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The University of Southampton
Medicine

Professor Sarah Ennis PhD

Professor of Genomics, Genomic Informatics Group Lead

Professor Sarah Ennis's photo

Professor Sarah Ennis is Professor of Genomics within Medicine at the University of Southampton.

Sarah Ennis holds a first class honours degree in Biochemistry from National University Ireland (Galway) and a PhD in Genetic Epidemiology (University of Southampton). Her career has evolved with the emerging field of Human Genomics and she now leads the Human Genetics & Genomic Medicine Research theme and her own research group in Genomic Informatics. Her group specialises in the analysis of next generation sequencing (NGS) data and these are focussed on, but not limited to: interrogation of targeted and whole genome sequence data to determine cryptic causes of Mendelian disease; large scale genomic data analysis, including data integration and machine learning to better understand the genetic basis of rare and common disease with the aim of stratifying diagnoses and targeting tailored treatment for better patient outcomes; the application of whole genome sequence data for the generation of optimally resolved genetic maps and the correlation of these maps with genetic motifs, recombination and selection.

SE holds an honorary NHS contract, works closely with clinical colleagues across various NHS Trusts and international research institutes and is Chief Investigator of studies that have recruited thousands of patients and families into clinical research.

Prof. Ennis’ group comprises senior postdoctoral researchers, clinical research staff and senior research nurses. She supervises a diverse group of MSc and PhD students as well as undergraduate student projects. She lectures in Biochemistry, Molecular Cell Biology and Genomics within the BM5 Medical Degree Programme and Module Lead within the MSc in Genomic Medicine.

Qualifications

BSc Hons., Biochemistry, National University of Ireland, Galway, 1998
PhD, Genetic Epidemiology, University of Southampton, 2003

Research interests

Genomic Analysis

Advances in sequencing technology have the potential to effect a step change in our approach to medical genetic research and clinical diagnostics. Processing and interpretation of large scale genomic data from patient samples has the potential to reveal common and rare genetic changes that predispose to disease. The development of new tools and skills necessary to analyse, interrogate and understand the importance of genomic variation is an essential prerequisite. The vast nature of the data necessitate analytical pipelines, variant annotation and variant prioritisation in order to extricate biologically relevant variation from background noise.

Sequence data can also be directed towards more generic biological questions pertaining to; understanding chiasma hotspots in recombination; inheritance patterns in families; extended regions of homozygosity and; factors acting in cis to modify chromosome stability.

Paediatric Inflammatory Bowel Disease

In 2010, Professor Ennis initiated local research into the genetics of paediatric inflammatory bowel disease (IBD). Patient and family recruitment is ongoing in collaboration with colleagues from Southampton University Hospital Trust and the NIHR Nutrition Biomedical Research Centre. This locally collected cohort of patients contributes to the UK & Ireland Paediatric IBD Genetics Group, as part of the UKIBDGC and is part of our current next generation sequencing work. Very detailed family history and clinical detail are collected for all participants. The cohort represents an increasingly important resource with over half of the children already having undergone complete exome sequencing. A PhD studentship part funded by the Gerald Kerkut Charitable Trust and the Crohn’s in Children Research Association (CICRA) supports this work.

This work with IBD has led to a natural collaboration with Dr Tony Williams, director of the Wessex Integrated Sciences Hub Laboratory whereby research interests are aligned in bridging the information gap between autoimmunity and genomics in early onset IBD. Dr Ennis supervises a recent clinical fellowship award by CICRA to 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.

Ophthalmic Genetics

A local collaboration with the Vision Laboratory, part of the Clinical Neurosciences Research Division and Southampton Eye Unit, has produced patents in medical diagnostics and research papers published in leading international journals such as The Lancet and Nature Genetics. This work has involved international collaboration with the University of Iowa, The Netherlands Institute for Neuroscience and deCODE genetics Inc.

Specifically research into the genetics of age related macular degeneration (AMD) and primary open angle glaucoma (POAG) using targeted investigation as well as whole genome association and copy number variant analyses have produced numerous scientific papers. More recently, we have begun applying next generation sequence technology to samples from patients with Cone Dystrophy and Nystagmus to ascertain causal mutation not found by conventional diagnostics.

Genetics of Cancer

Professor Ennis supervises a CRUK funded postdoctoral position in the Genomic Informatics Group to support research into genetic variation in cancer. Ongoing collaborations with local researchers to: examine genomic data from germline and tumour DNA samples from patients with chronic lymphocytic leukemia and Splenic Marginal Zone Lymphoma; understand the pathogenesis and clonal evolution of multiple myeloma through analysis of genome sequence data; Assess exome data from long and short term survivors of pancreatic cancer; 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.

