between inbred strains, and increase the amount of interesting gene variants present in the many available inbred lines. SPRET/Ei is an inbred strain derived from Mus spretus that has ∼1% sequence difference with the C57BL/6J reference genome. We obtained a listing of all SNPs and insertions/deletions (indels) present in SPRET/Ei from the Mouse Genomes Project (Wellcome Trust Sanger Institute) and processed these data to obtain an overview of all transcripts having nonsynonymous coding sequence variants. We identified 8,883 unique variants affecting 10,096 different transcripts from 6,328 protein-coding genes, which is about 28% of all coding genes. Because only a subset of these variants results in drastic changes in proteins, we focused on variations that are nonsense mutations that ultimately resulted in a gain of a stop codon. These genes were identified by in silico changing the C57BL/6J coding sequences to the SPRET/Ei sequences, converting them to amino acid (AA) sequences, and comparing the AA sequences. All variants and transcripts affected were also stored in a database, which can be browsed using a SPRET/Ei M. spretus variants web tool (www.spretus.org), including a manual. We validated the tool by demonstrating the loss of function of three proteins predicted to be severely truncated, namely Fas, IRAK2, and IFNγR1.

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