Medical Genomics Research Group
Group Leader: Professor Stephan Beck
The laboratory has broad interests in the genomics and epigenomics of phenotypic plasticity in health and disease. In addition to genetic variations, we study epigenetic variations such as DNA methylation, histone modifications and microRNAs and how they modulate genome function. Central to our research is the development of systems approaches for integration of multi-dimensional data and their application to epigenome-wide association studies (EWAS) in cancer and other common diseases to advance translational, regenerative and personalized medicine. The Medical Genomics Group offers state-of-the-art facilities and a stimulating environment for graduate and post-doctoral training.
This programme aims to establish integrated (epi)genomic analysis in a clinical setting, utilizing the NET BioBank at the Royal Free and UCL Hospitals. Neuroendocrine Tumors (NETs) are a heterogeneous group of neoplasms which arise from the hormone-producing cells of the bodyís nervous and endocrine systems and affect 1/50,000 in the UK population.
C2c: Cancer to chronic disease
Aberrant DNA methylations is an early event in carcinogenesis. The ongoing research into the use of minimally-invasive liquid biopsies holds great promise for enabling early diagnosis and improving cancer management through comprehensive detection of tumour specific genetic and epigenetic alterations. The aim of the C2c project is to develop a novel pipeline for the high-throughput targeted detection of tumour-specific DNA methylations marks using bisulfite sequencing at single base resolution in minute quantities of circulating cell free DNA (cfDNA). This project is focused on the analysis of circulating tumour DNA (ctDNA) for dynamic monitoring of cancer progression and evaluation of epigenetic biomarkers for predictive, prognostic, and diagnostic purposes.
The involvement of DNA methylation in health and disease is well established but not yet fully understood. The aim of this project is to develop novel experimental and computational methods for the analysis of 5-methyl-cytosine (5-mC) and 5-hydoxymethyl-cytosine (5-hmC). These include development of analysis tools and pipelines for whole genome sequencing, whole genome bisulfite sequencing, targeted bisulfite sequencing and genome-wide methylation arrays.
This project involves the development of eFORGE, a computational tool for the analysis of DNA methylation data from Epigenome-Wide Association Studies (EWAS).
Epigenomics of Common Disease
Genome-wide association studies (GWAS) have identified a multitude of genetic variants associated with complex traits including common diseases. However, their effect sizes are modest and the majority of causality remains unexplained for most common diseases. The aim of this project is to integrate GWAS with epigenome-wide association studies (EWAS) to gain a more complete picture of the aetiology of common diseases.
This NIHR Blood Transplant Research Unit project aims to identify and validate donor-specific biomarkers which are predictive of recipient outcome following hematopoietic stem cell transplantation. Such biomarkers would allow guidance of treatment strategy and improved donor selection, in a personalised medicine approach to transplantation.
This project involves the development of computational tools for the analysis of DNA methylation data from the Illumina 450k array.
Epigenetics of Urological Cancers
Bladder cancer is the fifth most common cancer in the UK with over 11,000 new cases and almost 5,000 deaths per year. This project aims to provide a better understanding of how aberrant DNA methylation can affect the aetiology of bladder cancer and how we can use this information to identify novel epigenetic biomarkers for the diagnosis and prognosis of the disease.
Induced pluripotent stem cells (iPSC) are pluripotent cells derived from reprogramming of non-pluripotent cells such as skin or blood cells. iPSC have great potential for regenerative and therapeutic medicine. The aim of this project is to assess the efficiency of different reprogramming protocols using methylome analysis.
Using a novel Open Consent protocol, PGP-UK will provide genomic, environmental and trait data under Open Access to advance personal and medical genomics and to promote Citizen Science.
The BRC-funded Cancer Genome Engineering (CAGE) Facility develops and provides TALE- and CRISPR-based genome engineering technologies for targeted genetic and epigenetic reprogramming to advance personal and medical genomics.
EpiTrain is an Integrated Training Network (ITN) providing high-level training and career development for PhD students and postdocs at local host institutions, complemented by exchange programs and topical workshops. The scope of the project is to develop a broad scale understanding of epigenetic processes in common disease.
This EU Network of Excellence aims to link epigenetics with systems biology. The multidisciplinary consortium will model and quantify the dynamics and mechanisms of epigenetic modulation at the cellular and organismal level. Our contribution is to explore and quantify the link between genotype and epigenotype.
This public/private translational consortium will develop methods for systematic generation and validation of oncology biomarkers to advance personalized therapy and medicine. Genomic, epigenomic and transcriptomic data will be generated and analyzed using a modeling system developed for the TREAT1000 project. Our contribution is the generation and analysis of epigenomic data.
This project represents the EU contribution to the International Human Epigenome Consortium (IHEC). It focuses on the analysis of haematopoietic epigenomes from healthy individuals and patients with common leukaemias and autoimmune disease. Our main contribution to BLUEPRINT is an epigenome-wide association study (EWAS) in Type 1 Diabetes.
This consortium will carry out integrated research on developmental determinants of aging and longevity with focus on epigenetic mechanisms. Our contribution to IDEAL is to determine the role of DNA methylation in haematopoietic stem cell aging.
NOCRC aims to develop and validate high performance blood based tests for colorectal cancer in a recently initiated screening program in Denmark quantifying existing and novel markers by sensitive and cost-effective methods. Our contribution is towards the development of a targeted bisulfite sequencing assay.