Table 1 Description of a range of genomic datasets in Africa for potential polygenic risk scores for disease risk in Continental Africa
Full name (Study) | Country | Ancestry/ethics | Number of samples | Disease/traits | Lifestyle/exposure variables | Genotyping platform | Reference | Controlled access on EGA/DbGAP/ accession number |
|---|---|---|---|---|---|---|---|---|
Uganda Genome Resource (UGR) | Uganda | Ugandans | 7 000 | Blood Pressure, lipid, Anthropometries, Full blood count, Liver Function, HbA1c, Kidney function, others | smoking, diet, physical activity, others | Illumina HumanOmni 2.5Â M BeadChip array | EGA: EGAD00010000965; EGAD00001001639 | |
Durban Diabetes Study (DDS) | South Africa | South African Zulu | 1,200 | Diabetes Mellitus, BP, lipid, Anthropometries, Full Blood Counts, Liver Function | smoking, diet, physical activity, others | Customised Illumina Multi-Ethnic Genotyping Array (MEGA) | [29] | Not known |
Durban Diabetes Case Control study (DCC) | South Africa | South African Zulu | 1 600 | Diabetes Mellitus, BP, lipid, Anthropometries, Full Blood Counts, Liver Function | smoking, diet, physical activity, others | Customised Illumina Multi-Ethnic Genotyping Array (MEGA) | [29] | Not known |
Africa America Diabetes Mellitus (AADM) | Nigeria, Ghana & Kenya | Sub-Saharan African | 5 000 | Diabetes Mellitus, BP, lipid, Anthropometries, Full blood count, Liver Function, Kidney function, others | smoking, diet, physical activity, others | Affymetrix Axiom PANAFR SNP array | [30] | dbGAP: phs001844 |
Research on Obesity and Diabetes among African Migrants (RODAM and HELIUS) | Ghana, Suriname, Morocco | Africans | 13 655 | Diabetes Mellitus, BP, lipid, Anthropometries, Kidney Function, others | smoking, diet, physical activity, others | Not Known | [31] | EGA: EGAD00001004106 |
Muhimbili Sickle Cohort (Haemoglobin GWAS study) | Tanzania | Tanzania | 1213 | Sickle cell disease, Anthropometries, Others | Â | Illumina Omni2.5 array | [32] | Not known |
Genomic and Environmental Risk Factors for Cardiometabolic Disease in Africans (AWI-GEN) | Burkina Faso, Ghana, Kenya and South Africa | Sub-Saharan African | 12 000 | Blood Pressure, lipid, Anthropometries, Full blood count, Liver Function, Kidney function, others | smoking, diet, physical activity, others | H3Africa Illumina Array | EGA EGAD00001004448 | |
H3Africa Diabetes study (H3Africa Diabetics) | Various across Sub-Sahara Africa | Sub-Saharan African | 12 621 | Diabetes Mellitus, BP, lipid, Anthropometries, others | smoking, diet, physical activity, others | Planned H3Africa Illumina Array | [35] | Not Known |
Genetics of rheumatic heart disease (RHDGen) Network | Various across Sub-Sahara Africa | Sub-Saharan African | 3 555 | rheumatic heart disease, BP, lipid, Anthropometries, others | Â | Planned H3Africa Illumina Array | [36] | Not known |
African Collaborative Center for Microbiome and Genomics Research (ACCME) | Nigeria | Nigerian | 11Â 700 | cervical cancer, Blood Pressure, lipid, Anthropometries, others | smoking, diet, physical activity, others | H3Africa Illumina Array | [37] | dbGAP phs001945 |
African Female Breast Cancer Epidemiology (AFBRECANE) | Nigeria | Nigerian | 1 000 | Breast Cancer, Blood Pressure, lipid, Anthropometries, others | smoking, diet, physical activity, others | Not Known | [38] | Not known |
KEMRI VaccGene study | Kenya | Kenya | 1 400 | Blood Pressure, Anthropometries, others | smoking, diet, physical activity, others | Not Known | Not known | |
