Genotype Imputation and Data Analysis for African Populations: A Practical Tutorial Using AfriGen-D Resources

This tutorial addresses an immediate practical need in African bioinformatics: the lack of training in African-specific genomic analysis tools. This hands-on tutorial will bridge this gap, providing practical training that participants can immediately apply to their research projects. The timing also aligns with the rapid growth of African genomics projects and new sequencing facilities across the continent. By focusing on end-to-end real-world applications, participants will gain immediately applicable skills using actual African genomic datasets.

Through practical exercises, participants will master data quality control specific to African genetic data, execute imputation and basic GWAS workflows, and learn to interpret results using the AfriGen-D Imputation Service, African Genomics Medicine Portal (AGMP), and African Genomics Variation Database (AGVD).

Keywords: Imputation, genotyping, data analysis, African populations, bioinformatics.

Skill level of training: Intermediate

Language: English

Credential awarded: None

Type of training: In Person

Venue

ISCB Africa / ACSCB 2025, Lagoon Beach Hotel, Cape Town

Date(s) of training: 17 April 2025, 1pm - 5pm
13:00-17:00 CAT

Organisers:

• Mamana Mbiyavanga, University of Cape Town
• Lyndon Zass, University of Cape Town
• Sumir Panji, University of Cape Town
• Nicola Mulder, University of Cape Town
• Hosted by ISCB Africa / ACSCB 2025

Registration for classrooms opens: 28 February 2025

Registration for classrooms closes: 7 April 2025

Link to classroom application form: https://www.iscb.org/cms_addon/registration_conference/africa2025

Notification date for successful classrooms: 8 April 2025

Application instructions:

Sponsors:

Afrigen-D, ISCB Africa ASBCB 2025

Intended Audience:

• Researchers, bioinformaticians, and students working with African genetic data. Basic understanding of genetics and familiarity with command-line interface required.
• 30 participants (to ensure adequate hands-on assistance)

Syllabus and Tools:

Licensing for course materials:

The default licensing attached to any workshop and materials will be a creative commons license. Please do specify if a different license is required or whether materials will not be available publicly. If materials cannot be linked to our website, please specify a contact person in order to gain access to materials in future.

Prerequisites:

Personal laptop with internet connection
Basic command-line knowledge
Familiarity with genetic data formats

Learning outcomes:

Navigate AfriGen-D catalogues for data discovery
Master data preparation and quality control using the AfriGen-D Imputation Service
Execute and monitor imputation workflows using the AfriGen-D Imputation Service
Perform post-imputation quality assessment
Perform basic GWAS analysis using the AfriGen-D Imputation Service
Annotate and interpret genetic variants using African-specific resources (AGMP and AGVD)

Limitations:

This workshop will only provide a foundation for continued learning in genotype imputation on the Afrigen-D Imputation Service

Programme:

Time	Topic	Trainers
17^th April 2025
13:00-13:15	Introduction to AfriGen-D Resources and Data Discovery	Sumir Panji, Lyndon Zass
13:15 - 13:30	Introduction to Genotype Imputation (Mamana/Ayton)	Mamana Mbiyavanga, Ayton Meintjes
13:30 - 14:00	Data Preparation and Quality Control (Hands-on)	Mamana Mbiyavanga
14:00 - 15:00	Imputation Workflow and Monitoring (Hands-on)	Mamana Mbiyavanga
15:00 - 15:15	Tea Break
15:15 - 15:45	Imputation Quality Assessment (Hands-on)	Mamana Mbiyavanga
15:45 - 16:10	Basic GWAS (Hands-on)	Mamana Mbiyavanga
16:10 - 16:15	Break
16:15 - 16:45	Variant Annotation and Interpretation Using AGMP/AGVD	Lyndon Zass, Ayton Meintjes
6:00	Workshop End