Poster Number
44
Poster Title
Characterization of African Biospecimen Using High-Throughput SNP-Genotyping: Lessons Learned and Future Direction
Authors
Ofonime Ebong1, Chinyere Anyika1, Jumi Popoola2, 54gene Team3, Colm O’Dushlaine4, and Abasi Ene-Obong1
1 Syndicate Bio Nigeria, 18, Samuel Ajayi, Magodo, Lagos, Nigeria
2 BioVana, 84, Emmanuel Keshi, Magodo, Lagos, Nigeria
3 54gene, 10, Nike Art Gallery Road, Ikate, Lagos, Nigeria
4 Insitro, South San Francisco, California, USA
1 Syndicate Bio Nigeria, 18, Samuel Ajayi, Magodo, Lagos, Nigeria
2 BioVana, 84, Emmanuel Keshi, Magodo, Lagos, Nigeria
3 54gene, 10, Nike Art Gallery Road, Ikate, Lagos, Nigeria
4 Insitro, South San Francisco, California, USA
Abstract
Introduction:
Africa harbours the highest level of genetic diversity worldwide, yet it remains significantly underrepresented in global genomic research. This study focused on Nigeria as a case study due to its highly diverse population, comprising over 300 ethnic groups, making it an ideal setting for exploring Genome-wide Association Studies (GWAS). SNP genotyping has become a key method for exploring genetic variation and identifying disease-associated markers in African populations. This process involves detecting differences in DNA, such as single-nucleotide polymorphisms (SNPs), insertions, deletions, and copy number variations (CNVs) by comparing individual sequences to a reference genome. The Illumina Infinium HTS Assay, a high-throughput genotyping platform, enables the analysis of up to 750,000 genetic markers per sample with high accuracy. Over 10,000 Nigerian samples were genotyped using this assay and the Infinium Global Screening Array-24 v3.0 beadchip. A custom African-focused beadchip, GENIISYS v1.0, developed by 54gene using data from whole genome and genome-wide association studies, was also utilized in processing a further 30,000 samples to improve the detection of unique variants. The study aimed to contribute to more inclusive global genomics by expanding the catalogue of African genetic diversity and informing future research in precision medicine.
Method:
A total of 40,000 samples from individuals with non-communicable diseases were collected across diverse geographical regions in Nigeria and processed for DNA extraction using the KingFisher Flex system. DNA quantity and quality were assessed using Quantifluor, QuantStudio 7, Multiskan SkyHigh, and DeNovix instruments. Samples that passed quality control were genotyped using the Illumina Infinium HTS Assay on the Global Screening Array-24 v3.0 and GENIISYS v1.0 beadchips. The workflow was automated with the Tecan and scanned on the iScan system. Primary genotyping analysis was performed using GenomeStudio, followed by secondary analysis using a custom bioinformatics pipeline to identify novel and population-specific variants.
Result & Conclusion:
High-throughput genotyping of over 40,000 samples and whole-genome sequencing of 1,000 Nigerian individuals from 50 ethnolinguistic groups enabled the identification of over 24 million high-quality variants. These efforts revealed striking genetic diversity, low levels of autozygosity, evidence of European/North African admixture in select groups, and unique patterns of natural selection across different populations. The development and deployment of the custom GENIISYS array (>800K markers) significantly improved the representation of African genomic variation for downstream analyses.
Implementing large-scale SNP-genotyping in African populations highlighted the importance of tailored QC pipelines, robust sample tracking systems, and culturally sensitive community engagement to ensure data quality and participant diversity.
Future efforts will focus on integrating phenotypic and clinical data with genomic information, expanding genotyping across more African regions, and developing improved arrays to capture rare and population-specific variants. This study reinforces the critical need for African-led genomic research and demonstrates how customized genotyping strategies can enhance global understanding of human genetic diversity and support precision medicine initiatives.
Africa harbours the highest level of genetic diversity worldwide, yet it remains significantly underrepresented in global genomic research. This study focused on Nigeria as a case study due to its highly diverse population, comprising over 300 ethnic groups, making it an ideal setting for exploring Genome-wide Association Studies (GWAS). SNP genotyping has become a key method for exploring genetic variation and identifying disease-associated markers in African populations. This process involves detecting differences in DNA, such as single-nucleotide polymorphisms (SNPs), insertions, deletions, and copy number variations (CNVs) by comparing individual sequences to a reference genome. The Illumina Infinium HTS Assay, a high-throughput genotyping platform, enables the analysis of up to 750,000 genetic markers per sample with high accuracy. Over 10,000 Nigerian samples were genotyped using this assay and the Infinium Global Screening Array-24 v3.0 beadchip. A custom African-focused beadchip, GENIISYS v1.0, developed by 54gene using data from whole genome and genome-wide association studies, was also utilized in processing a further 30,000 samples to improve the detection of unique variants. The study aimed to contribute to more inclusive global genomics by expanding the catalogue of African genetic diversity and informing future research in precision medicine.
Method:
A total of 40,000 samples from individuals with non-communicable diseases were collected across diverse geographical regions in Nigeria and processed for DNA extraction using the KingFisher Flex system. DNA quantity and quality were assessed using Quantifluor, QuantStudio 7, Multiskan SkyHigh, and DeNovix instruments. Samples that passed quality control were genotyped using the Illumina Infinium HTS Assay on the Global Screening Array-24 v3.0 and GENIISYS v1.0 beadchips. The workflow was automated with the Tecan and scanned on the iScan system. Primary genotyping analysis was performed using GenomeStudio, followed by secondary analysis using a custom bioinformatics pipeline to identify novel and population-specific variants.
Result & Conclusion:
High-throughput genotyping of over 40,000 samples and whole-genome sequencing of 1,000 Nigerian individuals from 50 ethnolinguistic groups enabled the identification of over 24 million high-quality variants. These efforts revealed striking genetic diversity, low levels of autozygosity, evidence of European/North African admixture in select groups, and unique patterns of natural selection across different populations. The development and deployment of the custom GENIISYS array (>800K markers) significantly improved the representation of African genomic variation for downstream analyses.
Implementing large-scale SNP-genotyping in African populations highlighted the importance of tailored QC pipelines, robust sample tracking systems, and culturally sensitive community engagement to ensure data quality and participant diversity.
Future efforts will focus on integrating phenotypic and clinical data with genomic information, expanding genotyping across more African regions, and developing improved arrays to capture rare and population-specific variants. This study reinforces the critical need for African-led genomic research and demonstrates how customized genotyping strategies can enhance global understanding of human genetic diversity and support precision medicine initiatives.