Malawi Genome Resource | Malawian | Malawian | 6 626 | Diabetes Mellitus, BP, lipid, Anthropometries, Kidney Function, others | smoking, diet, physical activity, others | H3Africa Illumina Array version 2 | [41] | Not known |
The Stroke Investigative Research and Educational Network (SIREN) | Nigeria | Nigerian | 8 000 | Stroke, Blood Pressure, Anthropometries and others | smoking, diet, physical activity, others | H3Africa Illumina Array | [42] | Not known |
Trauma and PTSD study | Rwanda | Rwandans | 400 | Trauma, Post-traumatic stress disorder (PTSD), Blood Pressure, Anthropometries and others | smoking, diet, physical activity, others | Planned H3Africa Illumina Array | Not known | |
Keneba Biobank | Gambia | Gambians | 10 000 | Blood Pressure, serum creatinine, Anthropometries and others | smoking, diet, physical activity, others | Planned H3Africa Illumina Array | [45] | Not known |
The Sickle Cell Disease Genomics of Africa (SickleGenAfrica) | Cameroon, Ghana, Nigeria and Tanzania | Africans | 7 000 | Sickle cell disease, Blood Pressure, Anthropometries and others | smoking, diet, physical activity, others | H3Africa Illumina Array | [46] | Not known |
The H3Africa Kidney Disease study | Ghana, Nigeria, Ethiopia, and Kenya | Africans | 11 964 | Kidney function, Blood Pressure, Anthropometries and others | smoking, diet, physical activity, others | Planned H3Africa Illumina Array | [47] | EGA EGAD00010002365; EGAD00001009333 |
Collaborative African Genomics Network (CAfGEN) | Botswana, Uganda, and Swaziland | Africans | 1 000 | HIV, Blood Pressure, Anthropometries and others | smoking, diet, physical activity, others | Illumina HiSeq 2500 | [48] | EGAD00001006224 |
The Tanzania Stroke Incidence Project (TSIP) | Tanzania | Tanzanian | 636 | Stroke, Anthropometries, Others | Â | Not Known | [49] | Not known |
Non-Communicable Diseases – Genetic Heritage Study (NCD-GHS) | Nigeria | Nigerian | 100 000 | Blood Pressure, lipid, Anthropometries, Full blood count, Liver Function, HbA1c, Kidney function, Cancer, Diabetes Mellitus others | smoking, diet, physical activity, others | Illumina Global Array | [50] | Not known |
H3AFRICA TRYPANOGEN PROJECT | Uganda Guinea Ivory Coast Burkina Faso Cameroon DRC Malawi Zambia | Africans | 233 | trypanosomiasis | lifestyle | Illumina HiSeq 2500 | [51] | EGAS00001002602 |
H3Africa Genomic Characterization and Surveillance of Microbial Threats in West Africa | Nigeria, Sierra Leone | West Africa | 2667 1345 | Lassa Fever | lifestyle | Illumina Omni 2.5Â M, Illumina Omni 5Â M | [52] | EGAD00010002509 |
NeuroGAP-Psychosis | Kenya, Ethiopia, Uganda, South Africa | South and East Africans | 17,000 | Schizophrenia, Bipolar disorder | lifestyle | Global Sequencing Array | [53] | dbGaP accession phs002528.v1.p1 |
NeuroDev project | Kenya, South Africa | South and East Africans | 5,000 | Autism spectrum disorder (ASD), Intellectual disability (ID), Attention deficit hyperactivity disorder (ADHD) | lifestyle | Global Sequencing Array | [54] | dbGap accession number phs001874 |
The African Biobank | Nigeria, Kenya, Tanzania, Zimbabwe and South Africa | Africans | 1,488 | Pharmacogenetics | lifestyle | PCR–RFLP | [55] | Not known |
MalariaGEN | Burkina Faso, Cameroon, Ghana, Kenya, Malawi, Mali, Nigeria, Papua New Guinea, Tanzania, The Gambia, Vietnam | Africa, Asia and Oceania | 17,000 | Malaria | lifestyle | Sequenom MassArray platform | EGAS00000000026 | |
Total | 262,303 | Â | ||||||