Genomics of gene regulation
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Headed by Daniel Gaffney, the group combined computational and statistical methods with high-throughput experimental techniques to understand the role played by changes in gene regulation in disease susceptibility and human evolution. A major focus of our group was the use of human induced pluripotent stem cells as models to study the functions of regulatory variation, as part of the Human Induced Pluripotent Stem Cells Initiative (HipSci) (Kilpinen, Goncalves et al, 2017). Recent publications and preprints from the group focused on IPSCs as models for context-specific specific changes in regulation in immune response (Alasoo et al, 2018), and in hard-to-access cells like neurons (Schwartzentruber et al, 2018). We also worked on statistical methods development for genetic mapping of gene regulatory variants (Kumasaka et al, 2016) and of interactions between regulatory regions (Kumasaka et al, 2018)
We welcomed applications from prospective postdocs and PhD students. Projects are available in the areas of genomics of gene regulation, molecular evolution and on population genomics of gene regulation. All our work involved data analysis, but there was also scope for projects with a component of laboratory work.
Much of our work applied the principles of association mapping to cell phenotypes, such as RNA levels or chromatin status. Association mapping is a powerful, unbiased approach for identifying genetic loci (sometimes referred to as quantitative trait loci, QTLs) that change a phenotype. Many maps of expression QTLs (eQTLs) have now been created, both as individual studies (for some recent reviews see here or here) and, more recently, as part of large consortia such as the GTEX project. Our most recent work was focused on using this approach in Induced Pluripotent Stem Cells (IPSCs) and cells derived from IPSCs, as part of our involvement in HIPSCI.
Previous team members
Genomics of inflammation and immunity
The goal of our research is to use high-throughput screens to gain causal insights into the biological basis of human disease, ...
Cellular Generation and Phenotyping
The Cellular Generation and Phenotyping (CGaP) core facility provides central cell biology support to the Sanger Institute, functioning as a contract ...
Cellular Genetics Informatics
Our team provides efficient access to cutting-edge analysis methods, environments and pipelines for Cellular Genetics programme, which leads and is involved ...
Programmes and Facilities
Health Data Research UK (HDR UK)
The Health Data Research (HDR) UK Cambridge site is part of the national institute for health data science (HDR UK) ...
We are focused on using single-cell approaches, so called “cell atlas” technologies and understanding human genetics at the cellular level. The ...
We work with the following groups
We are generously funded by the MRC to pursue research on human IPSCs.
We collaborate closely with Oliver Stegle's group at EBI on the HIPSCI project.
OpenTargets is a unique public-private initiative to apply cutting edge genetics research to the problem of drug taregt identification and validation. They have generously funded several projects in our lab on the application of CRISPR technology to human IPS-derived model systems