23 May 2017
10.00 – 11.30am
Big Data in Malaria Elimination
Malaria is one of the most important causes of morbidity and mortality in the developing world. Most of the deaths are in children infected by Plasmodium falciparum, a mosquito-borne protozoan parasite that invades red blood cells. Much progress has been made to reduce the burden of malaria. However, the remarkable adaptive capabilities of P. falciparum constantly undermine the efficacy of antimalarial drugs.
Next-generation whole-genome sequencing (WGS) has made it possible to sequence large numbers of P. falciparum genomes. Through significant advances in sample processing, it has now become possible to conduct large-scale population genetics studies using WGS data from dried blood spots collected in the most basic endemic settings. The MalariaGEN P. falciparum Community Project collaborates with dozens of clinical research groups and national malaria control programmes to maintain the world’s largest repository of malaria genetic data. Presently, our global studies use WGS data from nearly 7,000 clinical cases from 4 continents, and this number is rapidly increasing with falling sequencing costs. This dataset has enabled a number of significant advances in P. falciparum genetic epidemiology including the identification of genetic factors associated with resistance to artemisinin and piperaquine.Genomic data is gradually becoming incorporated in surveillance, control and elimination interventions, but this is not without challenges. It will be important for all public health and research partners to understand which capacities are to be developed in the country, and which to be acquired through partnerships.
After graduating as a physicist at Imperial College London, Olivo worked for two decades in software engineering, first as a software developer and later as a lecturer at the National University of Singapore. In the wake of the publication of the first human genome, he thought his computing skills would be best employed to fight disease, and completed a PhD in bioinformatics. In 2008, he joined the University of Oxford, where he has led large-scale analyses of malaria genomes. Being located at the Mahidol-Oxford Research Unit in Bangkok, Olivo has been able to collaborate in key clinical studies across Southeast Asia, focussing on the emergence and spread of drug resistance. His work has been published on several respected biomedical journals, including Nature, Science, NEJM, Nature Genetics, PNAS, Lancet ID. He is currently funded by the Bill and Melinda Gates Foundation to implement a genetic surveillance platforms to inform elimination strategies in endemic countries in the region, a project that brings together public health and research partners from eight countries.
Dr Olivo Miotto
Senior Informatics Fellow
Mahidol-Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok;
Centre for Genomics and Global Health, Oxford University, Oxford.
18 July 2017
2.00 – 3.00pm
Large scale bioinformatics data integration and data mining of resources for improved target identification and validation in various therapeutic areas.
Open Targets is a public-private partnership made up of four global leading institutions in the fields of pharmaceuticals, bioinformatics and genomics, namely GSK, EMBL-EBI, the Wellcome Trust Sanger Institute, and Biogen. We combine large-scale genomic experiments to identify and validate the causal links between targets, pathways and diseases. We have recently developed the Target Validation platform, a web application for data integration and visualisation, which supports both target- and disease-centric workflows.
Our platform enables biomedical researchers to discover and prioritise biological targets for new therapies. We derive evidence of association between a target and a disease from multiple public domain resources, including germline and somatic genetics. An association score, which takes into account the observed frequency, the experiment confidence, and the likely strength of the effect of the target on the disease was also provided. By drawing on expertise in product and platform development including product testing, UX design and site development, we have created this comprehensive and robust data integration for access and visualisation. In addition, programmatic retrieval of data via RESTful endpoints and/or using our API clients, in R and Python. The Target Validation Platform is aimed at users from both academia and industry, whether you want to browse a target on a gene by gene (or disease by disease) basis, carry out more complex queries using the API, or download all evidence and association objects for downstream analyses.
Chuang Kee is a proven research and informatics leader using computational and informatics platforms for life science and drug discovery applications. In his role as Data Integration Manager at OpenTargets (EBI), Chuang Kee manages data providers across various different groups and leads the data integration efforts. Chuang Kee join OpenTargets from Ensembl. Most recently the Senior Technical Officer in the production team, responsible for the large scale genomics processing pipelines, production infrastructure development, data coordination among various sub-teams to ensure timely delivery of Ensembl releases consist of thousands genomes. Before Ensembl, Chuang Kee was the Principal Scientist, VP at SDTC. He is responsible for the bioinformatics unit whose efforts were geared toward enhancing palm oil yield productivity via various cutting-edge high throughput assays. Prior to joining SDTC, Chuang Kee was the Senior Associate Scientists at Eli Lilly. He lead various cross functional, disciplines drug discovery informatics projects to support target identifications and validation in a variety of therapeutic areas. Chuang Kee has a MSc Bioinformatics from Chalmers University of Technology in Sweden.
Mr Chuang Kee
Data Integration Manager
Open Targets, European Bioinformatics Institute (EMBL-EBI)