Abstract
BackgroundExome sequencing has become a popular method to evaluate undirected mutagenesis experiments in mice. However, the most suitable mouse strain for the biological model may be relatively distant from the standard mouse reference genome. For pinpointing causative variants, a matching reference with gene annotations is essential, but not always readily available.ResultsWe present an approach that allows to use murine Ensembl annotations on alternative mouse strain assemblies. We resolved ENU-induced mutation screening for 8 phenotypic mutant lines generated on C3HeB/FeJ background aligning the sequences against the closely related, but not annotated reference of C3H/HeJ. Variants occurring in all strains were filtered out as specific for the C3HeB/FeJ strain but unrelated to mutagenesis. Variants occurring exclusively in all individuals of one mutant line and matching the inheritance model were selected as mutagenesis-related. These variants were annotated with gene and exon names lifted over from the standard murine reference mm9 to C3H/HeJ using megablast. For each mutant line, we could restrict the results to exonic variants in between 1 and 23 genes.ConclusionsThe presented method of exonic annotation lift-over proved to be a valuable tool in the search for mutagenesis-derived coding genomic variants and the assessment of genotype-phenotype relationships.
Highlights
Exome sequencing has become a popular method to evaluate undirected mutagenesis experiments in mice
Since the bulk of phenotype-causing mutations identified to date after ENU mutagenesis are exonic, exome sequencing would be a welcome method to speed up this process, provided that it
For a direct comparison, we mapped the raw reads from the exome sequencing experiment to both the mm9 and the C3H/HeJ reference sequences
Summary
Exome sequencing has become a popular method to evaluate undirected mutagenesis experiments in mice. ENU mutagenesis is a popular method to introduce single nucleotide mutations in the mouse genome [1]. Before massive sequencing technologies became available, phenotype-related ENU-induced mutations were shortlisted in a lengthy procedure of out-crossing and meiotic mapping that identified linkage chromosomes, or finer linkage regions of approximately 20 MB. Since the bulk of phenotype-causing mutations identified to date after ENU mutagenesis are exonic, exome sequencing would be a welcome method to speed up this process, provided that it. For the large-scale Munich ENU mutagenesis project [2] the C3HeB/FeJ (C3H) strain was chosen due to the observed high mutation loads and fertility rates following ENU treatment in early pilot studies. Once archived by cryo-preservation good results for in vitro fertilization and embryo transfer were observed [5,6]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
