27th Nov 2017

Developing skills in bioinformatics for pathogen genome analysis in Asia

Understanding pathogen genomes, how they evolve and which genes are essential for their ability to cause disease, is a key part of the battle to reduce the global disease burden. But capacity for research and skills for genome data analysis are limited in most low- and middle-income countries in Africa, Asia and South America and the Caribbean.

Contributing towards bridging this gap, Advanced Courses and Scientific Conferences (ACSC) recently held the Working with Pathogen Genomes course at the Oxford University Clinical Research Unit (OUCRU) in Ho Chi Minh City, Vietnam. This course has been going for over a decade and been held in different locations including Uruguay, Malawi and the UK.

Ten countries were represented from Asia-Pacific and Australasia – Thailand, Philippines, India, Vietnam, Japan, China, South Korea, Sri Lanka, Australia and New Zealand – by 24 participants. They are currently conducting research on a wide range of organisms to understand how factors such as pathogen virulence, host responses, and drug resistance affect human and livestock health, and food production.

This year the five-day computational course was led by Alison Mather (Quadram Institute, UK) with the goal of disseminating skills on how to analyse genomics data in bacterial and eukaryotic pathogen research and surveillance. There are an increasing number of institutions across South East Asia which now have genome sequencing technology and yet lack computational skills in handling the data being generated at such a fast rate. So the course was designed to provide hands-on training in the use of genome analysis software for genome exploration and comparative genomics. This was followed by mapping of Illumina sequence data, SNP calling, phylogenetics, genome assembly, genome annotation and RNA-seq.

Guy Thwaites, Director of OUCRU, kicked off the course with a seminar about ongoing research to tackle disease outbreaks, drug resistance, and the emerging burden of infectious and non-communicable diseases in South East Asia. Steven Baker, who heads a research group studying epidemiology and treatment of enteric infections, then talked about genomic surveillance of Salmonella Typhi in the region.

The UK-based team of instructors included Steve Doyle, Christine Boinett, and Martin Aslett, who gave talks about Next Generation Sequencing, molecular evolution and antimicrobial resistance, determinants of gastrointestinal bacterial pathogens, and the genetics of anti-helminth resistance. They were assisted by Nguyen Thi Nguyen, Hao Chung The and Pham Thanh Duy from OUCRU.

As part of the ACSC professional development programme, ‘train the trainer’ sessions were incorporated into the course programme to encourage participants to develop their educational practice and learn how to train others on return to their institution.

The course will be on twice in 2018: in South Africa in June, led by Adam Reid and hosted by Nicola Mulder at the University of Cape Town, and in Uruguay in November.

Interested in attending the course in 2018?

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