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GEH Data Access Committee

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Dr Etienne Patin
epatin@pasteur.fr

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This DAC controls 10 datasets

Dataset ID	Description	Technology	Samples
EGAD00001002714	We recruited 100 healthy, male donors of self-reported European descent (EUB) and 100 of self-reported African descent (AFB) (Ghent, Belgium). For each participant, peripheral blood mononuclear cells (PBMCs) were isolated from whole blood on Ficoll-Paque density gradients. Monocytes were then positively selected with magnetic CD14 microbeads and exposed for 6 hours to different ligands activating TLR4 (LPS), TLR1/2 (Pam3CSK4), TLR7/8 (R848) and to a human seasonal influenza A virus (IAV). High-quality RNA was obtained from unstimulated and stimulated monocytes for 970 of the 1000 samples (200 x 5 conditions), and was sequenced on an Illumina HiSeq2000. On average, 34 million 101-bp single-end reads were obtained per sample.	Illumina HiSeq 2000	970
EGAD00001004569	Exome sequencing of 317 rainforest hunter-gatherers (RHG) and neighbouring farmers (AGR) from Central Africa was performed based on the Nextera Rapid Capture Expanded Exome Kit (62-Mb content) with the Illumina HiSeq 2500. The population sample includes the Baka of south-eastern Cameroon and northern Gabon (wRHG), the Bantu-speaking Nzebi and Bapunu sedentary agriculturalists of Gabon (wAGR), and the BaTwa (eRHG) and BaKiga (eAGR) from Uganda. After QC filters, exomes of 300 unrelated individuals were obtained at high coverage (mean depth 68x), including 406,270 variants.	Illumina HiSeq 2500	317
EGAD00001006965	The Genomic Diversity in Africa Project (GDAP) started with the plan to develop a genomic resource from African populations, characterise genomic diversity and population history, and facilitate clinical studies in Africa. Currently, 25 individuals from 24 ethnolinguistic groups have been whole-genome sequenced at high depth totalling 585 individuals. An additional 41 individuals have been sequenced with 10X Genomics libraries. At this stage, the initial curation of this dataset has been finished and we are performing the analysis in coordination with our collaborators. The current state of the GDAP represents a very diverse panel of African populations that maximizes geographical and ethnic variation and represents a great starting point to achieve the aforementioned goals. However, southern sub-Saharan countries, Bantu speakers and hunter gatherer groups are currently underrepresented, despite being crucial to understand the evolutionary history of the continent. After extensive effort to collate studies documentation, we finally have the opportunity to sequence 600 new individuals from these groups, including countries as Gabon, Rwanda and Zambia, and address these deficiencies. We aim to proceed with the same strategy: to sequence at high depth 25 individuals with standard PCR free libraries, with 2 additional individuals with 10X Genomics Chromium libraries per ethnolinguistic group. The former allows a good representation of variants down to low frequency in any given population, and the latter allows accurate phasing and the analysis of structural variation. By including these new populations, we want to investigate three crucial questions in African history in addition to the initial objectives: the Bantu expansion, the evolutionary history of hunter gatherers and the transatlantic slave trade. Additionally, the expanded dataset will help us better discover the genetic variation present in Africa and characterize the African pangenome. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2021-02-12.	Illumina NovaSeq 6000	184
EGAD00010000496	Genome-wide SNP genotyping of African rainforest hunter-gatherers and neighbouring agriculturalists	Illumina HumanOmni1-Quad-Illumina GenomeStudio	260
EGAD00010000690	Genome-wide SNP genotyping of African rainforest hunter-gatherers and neighbouring agriculturalists by Illumina HumanOmniExpress		160
EGAD00010000692	Genome-wide DNA methylation epigenotyping of African rainforest hunter-gatherers and neighbouring agriculturalists by Illumina HumanMethylation450		372
EGAD00010001131	The 100 European-descent (EUB) and 100 African-descent (AFB) Belgians studied were genotyped for a total of 4,301,332 SNPs on the Illumina HumanOmni5-Quad BeadChips. Whole-exome sequencing was carried out for the same 200 individuals with the Nextera Rapid Capture Expanded Exome kit, on the Illumina HiSeq 2000 platform, with 100-bp paired-end reads. This kit delivers 62 Mb of genomic content per individual, including exons, untranslated regions (UTR), and microRNAs. Omni5 and exome datasets were merged, yielding a concordance rate between platforms of 99.93%.	Illumina HumanOmni5-Quad and exome sequencing	200
EGAD00010001209	Genome-wide SNP genotyping data for 1,235 western Africans by Illumina HumanOmniExpress-12 array, used in the EGAS00001002078 study	Illumina HumanOmniExpress-12	1235
EGAD00010001251	Epigenome of 36 rainforest hunther-gathering Baka of Cameroon by Illumina HumanMethylation450 array, used in the EGAS00001002226 study	Illumina HumanMethylation450	38
EGAD00010001452	Genome-wide SNP genotyping data for 102 Pakistani individuals by Illumina HumanOmni2.5-8 array, used in the EGAS00001002558 study	Illumina HumanOmni2.5-8	102