Human Heredity and Health in Africa Data Access Committee

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H3Africa DAC
dbac@h3africa.org

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This DAC controls 31 datasets

Dataset ID	Description	Technology	Samples
EGAD00001004220	41 samples from Zambia generated for the H3Africa Chip Design Study. The dataset includes BAM, FASTQ and decompressed gVCF files.	Illumina HiSeq 2500	41
EGAD00001004316	24 samples from Cameroon generated for the H3Africa Chip Design Study. The dataset includes BAM, FASTQ and decompressed gVCF files.	Illumina HiSeq 2500	24
EGAD00001004334	50 samples from Mali generated for the H3Africa Chip Design Study. The dataset includes BAM, FASTQ and decompressed gVCF files.	Illumina HiSeq 2500	50
EGAD00001004393	26 samples from Cameroon generated for the H3Africa Chip Design Study. The dataset includes BAM, FASTQ and decompressed gVCF files.	Illumina HiSeq 2500	26
EGAD00001004448	60 samples from Burkina Faso and Ghana generated for the H3Africa Chip Design Study. The dataset includes BAM, FASTQ and decompressed gVCF files.	Illumina HiSeq 2500	60
EGAD00001004505	49 samples from Nigeria generated for the H3Africa Chip Design Study. The dataset includes BAM, FASTQ and decompressed gVCF files.	Illumina HiSeq 2500	49
EGAD00001004533	48 samples from Botswana generated for the H3Africa Chip Design Study. The dataset includes BAM, FASTQ and decompressed gVCF files.	Illumina HiSeq 2500	48
EGAD00001004557	The dataset includes BAM, FASTQ and decompressed gVCF files for 50 samples from Benin generated for the H3Africa Chip Design Study.	Illumina HiSeq 2500	50
EGAD00001005076	This dataset is for TrypanoGEN Phase 1: Variant discovery, and includes 233 samples sequenced to approximately 10X coverage. Samples are from Guinea, Cote D’Ivoire, DRC and Uganda using Illumina HiSeq 2500.		233
EGAD00001005310	Basic phenotypic data (country, ethnicity and sex) for 348 samples of the H3Africa Chip Design Study. Divided into 8 datasets of 41 samples from Zambia, 24 samples from Cameroon, 50 samples from Mali, 26 samples from Cameroon, 49 samples from Nigeria, 48 samples from Botswana, 50 samples from Benin, 60 samples from Burkina Faso and Ghana.		348
EGAD00001006224	Whole Exome Sequencing data from a retrospective paediatric HIV-disease progression cohort defined on the World Health Organization's criteria for paediatric HIV progression. Data comprises of BAM and VCF files for 314 participants from 2 countries: Botswana and Uganda. DNA and RNA samples are linked in bio-repository.	Illumina HiSeq 2500	314
EGAD00001006244	Phenotype data for shotgun metagenomic sequencing data of nasopharyngeal fluid for studying nasopharyngeal colonization dynamics with Streptococcus pneumoniae and associated antimicrobial-resistance in a South African birth cohort. https://www.ebi.ac.uk/ena/data/view/PRJEB37312		196
EGAD00001006295	SNPs and INDELs of novel hereditary neurological disease genes in Mali using Beckman 8800, ABI 3730/3730xl.		10
EGAD00001006418	These samples were sequenced at the Broad Institute on an Illumina HiSeqX at 30x -- PCR Free. The CRAMS and VCF are as produced by Broad. The VCFs produced were generated by the Broad using GATK.		100
EGAD00001006425	The phenotypic data for ~12500 samples of the AWI-Gen Phase 1 Population cross-sectional study of older adults (mostly between 40 and 60 years), men and women. Six study sites in four sub-Saharan African counties including Ghana, Burkina Faso, Kenya and South Africa. Some groups are missing data for specific variables. Data includes questionnaire data (demography, health history, family health history, behaviour and infection data); anthropometry; and laboratory assays on blood and urine.		12032
EGAD00001006581	This is human phenotype data for participants in a gut microbiome study. This data was collected at the same time as the stool samples used for the microbiome component. Participants were also part of the AWI-Gen Phase 1 main study. https://www.ebi.ac.uk/ena/data/view/PRJEB40733		171
EGAD00001008577	Joint called VCF for whole genome sequence data from 410 samples described in the paper: PMID:33116287. It includes 314 high coverage (average 30X) samples sequenced on the Illumina X-Ten, also available as individual datasets under the H3Africa Chip study (EGAS00001002976) and 112 medium coverage (average 10X) samples from the TrypanGen study (EGAS00001002602) sequenced on Illumina HiSeq 2500. Supplementary table 3 of the paper describes the geographic breakdown of the samples. 16 samples from the Southern African Human Genome project have been removed from this VCF.		410
EGAD00001009333	The phenotypic data for 6431 samples of the KDRN Study from Ghana and Nigeria.		6431
EGAD00001009739	Phenotype data from pregnant mothers unexposed and exposed to the Rwandan genocide from 59 whole blood samples.		1
EGAD00001010922	Phenotype data for Lassa Fever cases and population controls from Nigeria and Sierra Leone associated with genotype data generated using Illumina Omni 2.5M and 5M.		2667
EGAD00001010923	Phenotype data for Lassa Fever cases and population controls from Nigeria and Sierra Leone associated with genotype data generated using Illumina H3Africa array version 1.		1345
EGAD00001011075	Phenotype data for 3421 Samples from Nigeria and Ghana, sequenced with the Illumina NestSeq 500.		3421
EGAD00001011348	TrypanoGEN+ phenotype data containing 183 samples from DRC, Malawi and Uganda.		183
EGAD00001011666	TrypanoGEN+ data containing fastq files of 183 samples from DRC, Malawi and Uganda using NextSeq500.	unspecified	183
EGAD00010001258	Pilot study on the interplay between genetic, epigenetic, and environmental risk factors for obesity and related cardiometabolic diseases with 973 samples from South Africa genotyped on Illumina Human MetaboChip array.	Human Cardio Metabochip	973
EGAD00010001996	The samples were genotyped on the H3Africa array (~2.3M SNPs) using the Illumina FastTrack Sequencing Service2. The default Illumina pipeline was used for the genotype calling (build GRCh37/hg19). The data was converted to PLINK using the h3abionet/h3agwas/call2plink pipeline and QC done using the h3abionet/h3agwas/qc pipeline		10776
EGAD00010002365	The 6431 samples were genotyped on the H3Africa array.	Illumina	6431
EGAD00010002383	Data from 59 whole blood samples from pregnant mothers, unexposed and exposed to the Rwandan genocide, was generated using Infinium MethylationEPIC BeadChip Kit.	IlluminaEpic	59
EGAD00010002509	SNP Genotyping for Lassa Fever cases and population controls from Nigeria and Sierra Leone using Illumina Omni 2.5M and 5M	Illumina Omni 2.5M, Illumina Omni 5M	2667
EGAD00010002510	SNP Genotyping for Lassa Fever cases and population controls from Nigeria and Sierra Leone using Illumina H3Africa array version 1	Illumina H3Africa array version 1	1345
EGAD00010002551	3421 Samples from Nigeria and Ghana, sequenced with the Illumina NestSeq 500	Illumina NestSeq 500	3421