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The University of Southampton

Genetic Epidemiology & Genomic Informatics

This initiative combines the expertise and resources of two closely linked groups that work synergistically to develop and apply methodologies for genomic analysis.

The Genetic Epidemiology Group was established in 1988 by Professor Newton Morton - a founding father of the field perhaps best known for developing lod scores for detection of linkage within families. The group developed the first single nucleotide polymorphism (SNP)-based linkage disequilibrium maps for multiple populations which have been used for disease association mapping, the study of human populations and in characterising patterns of extended homozygosity in the genome. The group is now led by Professor Andrew Collins and current interests include development of methodology for meta-analysis of SNP-based association data, development and application of machine learning approaches, disease gene mapping in breast cancer and leukaemia and the analysis of next generation sequence data.

The recently formed Genomic Informatics Group led by Dr Sarah Ennis specialises in the analysis of next generation sequencing data and together with the Genetic Epidemiology Group have developed analytical pipelines for the analysis of these enormous datasets. It benefits from one of the largest computational facilities in the UK, the IRIDIS cluster. Professor Collins and Dr Ennis have several ongoing collaborations, including those described below

Examples of current research interests

The genetics of paediatric inflammatory bowel disease with cross institutional collaborators from University Hospital Southampton NHS Foundation Trust, the NIHR Nutrition Biomedical Research Centre and Edinburgh University. Our locally collected cohort of patients contributes to the UK Paediatric IBD Genetics Cohort, as part of the UKIBDGC and is part of our current next generation sequencing work. The study, led by Dr. Ennis, has been adopted by the CLRN clinical Genetics Portfolio and has been co-adopted by Paediatrics. Recruitment is ongoing and currently comprises approximately 200 children with DNA and clinical information. Clinical data and DNA is also routinely collected for all parents and affected relatives. Next generation exome sequence data generation is ongoing with complete data in place for half the children. A PhD studentship part funded by the Gerald Kerkut Charitable Trust and the Crohn’s in Children Research Association (CICRA) supports this work.

Our work with IBD has led to a natural collaboration with Dr Tony Williams, director of the Wessex Integrated Sciences Hub Laboratory. Our research interests are aligned in bridging the information gap between autoimmunity and genomics in early onset IBD. A recent clinical fellowship award by CICRA the will fund ongoing research merging these two disciplines. Similar parallel projects investigating translational immunology in the context of next generation sequencing in Primary Immunodeficiency are also in place.

The group has various ongoing projects that apply next generation sequencing to oncology: Examining genomic data from germline and tumour DNA samples from patients with chronic lymphocytic leukemia and Splenic Marginal Zone Lymphoma in collaboration with Dr Jon Strefford; Genomic studies with Dr Surinder Sahota to understand the pathogenesis and clonal evolution of multiple myeloma through analysis of genome sequence data; Assessing exome data from long and short term survivors of pancreatic cancer in collaboration with Dr Gareth Thomas; Investigating rare cancers such as Pseudomixoma Peritonei in collaboration with surgical colleagues - Mr Alex Mirnezami, local pathologists – Dr Norman Carr and the Hampshire Hospitals Foundation Trust. Much of the method development and application of NGS to these projects has been underpinned by core funding from Cancer Research UK (CRUK) and their support of Dr Jane Gibson, a postdoctoral scientist working with Dr Sarah Ennis.

A body of work in conjunction supported by Leukemia and Lymphoma research with Professor Nick Cross of the Wessex Regional Genetics Laboratory and Dr Will Tapper, a senior postdoctoral scientist from our group, to investigate genetics and genomics of myeloid malignancies. The group hosts and supervises a PhD studentship working on generation of an analytical pipeline to apply RNA Sequence data to identify genomic translocations and specifically gene fusions leading to this form of malignancy.

Specific to breast cancer we collaborate with: Professor Diana Eccles to identify genes underlying risk and survival in early onset breast cancer and methods for meta-analysis in breast cancer association data, and with Professor Eccles and Professor Joerg Fliege (Mathematics), for developing machine learning approaches and applications in breast cancer; Projects to apply RNA sequencing data to assess the role of splicing in genes implicated in breast cancer are underway in collaboration with Dr Diana Baralle and Dr Michaela Raponi.

An established local collaboration with the Vision Laboratory, part of Clinical Neurosciences and Southampton Eye Unit, has produced patents in medical diagnostics. This work has involved international collaboration with the University of Iowa, The Netherlands Institute for Neuroscience and deCODE genetics Inc. Projects focus on various diseases including age-related macular degeneration, glaucoma, nystagmus and cone dystrophy.

In collaboration with other colleagues at University Hospital Southampton NHS Trust, we have other small projects examining the genetics of Mendelian and Syndromic disorders including familial end stage renal failure, skeletal dysplasia as well as rare diseases such as Bazex-Dupre-Christol syndrome, autosomal dominant adult onset leukodystrophy.

A collaboration with Professor Pat Jacobs at Salisbury District Hospital, Dr Anna Murray from the University of Exeter and Professor Tony Swerdlow from the Institute of Cancer Research looking at genetic predisposition to premature ovarian failure.

Industrial collaboration with Complete Genomics for the application of whole genome data to next generation linkage disequilibrium map generation and with Oxford Gene Technology for method development to improve quality assurance in high throughput genomics.

An international collaboration supported by the Santander Internationalisation fund and New Life Foundation to examine highly prevalent syndromic and non-syndromic cleft lip in Colombian patients in collaboration with Prof. Ignacio Briceno from Universidad de La Sabana, Bogota, Colombia.

Technical Information

Over recent years the University of Southampton has established one of the largest computational facilities in the UK. The IRIDIS cluster launched in February 2010. This facility enables high performance computing necessary for the efficient processing of next generation genomic data. In association with staff at the School of Electronics & Computer Science, IRIDIS is already established as a secure data repository and platform for numerous genomic analysis software packages that are components of the next generation sequence analysis pipeline.

Professor Collins and Dr Ennis are members of the Computational Modelling Group that brings together University of Southampton researchers using applied Computational Modelling to support the understanding and advancement of physical and natural sciences, engineering, medicine, economy, society, psychology, and other fields. This includes both the development of new computational methods and the application of existing simulation tools and software packages.

Professor Collins is a member of the Institute for Complex Systems Simulation

For publications please see individual researchers' home pages.


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