Archive: Mouse and Zebrafish Genetics Programme

ARCHIVE PAGE: The Mouse and Zebrafish programme ran until September 2016. The programme helped to produce the mouse and zebrafish reference genomes and created a formidable range of knock-out mice and zebrafish resources that power research worldwide. Many of the model organism experts continue to work at the Sanger Institute supporting our research programmes to carry out the high-throughput, large-scale data-generating experiments that are a feature of the Institute's genomic studies. This page is being retained as a historical record and is not being updated.

Summary

The Mouse and Zebrafish Genetics programme carried out research to understand biological processes and generated and distributed a wide range of community resources, accelerating research globally.

Its principal focus was on mouse and zebrafish genetics, information and biological resources. In-house research focused on the biological function of genes identified in other Sanger Institute programmes, such as Human Genetics and the Cancer Genome Project, or of potential importance to human development and health.

Research

Below are some of the research projects that the Mouse and Zebrafish Genetics programme delivered or supported:

Mouse Resource Portal

The Sanger Mouse Genetics Programme (Sanger MGP) was initiated in 2006 to advance the functional understanding of protein coding and non-coding RNA genes using a standardised high-throughput phenotypic screen designed to contribute to improved diagnosis and treatment of human disease.

Sanger Institute Gene Trap Resource

The Sanger Institute Gene Trap Resource was a major project that isolated and characterised gene trap mouse embryonic stem (ES) cell lines to generate reporter-tagged, loss of function mutations.

The project produced more than 10,000 characterised gene trap insertions in 129P2 ES cells that are stored frozen and are freely available to the research community. These lines can be requested from the Mutant Mouse Regional Resource Center (MMRRC) at UC Davis in California on a cost-recovery basis and free of restrictions.

Sequencing of Idd regions in the NOD mouse genome

The Wellcome Trust Sanger Institute undertook the genome sequencing of regions of the non-obese diabetic (NOD) mouse relevant to type 1 diabetes (T1D), also known as insulin-dependent diabetes (Idd). Comparing the sequences of Idd candidate regions between the diabetes-sensitive NOD mouse and the diabetes-resistant C57BL/6J reference mouse allowed identification of genomic variations putatively associated with diabetes in mice and, by extension, in humans.

Zebrafish Genome Project

The Sanger Institute started the zebrafish genome sequencing project in 2001 and has generated several genome assemblies of the Tuebingen strain. After the release of Zv9, the zebrafish genome project joined the Genome Reference Consortium (GRC) for further improvement and ongoing maintenance. The GRC has now released a new reference assembly, GRCz10. After the release of the next assembly GRCz11, planned for 2017, our GRC partners at ZFIN have agreed to take over the responsibility for further updates and maintenance. 

Zebrafish Mutation Project

The Zebrafish Mutation Project (ZMP) has created a knockout allele in over 16,000 protein-coding genes in the zebrafish genome, using a combination of ENU mutagenesis, whole exome enrichment and Illumina sequencing, in addition to a targeted CRISPR/Cas9 approach.

Groups

Below are research teams who were part of the Mouse and Zebrafish Genetics programme:

Adams Group | Experimental Cancer Genetics

In our research we use mice to model key aspects of human cancer development and progression.

Bradley Group | Mouse genomics

The Bradley laboratory is a multi-disciplinary environment with a number of parallel research themes.  One of our core disciplines is the development and use of genetic technologies which we primarily apply to the mouse genome, although we also embrace studies in other mammalian genomes.

Liu Group | Mouse cancer genetics

We use various approaches including genetics, genomics and cell biology to study gene functions in normal development and disease such as cancer. We are particularly interested in stem cell self-renewal, differentiation, and lineage choice.

Logan Group | Genetics of Behaviour

The Genetics of Behaviour laboratory use mice as a model system to identify the genes and neural circuits that underpin social and learned behaviours, perception and cognition.

Vertebrate Annotation | Computational Genomics

This group consists of manual annotators and software developers. The HAVANA team provides the manual annotation of human, mouse, zebrafish and other vertebrate genomes that appear in the Vega browser. Our software is written and developed by the Annosoft team. 

Vertebrate Genetics and Genomics | Mouse and Zebrafish Genetics

We explore molecular phenotypes through the transcript sequencing of whole vertebrate embryos and tissues either by traditional RNA-seq or 3' end transcript counting. Taking advantage of the high quality reference genomes of the zebrafish and mouse, we are able to capture the full complement of polyadenylated transcripts. This allows us to establish a baseline of gene expression across the development of unperturbed organisms or explore the transcriptional consequences of loss of gene function or environmental disturbance.