UGI Spring 2012 Newsletter

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UGI Spring 2012 Newsletter

Direct observation of the interconversion of normal and pathogenic forms of α-synuclein, Prof Nick Wood publishes in Cell

Research paper: X-linked megalocornea caused by mutations in CHRDL1 identifies an essential role for ventroptin in anterior segment development

Article: How a mother's genes can increase birth weight

Bloomsbury Centre for Genetic Epidemiology and Statistics Annual Scientific Meeting, 12 June, 2-6:30pm

Seminar: Dissecting the genetic architecture of cardiometabolic risk, 28 May, 1pm

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UGI Spring 2012 Newsletter

Welcome to the UGI Spring 2012 newsletter. Please contact Susmita Datta if you have any comments or information to be included in the next edition.

Welcome to new members of UGI

The Balloux Group

The Balloux group uses genomic data to investigate spatial genetic epidemiology of humans and humanpathogens. They address problems in epidemiology of, among other agents, the plague bacteria Yersinia pestis, malaria pathogen Plasmodium falciparum, and antibiotic resistant Staphylococcus aureus. In addition to their work on pathogens, they have a long standing interest in understanding the forces that shaped the current distribution of worldwide human genomic diversity. To test for possible targets of natural selection in the genome, Francois and his team are reconstructing the spread of our ancestors around the globe in unprecedented details, taking into account past changes in climate and the shape of continents. By knowing how and when people got to different parts of the world, they will then be able to distinguish which genetic variants have geographic distributions too extreme to be the result of mere chance, and thus have been likely targets of natural selection.

Professor Francois Balloux - Chair in Computational Biology Systems

Francois joined the UCL Institute of Genetics in October 2011. Prior to his UCL appointment he was the lead of the Statistical Molecular Genetics group at Imperial College London, where he concentrated on developing new methodological tools and reconstructing epidemics and outbreaks of human pathogens using genetic sequence data. Francois trained as a population geneticist and obtained his PhD in 2000 from the University of Lausanne (Switzerland). After a postdoc at the University of Edinburgh, he was offered a position in the Department of Genetics in Cambridge in 2002 where he led a group working mainly on human genetics. In 2007, he joined the Department of Infectious Disease Epidemiology and the newly founded MRC Outbreaks Centre, a move motivated by his desire to work at the interface between genetics and epidemiology and to contribute to research more directly relevant to Public Health.

Other members of Francois team include Dr Lucy Weinert, Dr Vera Warmuth, Dr Adrien Rieux and in June, the group will be joined by Dr Margarida Lopes.

The Luscombe Group

The Luscombe group's research focuses on the genomic analysis of regulatory systems. We study how the biology of an organism is shaped by regulation of gene expression. We investigate this at various levels of complexity, from single-celled bacteria and yeast to complex mammals. Expression of a gene - i.e. production of a protein - is a complex exercise requiring large, gluttonous protein machines which expend the cell's energy reserves. Hence, the organism needs to be judicious in choosing which proteins to produce when and where. Furthermore, the expression of all genes at all times would be detrimental to the organism. Expression must be rigorously regulated so that the right genes are ‘switched on or off’ in response toll changes in the internal and external environments of the cell.

Professor Nicholas (Nick) Luscombe - Professor of Computational Biology

Nick joined UGI in March this year. Following a degree in Natural Sciences at Jesus College, University of Cambridge (1993-1996), Nick studied for a Ph.D. with Janet Thornton at UCL (1996-2000) on the basis for specificity of DNA-binding proteins. He then moved to Yale University, USA, as an Anna Fuller Postdoctoral Fellow with Mark Gerstein (2000-2005), where he shifted research focus to genomics with a particular emphasis on yeast transcriptional regulation. He was a Group Leader at the EMBL-European Bioinformatics Institute (2005-2012) in Cambridge and built a computational biology laboratory with an emphasis on genomics and gene regulation. During this time, he joined the Okinawa Institute of Science & Technology as an Adjunct Faculty to establish a small group focused on developmental regulation (2011-present). He has now recently returned to UCL as a Chair in Computational Biology in the UCL Genetics Institute and holds a joint appointment as a Senior Group Leader at the Cancer Research UK London Research Institute. His laboratory will be joining the Francis Crick Institute in 2015.

