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Derdak, S.* ; Sabrautzki, S. ; Hrabě de Angelis, M. ; Gut, M.O.* ; Gut, I.G.* ; Beltran, S.*

Genomic characterization of mutant laboratory mouse strains by exome sequencing and annotation lift-over.

BMC Genomics 16:351 (2015)
Verlagsversion DOI
Open Access Gold
Creative Commons Lizenzvertrag
Background: Exome 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. Results: We 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. Conclusions: The 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.
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Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
Schlagwörter Annotations ; Exome Sequencing ; Genomic Variants ; Mouse Strains ; Mutagenesis ; Phenotype ; Sequence Homology; Enu Mutagenesis; Spermatozoa; Alignment; Mutation; Format; Wide; Mice; Tool
ISSN (print) / ISBN 1471-2164
e-ISSN 1471-2164
Zeitschrift BMC Genomics
Quellenangaben Band: 16, Heft: , Seiten: , Artikelnummer: 351 Supplement: ,
Verlag BioMed Central
Verlagsort London
Begutachtungsstatus Peer reviewed