African-wide Workshop on Repeat Expansions Detection and Complex Phenotypes Association

Four Universities, Covenant University, Makerere University, the University of Cape Town (UCT), and the University of California, San Diego (UCSD) are collaborating to present a two-week virtual workshop on repeat expansions detection and complex phenotypes association in Africa. This workshop is funded by the R01 DS-I Africa award number 1U01HG013442-01 and you can find more information about it at https://h3africa.org/index.php/2022/09/14/h3africa-cross-consortium-genome-analysis-of-repeat-expansions-in-wgs-data-project-spotlight/ and https://dsi-africa.org/project/28.

Africa has a higher proportion of genetic polymorphisms than non-African groups. However, the number of sequenced African genomes still lags far behind non-African groups. Recent efforts by H3Africa and other consortia have begun to address this challenge and revealed Africa as a vast source of uncharacterized genetic variants. For example, the H3Africa Consortium recently sequenced 426 African individuals and identified 3 million previously undescribed variants, including 62 novel loci under strong natural selection. However, only genomes of several dozen of the approximately 2,000 ethnolinguistic groups have been analyzed, and these efforts have mainly focused on SNPs and small indels.

Repeat expansions in human genomes cause neurological disorders and complex blood diseases. Therefore, it is urgent to establish an INTERnational Research Training PROgram for REPEAT expansions Detection and association with complex traits (INTERPROREPEATD), particularly in African populations. This workshop aims to identify potential candidates for targeted research training from various African institutions. The multidisciplinary workshop invites applications from BSc and MSc/BEng and MEng final year students in Bioinformatics (preferably those with a previous background in Computer Science and Engineering), Computer Science, Mathematics, and Statistics (with a strong computing background expected) and Engineering (preferably from Electronic and Information Engineering (EIE)).

Course content

The workshop will last for 10 days, which is equivalent to two weeks.

Module One – Introduction (Day 1 and 2)

• A brief review of NGS and its technologies, genotyping, genetic variation and its types, resources, and databases for NGS
• Bash/shell scripting, working in batch environment, job submission on HPC, installing software and tools using command line
• NGS file format, NGS analysis tools, e.g., bcftools

Module Two – Overview of Tandem Repeats (Day 3 and 4)

• Description of tandem repeats, types of TRs and their characteristics, applications of TRs in health research
• Short TRs (STRs) genotyping, tools for identifying STRs: strengths and weakness

Module Three – STRs Analysis (Day 5 – 7)

• Software Installation of selected tools
• STRs identification using selected tools, at least two
• Functional annotation of identified STRs
• Association Analysis

Module Four – Hackathon (Day 8 – 10)

• Brief description of the projects (motivation, datasets, methods, milestones, expected results, etc) – (to be done on Day 4)
• Assigning the participants into groups and one teaching assistant per group – (to be done on Day 4)
• Project teams start meeting up with their teaching assistants after the daily sessions as from Day 5
• Participants work in groups.
• Daily review of work done to be presented by a group representative following the milestones/deliverables for each day
• Presentation of project outcomes and submission of project write-up
• Announcement of hackathon results

Invited Talks from Keynote and invited speakers (30-minute – 1-hour slots will be created as needed during the workshop)

• We expect to have invited talks from selected PhD students, Postdocs, and keynote speakers on selected topics relating to TRs identification.
• Potential speakers are those who have developed tools/databases for TRs and those who have used the tools for TRs analyses, etc.

Application closes on April 30th, 2024

Date: Wed, May 8 - Tue, May 21 2024, All day CAT

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