Gaffney Group

Genomics of gene regulation

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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.

Previous team members

Photo of Kaur Alasoo

Kaur Alasoo

PhD Student

Photo of Dr Clara Alsinet-Armengol

Dr Clara Alsinet-Armengol

Postdoctoral Fellow

Photo of Nicoletta Bruno

Nicoletta Bruno

Former Research Assistant at the Sanger Institute

Photo of Dr Angela Goncalves

Dr Angela Goncalves

Former Postdoctoral Fellow at the Sanger Institute

Photo of Gerda Kildisiute

Gerda Kildisiute

PhD Student

Photo of Dr Andrew Knights

Dr Andrew Knights

Senior Staff Scientist

Photo of Dr Natsuhiko Kumasaka

Dr Natsuhiko Kumasaka

Staff Scientist

Photo of Sebastian Lukasiak

Sebastian Lukasiak

Postdoctoral Fellow

Photo of Dr Maria Nascimento Primo

Dr Maria Nascimento Primo

Postdoctoral Fellow

Photo of Julia Rodrigues

Julia Rodrigues

Research Assistant

Photo of Jeremy Schwartzentruber

Jeremy Schwartzentruber

Former statistical geneticist at Open Targets


We work with the following groups


Wellcome Trust


Medical Research Council

We are generously funded by the MRC to pursue research on human IPSCs.


The Stegle group at EBI

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



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