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The University of Southampton

Human Genetics and Genomic Medicine

Southampton has a strong track record in human genetics and medical genomics and there is a broad research program from genetic medicine and the study of single gene disorders, through identification of genetic factors in common complex disease, the identification of somatically-acquired mutations in cancer to clinical application of genomic technology for molecular diagnosis and treatment optimisation in cancer. One of the strengths of genetics research in Southampton has been the close links between clinicians, clinical scientists and basic scientists.

Genetic Variation and Disease

From the seminal studies of Professor Patricia Jacobs FRS on chromosome disorders, using molecular technologies to characterise human chromosome abnormalities, to the use of large cohorts in genome wide association studies for common disease such as asthma and COPD, age related macular degeneration and glaucoma, and inflammatory bowel disease, to the use of next generation sequencing technology for exome sequencing to identify rare genetic variation in both common disorders, Mendelian disease, and cancer, Southampton has been at the forefront of the application of genetic technology to understanding disease.

Genetic epidemiology and genomic informatics

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 that 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 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 IRIDIS3 cluster

Dr Christopher Woelk leads a bioinformatics group that utilises whole genome gene expression technologies (e.g., microarray and RNA-Seq) to investigate the mechanism of human disease, and to construct diagnostic and prognostic classifiers.

Clinical Genetics Research Group

The Clinical Genetics Research group (previously called the Academic Unit of Genetic Medicine (ACUGEMS)) comprises clinicians and counsellors with an academic interest, and academics with a clinical genetics role

The main research themes are:-

Cancer genetics Professor Diana Eccles leads a large breast cancer program including Dr Ellen Copson. The group collaborate on many national and international studies on the relationship between genetics and outcome  (e.g. POSH)

Genomics law and ethics led by Professor Anneke Lucassen who directs a programme of research into the social, ethical and legal aspects of developments in genetics as part of CELS (Clinical Ethics and Law at Southampton).

Genetics and epigenetics of development disorders and genetic diseases led by Prof Karen Temple. The main research interests are in Dysmorphology, imprinting disorders and molecular pathogenesis of splicing in human genetic disorders (Dr Diana Baralle)

Genetics of congenital abnormalities Dr Diana Wellesley leads the Wessex Antenatally Detected Anomalies Register (WANDA) and current research includes environmental pollution and congenital anomalies, sex chromosome trisomies, long term follow up of specific congenital anomalies, and gastroschisis.

Other clinical genetics research includes Dr Simon Hammans in neurogenetics and in particular mitochondrial disorders and Dr Katherine Lachlan into PTEN mutation carriers.

Molecular genetics and cancer

Professor Nick Cross is Director of the Wessex Regional Genetics Laboratory and leads a research programme focused on myeloproliferative neoplasms (MPN) and related haematological malignancies. Their current areas of research are (i) the use of exome sequencing in combination with genomic arrays to identify mutations associated with acquired uniparental disomy, (ii) understanding the role of these mutations in the development of malignancy and (iii) identification of genetic factors that predispose to MPN.

Chromosomal abnormalities are the hallmark of human cancer and can aid in appropriate patient management. In chronic lymphocytic leukaemia (CLL), they can provide guidance on the most appropriate treatment regime and identify those patients likely to develop progressive disease or those that might exhibit limited response to treatment. Dr Jon Strefford leads The Cancer Genomics Group which employs state-of-the-art technology, including microarray approaches and next generation sequencing, to identify somatically-acquired mutation in CLL tumour specimens. These changes are then characterized at the mRNA and protein levels using standard molecular approaches, with the ultimate aim being functional characterisation with collaborators within the Faculty of Medicine.

Opthalmic Genetics

There is considerable interst in the genetics of ophthalmic disorders in Southampton. Mr Jay Self using next-generation sequencing techniques to unpick the heterogeneity of presumed idiopathic nystagmus. He hopes to use this information to explore the complex underlying pathophysiologies in addition to working towards a clinically useful genetic test for use in clinics and to aid preparation for robust clinical trials in genetically distinct cohorts.

Professor Andrew Lotery and Dr Sarah Ennis have undertaken genetic studies in age related macular degeneration (AMD) susceptibility and pharmacogenomics. Professor Lotery is also Chief Investigator on a multi-centre genetic study of primary open angle glaucoma (POAG) and together with the Wessex Regional Genetics Laboratory has established a test for glaucoma, now available on the NHS.

Human chromosome abnormality research

Staff at the Wessex Regional Genetics Laboratory have a long-standing interest in the study of chromosome abnormalities and research carried out there has made a significant contribution to this field. We have applied molecular techniques to study several classes of human chromosome abnormality to try and determine how and when they are formed. These studies are now being expanded to include much smaller abnormalities characterised by array CGH.

Current research areas

Transient neonatal diabetes & imprinting disorders
David Robinson, Deborah Mackay, Karen Temple

Monogenic disease
Andrew Lotery, Deborah Mackay, Karen Temple, David Wilson, Jay Self 

Ophthalmic Genetics
Andrew Lotery, Jay Self

Genetic Epidemiology: Complex Disease
Andy Collins, Sarah Ennis, Anthony WiskinJohn Holloway, Patricia Jacobs, Andrew Lotery

Gene function, Mechanisms and Models of Disease
Franchesca Houghton, Ita O'Kelly, Deborah Mackay, Dieter Riethmacher, David Wilson

Genetic Epidemiology and Genomic Informatics
Andy Collins, Sarah Ennis, Will Tapper, Christopher Woelk

Social, ethical and legal aspects of developments in genetics
Anneke Lucassen

Familial Cancer Predisposition
Diana Baralle, Andy Collins, Diana Eccles, Anneke Lucassen, Igor Vorechovsky

Molecular Genetics of Haematological Malignancy
Nick Cross, Fiona Ross, Jon Strefford

mRNA splicing and disease
Diana Baralle, Michela Raponi, Igor Vorechovsky

Technology Development and Diagnostics
Andy Collins, John Crolla, Chris Mattocks, Nick Cross, Patricia Jacobs FRS, Helen White

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