Biology subjects

Wardle-Jones, H.

Publications and source records attributed to Wardle-Jones, H..

3 recordsLinked to original sources

bioRxiv2021

The production of 4,182 mouse lines identifies experimental and biological variables impacting Cas9-mediated mutant mouse line production

The International Mouse Phenotyping Consortium (IMPC) systematically produces and phenotypes mouse lines with presumptive null mutations to provide insight into gene function. The IMPC now uses the programmable RNA-guided nuclease Cas9 for its increased capacity and flexibility to efficiently generate null alleles in the C57BL/6N strain. In addition to being a valuable novel and accessible research resource, the production of 3,313 knockout mouse lines using comparable protocols provides a rich dataset to analyze experimental and biological variables affecting in vivo gene engineering with Cas9. Mouse line production has two critical steps - generation of founders with the desired allele and germline transmission (GLT) of that allele from founders to offspring. A systematic evaluation of the variables impacting success rates identified gene essentiality as the primary factor influencing successful production of null alleles. Collectively, our findings provide best practice recommendations for using Cas9 to generate alleles in mouse essential genes, many of which are orthologs of genes linked to human disease.

genetics↗

bioRxiv2020

High laboratory mouse pre-weaning mortality associated with litter overlap, advanced mother age, small and large litters

High and variable pre-weaning mortality is a persistent problem among the main mouse strains used in biomedical research. If a modest 15% mortality rate is assumed across all mouse strains used in the EU, approximately 1 million more pups must be produced yearly to compensate for those which die. A few environmental and social factors have been identified as affecting pup mortality, but optimizing these factors does not cease the problem. This study is the first large study to mine data records from 219,975 pups from two breeding facilities to determine the major risk factors associated with mouse pre-weaning mortality. It was hypothesized that litter overlap (i.e. the presence of older siblings in the cage when new pups are born), a recurrent social configuration in trio-housed mice, is associated with increased newborn mortality, along with high mother age, large litter size, as well as a high number and age of older siblings in the cage. The estimated probability of pup death was two to seven percentage points higher in cages with compared to those without litter overlap. Litter overlap was associated with an increase in percentage of litter losses of 19% and 103%, respectively, in the two breeding facilities. Increased number and age of older siblings, high mother age, small litter size (less than four pups born) and large litter size (over 11 pups born) were associated with increased probability of pup death. Results suggest that common social cage configurations at breeding facilities are dangerous for the survivability of young mouse pups. The underlying mechanisms and strategies to avoid these situations should be further investigated.

animal behavior and cognition↗

bioRxiv2019

Human and mouse essentiality screens as a resource for disease gene discovery

Although genomic sequencing has been transformative in the study of rare genetic diseases, identifying causal variants remains a considerable challenge that can be addressed in part by new gene-specific knowledge. Here, we integrate measures of how essential a gene is to supporting life, as inferred from the comprehensive viability and phenotyping screens performed on knockout mice by the International Mouse Phenotyping Consortium and from human cell line essentiality screens. We propose a novel, cross-species gene classification across the Full Spectrum of Intolerance to Loss-of-function (FUSIL) and demonstrate that genes in five mutually exclusive FUSIL categories have differing characteristics in the biological processes they regulate, tissue expression levels and human mutation rates. Most notably, Mendelian disease genes, particularly those associated with developmental disorders, are highly overrepresented in the developmental lethal category, representing genes not essential for cell survival but required for organism development. Exploiting this finding, we have screened developmental disorder cases from three independent disease sequencing consortia and identified potentially pathogenic, de novo variants shared in different patients for several developmental lethal genes that have not previously been associated with rare disease. We therefore propose FUSIL as an efficient resource for disease gene discovery.

genomics↗