Other members of Nick’s lab include:

Bori Gerle - Postdoctoral Fellow

Bori is interested in transcriptional gene regulation by epigenetic mechanisms. She did her PhD with Thomas Jenuwein at the Institute of Molecular Pathology in Vienna where she characterised an embryonic stem cell line lacking particular histone methyltransferase enzymes. By comparing the behaviour of impaired cells to normal ones, she then examined the importance of these enzymes - and the histone methylation marks they make - in controlling differentiation and reprogramming. For her post-doc, Bori is investigating whether histone-modifying enzymes expressed by bacterial pathogens play a role in modulating the host cell’s response during infection.
Ale Vigilante - Postdoctoral Fellow

Alessandra studies how transcription factors encoded in the human genome are utilised in different cell types. Previously, she completed her PhD with Marilu’ Chiusano at the University of Naples Federico II, Italy performing genome-wide analyses of Arabidopsis thaliana. She examined patterns of gene duplication and then studied the transcription factors encoded in the genome. She joined the Luscombe laboratory in 2011 first as a visiting PhD student, and then now as a post-doc. Her current goal is to study how the regulatory function of transcription factors is controlled by alternative splicing, and to examine their dynamic usage in different cell types and along courses of biological processes like differentiation.

New UGI Manager

UGI has a new Institute Manager, Dr Susmita Datta, who succeeds Claire Glen who has taken up a new appointment in UCL, Maple House. Susmita was appointed to the post of UCL Genetics Institute Manager in March 2012. Prior to her arrival she was based at the Wellcome Trust for 5 years and then went to work for Cancer Research UK, where she gained experience in many aspects of science funding in the United Kingdom and abroad. She was born and educated in London and holds a BSc Hons in Genetics gained from Queen Mary, University of London. She then went on to complete a Masters in Human Molecular Genetics from Imperial College. Her first experience of laboratory life was as a Research Assistant for Professor Jonathan Flint, at the Wellcome Trust Centre for Human Genetics, Oxford, where she researched the Genetic Basis of Anxiety and Depression in mice. This culminated in her intention to do a PhD in Psychiatric Genetics which she then went on to complete on the Molecular Genetics of Schizophrenia at University College London, under the supervision of Professor Hugh Gurling.

Congratulations to Dr Julie Bertrand

Julie has been awarded the MRC Career development award in biostatistics in March 2012. For the last 2 years she has done a post-doctorate at the UGI, on the pharmacogenetics of anti-retroviral agents funded by the French National research Agency on AIDS and Hepatitis (ANRS). Her 3 years-research project aims to integrate cutting-edge methods developed in genetic statistics into the nonlinear mixed effect models framework required to handle pharmacokinetic profiles. Using insights into drug response acquired from modelling, the goal is that individualized therapy based on genetic and other biomarkers will enable the physician to rapidly deliver a treatment with good efficacy and toxicity profiles.

Julie is also involved in a multi-disciplinary group involved in pharmacometric methodology and applications (the London Pharmacometric Interest Group, LPIG) meeting weekly at the ICH and she co-supervises an Mres project in the MSc in Clinical and Experimental Medicine-Drug Discovery.

Bloomsbury Centre for Genetics Epidemiology and Statistics (BCGES)

BCGES Annual Scientific Meeting, 12 June 2012, 2:00 – 6:30pm

This year the meeting features talks on pathogen and population genomics by Stephen Bentley (Sanger Institute) and Francois Balloux (UCL) with a range of further speakers from UCL and LSHTM on infectious and non-communicable genetic epidemiology, epigenetics, high-throughput sequence analysis and other topics at the leading edge of genomics research. To view the full programme and to register please visit our Eventbrite page.

The centre will also run two short courses in September 2012.

Course 1: Introduction to Genetic Epidemiology in the GWAS era (4 – 7 September 2012)

Genetic epidemiology holds great potential for personalised medicine and improved biological knowledge of disease processes. This course provides an introduction to the design, analysis and interpretation of genetic studies of disease, with a focus on state of the art analysis of genomewide association scans. Throughout the course participants will gain practical experience of analysing genetic data in population and family studies. By the end of the course participants will have an understanding of the fundamental concepts of genetic epidemiology, will have a working knowledge of the terminology and current status of the field, and will be able to perform many basic analyses of genetic data.

For more detailed information and to apply please go here.

