GEID Philippines 2017

International Workshop in Genomic Epidemiology of Infectious Diseases in the Philippines

Course Dates: 3-7 July 2017

Workshop: Genomic epidemiology of infectious diseases

 

London School of Hygiene and Tropical Medicine (LSHTM), United Kingdom in partnership with the University of the Philippines (UP) and the Philippine Genome Centre (PGC), Philippines. 

Supported by the Newton Fund Researcher Links Programme.


UK coordinator: Professor Taane Clark, LSHTM.


Filipino coordinator: Dr Maria Anita Bautista, PGC.


UK mentors: Professor Martin Hibberd (LSHTM), Dr. Julius Hafalla (LSHTM).

Filipino mentors: Professor Carmencita Padilla (UP Manila), Dr. Raul Destura (PGC and UP Manila). 

Date and location

Date: 03-07 July 2017 (Computational workshop from 04-06 July 2017) 


Venue: Institute of Biology and Computational Science and Research Centre, National Science Complex, University of the Philippines, Diliman, Quezon City 

Background 

Infectious diseases, such as HIV-AIDS, malaria, pneumonia and tuberculosis, account for 25% of global mortality and more than half of all deaths in children under the age of five years. The genetic epidemiology of these diseases can be complex, especially as they may involve several genomes, including the host, pathogen(s) and a vector. There is also a need to look beyond the genome to consider other ‘omes, such as the transcriptome, in a more systems biology framework. 

High throughput genotyping and sequencing technologies are providing insights into these genomes, metabolomes, transcriptomes and proteomes, thereby revolutionising genetic epidemiological studies and biomedical research. The use of SNP chips in large-scale genome-wide studies of association and genetic selection has revolutionised the study of human disease susceptibility. Whole genome studies of pathogens using high throughput sequencing technologies is leading to the ability to track microbial evolution over time and space, as well as identify variants correlated with phenotypes such as anti-microbial resistance. Further, RNAseq methodologies are being used to measure transcript abundance and differential gene expression across isolates. 

To take full advantage of new ‘omic technologies requires the ability to analyse large amounts of data using methods from bioinformatics, population genetics and statistics – the focus of this Workshop. Specifically, the Workshop offers hands-on experience of processing sequencing data to construct genomes, identifying genomic variants and applying downstream methods, such as phylogenetics. Further, the course covers transcriptomic and proteomic analysis in human and pathogen settings. High profile examples, including malaria, TB and MRSA, will be used to illustrate the concepts, and there is a strong emphasis on how to implement the methods in practice, with the majority of sessions computer-based. 

The programme, Newton Researcher Links provides opportunities for early career researchers from the UK and internationally to interact, learn from each other and explore opportunities for building long-lasting research collaborations. As part of this programme, we are now recruiting Early Career Researchers to participate in the above Workshop. 

The Workshop will provide a unique opportunity for sharing research expertise and networking. During the Workshop early career researchers will have the opportunity to present their research in the form of short oral presentations and discuss this with established researchers from the UK and the Philippines. There will be a focus on building up links for future collaborations, and participants will be selected on the basis of their research potential and ability to build longer term links. 

The British Council and the Philippine’s Department of Science and Technology (DOST) will cover the costs related to the participation to the Workshop, including: travel, accommodation and meals. Although this cost will not be covered by the British Council or DOST, participants are encouraged to purchase an adequate travel and medical insurance. The British Council accepts no responsibility for any problems which may occur when the participants are in-country. 

Objectives 

This five-day Workshop will be held in the National Science Complex, University of the Philippines, Diliman, Quezon City, Philippines, aimed at early career researchers from the UK and the Philippines. This Workshop will bring together global experts on the study of genomic epidemiology of infectious diseases, particularly those affecting the Philippines. The Workshops aims to promote collaborations that will enhance the use of tools in bioinformatics, population genetics and statistics in infectious disease research. 

Days one and five of the Workshop, which will be held at the Institute of Biology auditorium, will focus on presentations and discussions relating to the role of genomics in the prevention and control of infectious diseases, with a focus on the Philippines. The other days, which will be held at the Computational Science and Research Centre, will focus on genomic analyses. By the end of the Workshop, participants will be able to: (a) process raw sequence into a set of informative variants, through mapping to a reference genome or using de novo or reference-free assembly approaches, (b) conduct transcriptomic and proteomic analysis, in an integrated systems biology approach, and (c) perform downstream population genetic and association analysis. 

Eligibility criteria

Applications must be submitted using the Researcher Links Application Form.
Applications must be submitted before the deadline. 
Participants must be Early Career Researchers: Early Career Researchers are defined as holding a PhD and having a maximum of up to ten years post-PhD research experience. MSc graduates and Research Assistants with extensive research experience are also encouraged to apply. 
Participants must have a research or recognized research institution post, research contract, or fellowship) at a recognized institution either in the UK or Philippines.
Please note that participants are expected to attend all sessions of the Workshop. Those who are not chosen to participate in the five-day Workshop are welcome to attend presentations and discussions on days 1 and 5. 

Application and deadline

For UK applicants, please send your application to Taane.Clark@lshtm.ac.uk (for UK applicants) and enter ‘Genomic epidemiology of infectious diseases’ in the email subject line. 

For Philippine applicants, please register through this link.

The full application must be completed and submitted by Saturday, 10 June 2017 (for Philippine and UK applicants). 

Equal Opportunities

Wherever possible, gender balance and diversity will be sought in the selection of candidates, and extra support to enable participation of Early Career Researchers with special needs will be given.