Single Cell Genomics - Latin America and the Caribbean

Single-cell sequencing technologies are powerful tools used to assess genomic, transcriptomic and proteomics information at the single-cell level. In recent years, the application of techniques that use single-cell sequencing have become increasingly common in several areas of research: including medicine, agriculture, and other life sciences disciplines. Single-cell sequencing may be used to study many aspects of an organism’s biology, both in health and disease, and the results of these studies contribute immensely to advancing the understanding of organisms as a whole. 

Illustrated by the successful formation of scientific networks within the Human Cell Atlas, there is growing interest among scientists and increased need for building capacity for single cell technologies. However, there is a lack of infrastructure, limited funding, and expertise  relevant for applying these advanced technologies in Latin America. Therefore, this short course offers hands-on laboratory training and bioinformatics analysis in single-cell technologies to contribute to capacity development in Latin America. 

Target Audience

Early and mid-career scientists, PhD students, and postdoctoral researchers based in Latin American countries who are engaged or planning to engage in single-cell research.

This hands-on laboratory and bioinformatics course will offer a series of lectures, practical sessions, and guest seminars which include the following:

• Introduce the application and analysis of single-cell sequencing approaches.
• Provide detailed breakdown of steps involved (molecular biology) in the current state of the art single cell RNA preparation methods.
• Teach best practises for planning and performing single cell experiments 
• Teach ways to perform QC at key stages of single cell RNA sequencing sample preparation, how to understand results, and what to do if something goes wrong.
• Provide a general overview of sequencing data output and workflow required for pre-processing single cell data. 
• Provide bioinformatics training using published / publicly available datasets.

Learning Outcomes

At the end of this course, participants will be able to:

1. Describe the experimental aspects of the single-cell RNA-seq technology and distinguish its advantages and pitfalls.
2. Plan and perform single-cell RNA-seq experiments from wet lab to data analysis.
3. Recognise the basic structure for R scripting to analyse single-cell RNA-seq data.
4. Discuss the methodological aspects of the data analysis in single-cell RNA-seq experiments.
5. Interpret the outcomes of a single-cell RNA-seq pipeline in light of a biological question.
6. Access single-cell RNA-seq data repositories.
7. Execute downstream analysis of single-cell RNA seq-read data. 

Prerequisites

The hands-on bioinformatics modules will be taught using R. Therefore, participants are required to have some familiarity with the R language. This will be essential for participants to fully benefit from the course. All candidates will be requested to undertake pre-course activities to gain the fundamental knowledge needed during the course.

Scientific Organising Committee 

Patricia Abrão Possik
National Institute of Cancer (INCA), Brazil

David Adams
Wellcome Sanger Institute, UK

Mariana Boroni
National Institute of Cancer (INCA), Brazil

Vinicius Maracaja-Coutinho 
University of Chile, Chile

Instructors & Teaching Assistants 

Erick Armingol
University of California, San Diego, USA

Lia Chappell
Wellcome Sanger Institute, UK

Yesid Cuesta Astroz 
Colombian Institute of Tropical Medicine (ICMT), Colombia

Benilton de Sá Carvalho 
Unicamp, Brazil

Anita Scoones
Earlham Institute, UK

Patricia Severino
Albert Einstein Research & Education Institute, Brazil

Danielle Carvalho
National Institute of Cancer (INCA), Brazil

Flavia Aguiar
National Institute of Cancer (INCA), Brazil

Gabriela Rapozo
National Institute of Cancer (INCA), Brazil

Cristóvão Lanna
National Institute of Cancer (INCA), Brazil

Leandro Santos 
National Institute of Cancer (INCA), Brazil

Diego Gomes
National Institute of Cancer (INCA), Brazil

Speakers 

Gary Bader
University of Toronto, Canada

Carla Jones 
Wellcome Sanger Institute, UK

Marcela Sjöberg Herrera
Pontificia Universidad Católica de Chile, Chile

Irene Papatheodorou
European Bioinformatics Institute, UK

Helder Nakaya
University of São Paulo, Brazil

Alejandra Medina-Rivera
UNAM, Mexico

Ivana Jelic
CZI, USA

Max Lombard
CZI, USA

Marcelo Mori
Unicamp, Brazil

Fernando Rivadavia
Illumina, Latin America

Carlos Ortiz
Cinvestav, Mexico

Organisers

Alice Matimba
Wellcome Connecting Science - UK

Cassandra Soo
Wellcome Connecting Science - UK

Isabela Malta
Wellcome Connecting Science - UK

Karon Chappell
Wellcome Connecting Science - UK

Martin Aslett
Wellcome Connecting Science - UK

Mônica Lisboa Torres
National Institute of Cancer (INCA), Brazil

Target Audience

This course is for early and mid-career scientists, PhD students, and postdoctoral researchers based in Latin American countries who are engaged or planning to engage in single-cell research. The course will be taught in English but there will be support from Portuguese and Spanish speaking instructors.

How to Apply
Please click the Apply button above to begin the online application process. Places are limited and will be awarded on merit. If you have any problems with the online application process, please contact us.

Please note: Applications must be supported by a recommendation from a scientific or clinical sponsor (e.g. supervisor, line manager or head of department). A request for a supporting statement will be sent to your nominated sponsor automatically during the application process. Applicants must ensure that their sponsor provides this supporting statement by the application deadline. Applications without a supporting statement cannot be considered.

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Cost
The course is subsidised by Wellcome Connecting Science, Chan Zuckerberg Initiative and Illumina, and is free to attend.

Bursaries
A number of bursaries are available for each course. These are awarded on merit to cover travel, accommodation and sustenance.

Bursaries can be applied for as part of the course application form. Applicants will be notified of a bursary award along with their place on the course, usually within one month of the application deadline. The decision of the selection committee is final.

Please note that both the applicant and sponsor are required to provide a justification for the bursary as part of the application.