Professor Ennis co-supervises a PhD studentship investigating methods to detect novel chromosomal fusion events that lead to cancer. She collaborates with clinical geneticists expert in the process of splicing to identify protein isoforms that are alternatively expressed in breast cancers.

Familial Nephropathy

Professor Ennis co-supervises an MD/PhD to identify the nature and prevalence of familial nephropathy with Dr. Venkat-Raman from the Wessex Renal Transplant Centre at Queen Alexandra Hospital Portsmouth. This project also aims to achieve precise genetic diagnoses in cases of uncertain aetiology. She also collaborates with consultant nephrologists at Southampton to investigate the inheritance of disease causing mutations in specific cases of congenital and childhood onset kidney disease.

Data Integration

The volume of data in clinical research is increasing exponentially. In addition to the significant advanced in genomic sequencing patient DNA, there have been parallel advances generating RNA sequence data from specific tissues, sequencing microbial populations within the body, using NMR to characterise the metabolic spectrum. This is in addition to the increasingly rich longitudinal clinical data that can be gleaned from healthcare systems. The Genomic Informatics group works closely with the Southampton NIHR BRC Data Science team to optimise methods for the digital extraction of anonymised clinical data. In addition the group works close with colleagues is mathematical modelling and machine learning to develop methods for the integration of diverse data types in healthcare research.     

Research group

Human Development and Health

Affiliate research group

Human Development and Physiology

Faculty and University roles

Research Lead for ‘Human Genetics & Genomic Medicine’
Cross-Faculty Lead for ‘Omics
Member of Senate
Lead organiser for the annual Southampton BiOmics conference  

Expert reviewer for multiple journals including:

Bioinformatics; BMC Genomics; BMC Medical Genetics; Brain; Clinical Genetics; Clinical & Experimental Allergy; European Journal of Human Genetics; Human Mutation; Genetic Epidemiology; Genetics; Genome Medicine; Genomics; Human Genetics; Human Mutation; Journal of Allergy & Clinical Immunology; Nature Communications; New England Journal Medicine; The Lancet; The Lancet Neurology; The Lancet Gastroenterology & Hepatology; The Lancet Oncology; The Lancet Respiratory Medicine.         

Expert panellist:

Medical Research Council (MRC); ANR France; European Commission; Genome British Colombia; Portuguese Foundation for Science and Technology (FCT); Israel Science Foundation; King Abdulaziz University (KAU), Saudi Arabia ; WELBIO Research Institute, Belgium; Nuffield Foundation; German Federal Ministry for Education and Research (BMBF) and the E-Rare group of national research funding agencies; National Institute of Health Research (NIHR); Academy of Finland; Scientific Advisory Panel – Crohn’s in Childhood Research Association; Medical Advisory Committee - Sparks for Children’s Health.

Genomics England:

Bioinformatics Lead for Wessex Genome Medicine Centre (GMC); GeCIP Subdomain Lead (Population Genomics); GeCIP Member (Chronic Lymphocytic Leukaemia, Haematological Malignancy, Paediatric, Renal, RNA Splicing and transcriptomics, Advanced analytics).

Societies:

Member of the Genetics Society; The Galton Institute; European & American Societies of Human Genetics; British Society of Paediatric Gastroenterology, Hepatology & Nutrition (BSPGHAN).     

Chief Investigator:

NIHR Portfolio Study 11158 ‘Genetics of Paediatric Inflammatory Bowel Disease’; REC reference - 09/H0504/125; Protocol number - RHM CHI0497; IRAS project ID – 29087
Use of NGS technologies for resolving clinical phenotypes; REC reference - 17YH/0069; Protocol number RHM NEU0302; IRAS project ID – 212945

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Articles

Book Chapter

Conference

Letters/Editorials

Reviews

Undergraduate

Lecturer Biochemistry, Molecular Cell Biology and Genomics: University of Southampton 5 year Medical Degree
Third Year Project Supervisor
Personal Tutor

MSc

Module Lead for Genomics of Common & Rare Disease: University of Southampton MSc Genomic Medicine
Dissertation Project Supervisor

Postgraduate

Supervisor of PhD student projects: 9 ongoing (Main Supervisor for 6); 10 completed.
External examiner: University College London; Institute of Cancer Research; Oxford University; Universities of Exeter, Bristol, Leeds; German University of Cairo.

Other

Course Lead: Primer in Genomic Medicine

Professor Sarah Ennis
Phone: (023) 8120 8614 Fax: (023) 8120 4264 Email: se@soton.ac.uk

Room Number NNN: SGH/DB/MP808

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