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H3Africa - Pharmacogenomic diversity across 12 understudied African populations from whole-exome sequencing

Cohort study characterizing pharmacogenomic diversity across 12 previously understudied African populations. 127 individuals were recruited from the AIBST biobank under MRCZ ethics approval, spanning Kikuyu, Luo, Maasai and psychiatric-patient groups (Kenya); two ethnicity-unspecified cohorts (Tanzania); Igbo, Hausa, Yoruba (Nigeria); Venda (South Africa); and San and Shona (Zimbabwe). The cohort emphasizes ethnic groups absent or underrepresented in 1000 Genomes, gnomAD, and AGVP. Characteristics under investigation are pharmacogene variant frequencies, population-level differentiation, novel-variant pathogenicity, and predicted metabolizer phenotypes relevant to HIV, tuberculosis, and malaria therapeutics. Participants are healthy adults; this is not a case-control design. Data sharing is consented under AIBST/MRCZ terms for biomedical research, broadly aligned with Data Use Ontology codes for general research use (GRU) and health/medical/biomedical research (HMB).

Type: Other
Archive: European Genome-phenome Archive (EGA)

2 Datasets

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001016422	Whole-exome sequencing dataset for 127 individuals from 12 African populations (Kenya, Tanzania, Nigeria, South Africa, Zimbabwe). Library preparation used Agilent SureSelect 50 Mb capture; paired-end 76 bp sequencing on Illumina HiSeq2500 at 12x average depth. Reads aligned to GRCh38 with BWA-MEM2, duplicate-marked, base-quality recalibrated with GATK. Joint variant calling with DeepVariant v1.6 + GLnexus v1.4.1 in WES mode, with calling extended 2 kb beyond exome targets. Deposit: 127 per-sample CRAM files (GRCh38, recalibrated; LZMA-encoded, samtools 1.20; 224 GB total) plus one joint-called multi-sample VCF (~555 MB).		1
EGAD00001016423	Whole-exome sequencing dataset for 127 individuals from 12 African populations (Kenya, Tanzania, Nigeria, South Africa, Zimbabwe). Library preparation used Agilent SureSelect 50 Mb capture; paired-end 76 bp sequencing on Illumina HiSeq2500 at 12x average depth. Reads aligned to GRCh38 with BWA-MEM2, duplicate-marked, base-quality recalibrated with GATK. Joint variant calling with DeepVariant v1.6 + GLnexus v1.4.1 in WES mode, with calling extended 2 kb beyond exome targets. Deposit: 127 per-sample CRAM files (GRCh38, recalibrated; LZMA-encoded, samtools 1.20; 224 GB total) plus one joint-called multi-sample VCF (~555 MB).		1