By Olimatou Coker
The Medical Research Council Unit The Gambia (MRCG) and the London School of Hygiene and Tropical Medicine (LSHTM) in collaboration with Wellcome Sanger institute UK Tuesday commenced a 5-day training workshop for 42 subregional leading health and clinical researchers on advanced bioinformatics.
The advanced bioinformatics course has been developed for the GPS and JUNO projects.
The Global Pneumococcal Sequencing project is a worldwide genomic surveillance network of Streptococcus pneumoniae which provides evidence for pneumococcal disease control. The JUNO project is a global genomic surveillance of Streptococcus agalactiae which is a major cause of neonatal invasive disease worldwide. One of the core aims of the GPS and JUNO projects is to strengthen the capacity of regional project collaborators in generating and analysing genomic data.
The advanced bioinformatics course is aimed at researchers who are part of these global surveillance networks and have an interest in learning how to carry out next generation sequencing (NGS) and analysis of bacterial genomes (i.e., Streptococcus pneumoniae and/or Streptococcus agalactiae). This course will concentrate on the application of cutting-edge genomic techniques that are currently being implemented.
Participants will gain practical experience in bioinformatics analysis with a focus on NGS data quality control, assembly, reference mapping, in silico isolated characterisation, developing a portable bioinformatics pipeline, and downstream analyses such as phylogenetic inference. There will be lectures and demonstrations of the potential applications of NGS in academic research and/or in public health settings, with practical case studies in assessing transmission.
It is also said that there will be lectures and demonstrations of the potential applications of NGS in academic research and/or in public health settings, with practical case studies in assessing transmission. We will also cover limitations and pitfalls of these techniques.
Addressing the trainees, prof Martin Antonio, principal investigator and leading scientist in Molecular Biology and co-director of the Center for Epidemic Preparedness, said over the years the MRC Gambia has had dreams of introducing genomic science and bioinformatics.
“The unit, acts as a hub for their colleagues in West Africa. It has the equipment for performing this particular assay, as well as the analysis of the program. So, the training workshop is targeting a couple of bacterial pathogens that cause a lot of outbreaks and havoc in our country. I remember decades ago we had an outbreak due to meningitis disease in the Basse area which affected the population not just in Basse but also the way the government responded. So, it’s really important to make sense and identify the different causes,” he said.
Prof Antonio added that the outcome of the 5 days training will be vital for the trainees and their respective countries.
“They will be able to work with not just their administrations but also with their government in order to perform analysis due to genome sequencing, and the data can be shared with the various institutions and be used by policymakers to direct the affairs of the state. Also, as part of this training, we will ensure that we produce our own local data,” he said.
Stephen Bentley, group leader of Wellcome Sanger Institute, said: “We are working with partners around the world to apply genomics to understand these pathogens and how to prevent infections. So, the Sangha, as Martin mentioned, is a world leading Genomics Institute and we do lots of leading-edge research and partnerships like these would allow that kind of learning to quickly get to the ground level and be applied in disease prevention.”
He said the major focus of the workshop is to enable as many people as possible from as many countries to learn how to apply the technology as it can be currently used.