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.
We utilise and develop computational tools for the analysis of biological data, primarily obtained from studies of DNA methylation. The data predominantly comes from either second generation sequencing platforms or methylation arrays.
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, including T1D, T2D and UC.
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).
MeDUSA is a computational pipeline bringing together numerous software packages to perform a full analysis of MeDIP-seq data, including sequence alignment, quality control (QC), and determination and annotation of DMRs.
Gliomas are the most common form of primary brain tumours. Glioma cancer stem cells (CSC) are cells that possess characteristics associated with normal stem cells but are tumourigenic and can cause relapse and metastasis by giving rise to new tumours. Using methylome analysis, this project aims to characterize epigenetic changes that occur during the differentiation of glioma CSC to committed progenitor cells.
IT Future of Medicine (ITFoM) is one of six flagship pilot projects will take advantage of recent technological advances to produce computational models of individual patients - virtual patients! These models will follow each patient through their healthcare system enabling physicians to virtually test and optimise personalised treatments
Head and Neck Squamous Cell Cancer (HNSCC) is the sixth most common cancer worldwide and increasingly caused by infection with human papilloma virus (HPV). The aim of this project is to analyse HPV and non HPV-associated HNSCC epigenomes for differences in DNA methylation and microRNA expression for translation into biomarkers and therapeutic targets.
Ulcerative Colitis (UC) is a type of Inflammatory Bowel Disease (IBD) where inflammation develops in the large intestine (the colon and rectum). This project identified novel epigenetic variations associated with UC by conducting an EWAS on monozygotic twins discordant for the disease.
Nerve Sheath Tumour Methylome
Using comparative methylome analysis of benign and malignant peripheral nerve sheath tumors (MPNST), Feber et al. identified loss of DNA methylation at satellite repeats as candidate biomarker for disease progression and challenged the dogma of global hypomethylation in cancer.
ZooArray: Epigenetic Insights into Vertebrate Genomes
Epigenetic modifications play crucial roles in organizing chromatin structure, specifically in regions which control gene expression and regulate other cellular processes. The aim of this project is to elucidate and characterize the epigenetic states of evolutionarily conserved sequences.
The EU-FP7 funded HEROIC Project was conducted between 2005-2010 and provides a resource (Ensembl Projects) for functional studies into chromatin remodeling, mouse embryonic stem (ES) cell differentiation and regulation of the (epi)genome in general.
The EU-FP5 and Wellcome Trust funded HEP was conducted between 1999-2006 and provides an epigenetic resource of chromosomal DNA methylation reference profiles of human tissues and cell lines
The MHC Haplotype Project provides genetic resources for association studies into inflammatory, autoimmune and infectious disease as well as forming a framework for population genetic studies.
The LRC Haplotype Project
The LRC Haplotype Project provides genetic resources for association studies into inflammatory, autoimmune and infectious disease as well as forming a framework for population genetic studies.