Genomic Mutation Identification in Mice Using Illumina Sequencing and Linux-Based Computational Methods.

Williams, John A and Powell, George and Mallon, Ann-Marie and Simon, Michelle M (2019) Genomic Mutation Identification in Mice Using Illumina Sequencing and Linux-Based Computational Methods. Current protocols in mouse biology, 9 (3). e64. ISSN 2161-2617.

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Official URL: https://currentprotocols.onlinelibrary.wiley.com/d...

Abstract

Genetically modified mice are an essential tool for modeling disease-causing mechanisms and discovering gene function. SNP genotyping was traditionally used to associate candidate regions with traits in the mouse, but failed to reveal novel variants without further targeted sequencing. Using a robust set of computational protocols, we present a platform to enable scientists to detect variants arising from whole-genome and exome sequencing experiments. This article guides researchers on aligning reads to the mouse genome, quality-assurance strategies, mutation discovery, comparing mutations to previously discovered mouse SNPs, and the annotation of novel variants, in order to predict mutation consequences on the protein level. Challenges unique to the mouse are discussed, and two protocols use self-contained containers to maintain version control and allow users to adapt our approach to new techniques by upgrading container versions. Our protocols are suited for servers or office workstations and are usable by non-bioinformatics specialists. © 2019 by John Wiley & Sons, Inc.

Item Type: Article
Subjects: QU Biochemistry
Divisions: Clinical Support > Pathology
Related URLs:
Depositing User: Mr Philip O'Reilly
Date Deposited: 03 Jan 2020 15:26
Last Modified: 03 Jan 2020 15:26
URI: http://www.repository.uhblibrary.co.uk/id/eprint/2737

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