Course 2: High throughput sequencing in disease studies (10 – 13 September 2012)

Rapidly developing technologies now allow genomes to be sequenced more quickly and cheaply than ever before. This course will cover state of the art methods and applications of next generation sequencing. The course runs over 4 days and participants will be introduced to tools for analysing high throughput sequence data, including methods for measuring copy number variants and allele-specific expression, and conducting disease association analysis with sequence data. There will be considerable opportunities to gain practical experience with new data types such as whole genome sequence, RNA- and ChIP-seq data. By the end of the course participants will have a broad knowledge of the state of the art and will be well equipped to analyse their own data.

For more detailed information and to apply please go here.

If you would like to join the e-mail list that will announce future seminars in statistical genetics and genetic epidemiology and other related events of broad interest, you can subscribe here.

UGI MSc courses

MSc in Genetics of Human Disease

This year we have 18 students on the course, among them 8 are from the UK, 6 from the EU and 4 are overseas. With the taught part of the current programme complete and the exams finished, the students will then be full time in carrying out their research projects.

In the coming academic year students on this Masters course will be offered one additional optional taught Module of “Clinical Applications for Pharmacogenetic Tests”, which is organised by Professors Steve Humphries and Aroon Hingorani). It was offered currently to the students on the MSc in Pharmacogenetics and Stratified Medicine and their feedback on the content of module is very positive. Pharmacogenetics is a new emerging field of biomedical science which has evolved from the analyses of the entire human genome. Students who will choose this module will be able to learn the application of genome science to study of human variability in drug response.

MSc in Pharmacogenetics and Stratified Medicine

The course is in its first year of operation. We welcomed 11 students this year, among them 4 from the UK, 2 from the EU and 5 are overseas. From the feedback of the student representatives to the Student Consultative Committee we are pleased to report that the students are enjoying their studies.

In 2012 the School of Pharmacy University of London merged with UCL, and from the next academic year this course will be a joint venture of UCL and the School of Pharmacy. Since the decision on the merger the UGI MSc management team has had a series of successful talks with the Department of Pharmaceutical and Biological Chemistry, School of Pharmacy. We are pleased to announced that two new optional modules Pharmacogenomics, adverse drug reactions and biomarkers (15 credits; organisers: Dr Michael Munday and Dr Rosemary Smyth) and Anticancer personalised medicines (15 credits; organiser: Dr Geoff Wells) will be delivered by the School of Pharmacy in the coming academic year. Thus, students will have a choice of 8 optional modules.

The taught part of the current programme is now complete and currently all our students are sitting exams. They will then be immersed full time in doing their research projects. We wish them well!

Please contact Elvira Mambetisaeva at e.mambetisaeva@ucl.ac.uk if you have any comments or information regarding the UGI MSc courses to be included in the next edition.

UGI email distribution list

The UGI has recently set up a new email distribution list. If you would like to subscribe to receive information about events organised by UGI please go here (insert link https://www.mailinglists.ucl.ac.uk/mailman/listinfo/ugi-events)

UGI is on Facebook

We have also recently set up a Facebook page where you can find all the latest information and events taking place. Visit us at www.facebook.com/uclgeneticsinstitute

Become a UGI affiliate

Being a UGI Affiliate brings the following benefits:

1. Access to the core team for research support, for example, to provide data analysis or to provide assistance with grant applications. The core team consist of: the Bioinformatician (Sonia Shah), Statistical Geneticist (Delilah Zabaneh), UGI Manager (Susmita Datta) and Executive Officer (Elvira Mambetisaeva). Affiliates have access to the core team by submitting a short request form to the UGI Manager. The costs of the core team used in the generation of research data (Bioinformatican and Statistical Geneticist) should be recovered from any grant obtained, their time and therefore cost should be included in any future grant application.

3. The UGI organises a series of workshops and seminars with the aim of facilitating interaction and fostering collaboration in genetics research. Affiliates will have the opportunity to co-organise and suggest such events.

2. Affiliates will have the opportunity to identify strong candidates for postgraduate study through interaction and engagement with the master’s students from the MSc in the Genetics of Human Disease. Affiliates will be asked to consider providing an MSc student project for this course (bench fees provided) and other masters courses as they become available (MSc Statistical Genetics and MSc in Pharmacogenetics).

If you are interested in becoming a UGI Affiliate please contact Susmita Datta.