Gaffney Group

Genomics of gene regulation

Archive Page

This page is maintained as a historical record and is no longer being updated.

The genomics of gene regulation group was interested in understanding the role of gene regulatory variation in human disease and evolution.

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.