DAC

Human Heredity and Health in Africa Data Access Committee

Dac ID Contact Person Email Access Information
EGAC00001000648 H3Africa DAC dbac [at] h3africa [dot] org https://catalog.h3africa.org/

This DAC controls 22 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. 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. 233
EGAD00001005310 The phenotypic data 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. Illumina HiSeq X Ten 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. Illumina HiSeq 2500 314
EGAD00001006244 Shotgun metagenomic sequencing data for 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. 10
EGAD00001006418 These sequences were sequenced at the Broad 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
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