In 2019, Tuberculosis (TB) was the leading cause of mortality due to infectious disease worldwide, with an estimated 10 million new cases and 1.5 million deaths. Despite having a low HIV prevalence and a successful TB control program, Peru has the second-highest estimated TB rates in the Americas and reported 29% of all multidrug-resistant (MDR) cases for the region in 2018. Recent advances in Next-Generation DNA Sequencing (NGS) and bioinformatics offer new and exciting tools to study TB transmission and enhance global surveillance of drug-resistant TB. However, infrastructure and capacity to conduct NGSbased studies in Peru are still limited.
To support this, the Instituto de Medicina Tropical Alexander von Humboldt (IMTAvH) and the Facultad de Ciencias y Filosofía of Universidad Peruana Cayetano Heredia (UPCH) in collaboration with the University of Antwerp (Global Health Institute, GHI and; Tuberculosis Omics Research consortium, TORCH) and Universidad Nacional San Agustín de Arequipa, is launching a 3-week course that offers trainees an introduction to NGS and bioinformatics data analysis, plus the opportunity to a develop TB-oriented pilot research projects throughout the course.
Training will focus on NGS applied to TB research and surveillance in academic and public health settings. Up to eight selected trainees will complete a 3-week training at UPCH in Lima and Arequipa, followed by long-term mentoring and assistance, to facilitate the participants' application of the newly acquired skills in their workplaces.
The course is aimed at Peruvian PhD or MSc students, post-doctoral researchers, clinicians, and healthcare professionals, currently-engaged-in or soon-to-begin NGS-based TB research or surveillance.
Eligible candidates should have previous theoretical and practical training in molecular biology techniques and good lab performance. Active involvement in tuberculosis research is required, and public health workers are encouraged to apply. The course will be taught in English and promote active discussions, so intermediate/advanced English skills are required.
At the end of the training you should:
- Have a comprehensive knowledge of NGS and its applications
- Have the practical skills to perform sequencing-based experiments
- Be able to use bioinformatics tools to perform analysis of NGS data
- Be able to develop a relevant to a public health research project using NGS
The 3-week programme will include lectures, discussions and laboratory and computationalbased practicals. It will cover:
- Basics of NGS and available platforms.
- Illumina sequencing technology, instrument workflow: run set up, operation and run monitoring.
- Isolation and culture of M. tuberculosis from patient samples.
- Genomic DNA extraction, quantification of input DNA, library normalization, quality control, and sequencing.
- Output files, location and use. Initial quality assurance, management, storage and data sharing.
- Assembly: reference genomes, mapping, variant calling, reporting.
- Tuberculosis research, surveillance and public health.
- Joint analysis and interpretation of genomic data.
Selection and Financial Support
Following a competitive selection process, a maximum of 8 candidates will be selected to participate in the program. We will work in Lima the first week and the last two weeks in Arequipa. The program will cover travel costs, accommodation, and daily allowance for participants living outside Lima and Callao during the first week; for those living outside Arequipa during the second and third weeks.
How to apply
Please complete the following application form: https://forms.gle/8XGpuoxZNmfspYZ78
The final decision from the selection committee will be available by March 4th, 2022.
You will be contacted by e-mail to inform you whether your application has been successful.
- Annelies Van Rie, Global Health Institute, University of Antwerp, Belgium.
- Conor Meehan, Nottingham Trent University, United Kingdom
- Pablo Tsukayama, Universidad Peruana Cayetano Heredia, Peru
- Christopher Delgado Ratto, Global Health Institute, University of Antwerp, Belgium.
This course is supported by: "Improved infectious diseases control in Peru through sustainable capacity building for bioinformatics and genome sequencing"- VLIR UOS JOINT E2019JOI018A102