EGAGenomicsOtherhttps://ega-archive.org/studies/EGAS00001002602EGAEGA study EGAS00001002602H3Africa TrypanoGEN MainEGArestrictedgenetic, familial, susceptibility, inherited genetic, constitutitional genetic, hereditary, Trypanosomiases.HSPABP2, l(1)G0014, human being, Activity, single-organism developmental process, determination, Laboratory, postnatal development, 2210017D18Rik, dCHIP, SCF receptor activity, Infestations and Infections, CG4399, growth and development, Xkl-1, SCAR16, CG30327, African trypanosomiasis, Medical Specialties, Human, CG11478, Speciality, Republic of Guinea, KL receptor activity, Medical Specialities, Gsfsco1, DmelCG5203, Homo sapiens, scfr, Specialities, Congo (Brazzaville), Core Genome, SCO5, Republic of Zambia, SCO1, Research Activity, Gsfsow3, Laboratory Research, Medical, SCFR, Gsfsco5, su(w[sp]), Man, 2310040B03Rik, East, SOW3, Priorities, study, DmelCG42257, Fdc, Guinea, Insurance Medicine, NY-CO-7, Man (Taxonomy), Genomes, Research, Ivory Coast, Chip, ChIP, Accessory Genome, French, CHIP, werinnua, Cameroons, W, clinical infection, genetic, chip, Infestation and Infection, drugs, medicine, 65K, DmelCG3924, CG42257, Dmel_CG30327, Medicine, AW046544, Bs, Republic of Uganda, snp, Infections and Infestations, Development and Research, Medicines, Research Priority, Insurance, UBOX1, 10X sequencing, 0610033N24Rik, constitutitional genetic, Sl, HAT, PP1131, sleeping sickness, proto-oncogene c-Kit, Republic of, Specialties, cg11478, niger, l(2)k04405, Northern Rhodesia, Medical Specialty, African sleeping sickness, T5E21.12, French Guinea, Modern, familial, CG5203, Research Priorities, Tr-kit, 10x sequencing, Republic of Niger, l(2)04405, Pangenome, Republic of the Congo, DmelCG4399, development, Medical Speciality, PBT, Priority, African Trypanosomiasis, KIT ligand receptor activity, ramtil, CG6393, l(1)G0500, chemical analysis, Research Activities, Trypanosomiases., Infection, Specialty, kl1-A, Rhodesia, University, Africam sleeping sickness, Republic of Cote diIvoire, KIT, human African trypanosomiasis, Republic of Cameron, T5E21_12, XKrk1, SDCCAG7, Research and Development, tyrosine-protein kinase Kit, Dmel_CG6393, pbt, c-KIT, dLdb, Ldb, LDB, anon-WO03040301.224, postnatal growth, Chromatin Immunoprecipitation, Infection and Infestation, Northern, whole genome, kit, United Republic of Cameroon, CD117, Trypanosomiases, CG3924, human, EAST, Activities, Insurance Medicines, c-kit, Pan-genome, dLDB/Chip, C-Kit, Ssm, Modern Man, xkl-1, inherited genetic, assay, EG:133E12.4, ramtilla, hereditary, growth, krk1falseH3Africa - An integrated approach to the identification of genetic determinants of susceptibility to trypanosomiasisThe objective of the TrypanoGEN project is to discover genetic variants associated with different responses to sleeping sickness infection. The project was designed in two phases:Phase 1) Variant discovery; 222 samples were sequenced to approximately 10X coverage on an Illumina 2500 with 2x150bp reads, at the University of Liverpool Center for Genomic Research. In addition, 77 samples from Cameroon and Zambia were sequenced to approximately 30X Coverage at Baylor College of Medicine. The sequenced reads were mapped onto the 1000 genomes project human_g1k_v37_decoy reference genome using BWA. The SNP calling on all the samples was done using the genome analysis tool kit GATK v3.4. Samples were selected from seven populations where Trypanosomiasis is endemic: Nilo-Saharan speakers from North-West Uganda and Niger-Congo speakers from South-East Uganda, DRC, Ivory Coast, Guinea, Cameroon and Zambia. The samples included 182 controls, 97 cases, 17 latent infections and 3 suspect cases. Phase 2) Variants discovered in Phase 1 will be used in the development of the H3Africa SNP chip. This chip will then be used in a GWAS study to identify variants associated with trypanosomiasis.2022-11-21 11:00:01EGAS000010026029606EGAD00001005076EGAC00001000648