Next Generation Sequencing and Bioinformatics for Malaria research and surveillance in Peru

Malaria continues to be the most important parasitic disease in the Peruvian Amazonia.

In the world, DNA sequencing has played a major role in the identification of common transmission pathways, as well as the surveillance of drug-resistant malaria. The arrival of new technologies as Next Generation Sequencing (NGS) had offered a unique opportunity to improve public health, thus they are of increasing importance in biomedical research. However, technical capacity to conduct NGS-based research in Peru is still scarce.

To overcome this, the Instituto de Medicina Tropical Alexander von Humboldt (IMTAvH) of Universidad Peruana Cayetano Heredia (UPCH), in collaboration with the Global Health Institute (GHI) of University of Antwerp, launched a course that offered trainees an introduction to NGS and bioinformatic data analysis.

This training has a focus on NGS applied to infectious diseases in Academic Research and Public Health settings. Selected trainees complete a 3-week training at UPCH in Lima-Peru, followed by a long-term mentoring and assistance, to facilitate the participants’ application of the newly acquired skills in their own work places.

Why do we organise this workshop?

To achieve greater equity and maximum impact, it is important that innovation and technologies are not only developed in -or targeted at- high income countries but also focus on low income countries. To benefit all populations, innovations should be implemented at a much faster pace in public institutions in resource-limited settings. We are convinced that now is the right time to develop NGS sequencing and bioinformatics capacity in academic and public institutions (universities and reference laboratories) in Peru.

More than just a workshop

NGS training

Wet-lab and bioinformatics training by leading experts in NGS

Research proposals development

Close acompainment for the developing of NGS-related research proposals

Long-term mentorship

Direct contact with NGS experts across the world

A 3-week programme

Some of the topics covered in this training are:

  • Basics of Next Generation Sequencing and available platforms. Illumina sequencing technology
  • Gene target PCR enrichment, quantification of input DNA, library normalization, quality control of libraries and library pooling
  • Quality assurance, management, storage and data sharing
  • Assembly: reference genomes, mapping, variant calling, reporting
  • Malaria research, surveillance and public health

Outcomes

At the end of this workshop the participants are expected to:

  • Have a comprehensive knowledge of NGS and its applications
  • Have the technical skills to perform sequencing-based experiments
  • Be able to use bioinformatics tools to perform analysis of NGS data
  • Be able to develop relevant to public health research projects using NGS

The faculty

Udhayakumar Venkatachalam

Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, USA

Jean-Pierre Van geertruyden

Global Health Institute, University of Antwerp, Belgium.

Dionicia Gamboa

Malaria Laboratory, Universidad Peruana Cayetano Heredia, Peru.

Eldin Talundzic

Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, USA.

Julia Kelley

Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, USA.

Annelies Van rie

Global Health Institute, University of Antwerp, Belgium.

Christopher Delgado Ratto

Global Health Institute, University of Antwerp, Belgium.

Johanna Helena (Eline) Kattenberg

Institute of Tropical Medicine, University of Antwerp, Belgium.

We encourage research that is locally relevant

Each trainee is be mentored by UPCH, CDC and Belgian researchers in the development of a research proposal during which they will directly apply what they learned during the training. They will be asked to address an infectious disease that poses a significant public health problem in Peru.

The goal is that trainees become independent researchers. Therefore, trainees are encouraged to submit a research proposal for external funding, an essential step in the development towards an independent research/scientist career. In addition, we will create a network of trainees and alumni who will collaborate, participate in peer review other’s proposals, and continued learning through journal clubs.

Planting the first seeds...

NGS is not yet fully integrated in the surveillance programs run by reference laboratories or in infectious disease research performed by academic scientists in public universities. We aim to plant the first seeds for infectious disease bioinformatics and sequencing in Peru; an effort we believe will result in the critical mass required to create a network of Peruvian research groups working on molecular epidemiology of infectious diseases.

This 3-week course is supported by

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