H3Africa - An integrated approach to the identification of genetic determinants of susceptibility to trypanosomiasis

The 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.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 10 Publications

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
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

Publications	Citations
Candidate gene polymorphisms study between human African trypanosomiasis clinical phenotypes in Guinea. Kaboré JW, Ilboudo H, Noyes H, Camara O, Kaboré J, Camara M, Koffi M, Lejon V, Jamonneau V, MacLeod A, Hertz-Fowler C, Belem AMG, Matovu E, Bucheton B, Sidibe I, TrypanoGEN Research Group as members of The H3Africa Consortium. PLoS Negl Trop Dis 11: 2017 e0005833	18
A polymorphism in the haptoglobin, haptoglobin related protein locus is associated with risk of human sleeping sickness within Cameroonian populations. Ofon E, Noyes H, Mulindwa J, Ilboudo H, Simuunza M, Ebo'o V, Njiokou F, Koffi M, Bucheton B, Fogue P, Hertz-Fowler C, MacLeod A, Simo G, TrypanoGEN Research Group, as members of The H3Africa Consortium. PLoS Negl Trop Dis 11: 2017 e0005979	12
No evidence for association between APOL1 kidney disease risk alleles and Human African Trypanosomiasis in two Ugandan populations. Kimuda MP, Noyes H, Mulindwa J, Enyaru J, Alibu VP, Sidibe I, Mumba Ngoyi D, Hertz-Fowler C, MacLeod A, Tastan Bishop Ö, Matovu E, TrypanoGEN Research Group as members of The H3Africa Consortium. PLoS Negl Trop Dis 12: 2018 e0006300	12
Association of APOL1 renal disease risk alleles with Trypanosoma brucei rhodesiense infection outcomes in the northern part of Malawi. Kamoto K, Noyes H, Nambala P, Senga E, Musaya J, Kumwenda B, Bucheton B, Macleod A, Cooper A, Clucas C, Herz-Fowler C, Matove E, Chiwaya AM, Chisi JE, TrypanoGEN Research Group as members of The H3Africa Consortium. PLoS Negl Trop Dis 13: 2019 e0007603	8
Copy number variation in human genomes from three major ethno-linguistic groups in Africa. Nyangiri OA, Noyes H, Mulindwa J, Ilboudo H, Kabore JW, Ahouty B, Koffi M, Asina OF, Mumba D, Ofon E, Simo G, Kimuda MP, Enyaru J, Alibu VP, Kamoto K, Chisi J, Simuunza M, Camara M, Sidibe I, MacLeod A, Bucheton B, Hall N, Hertz-Fowler C, Matovu E, TrypanoGEN Research Group, as members of The H3Africa Consortium. BMC Genomics 21: 2020 289	9
High Levels of Genetic Diversity within Nilo-Saharan Populations: Implications for Human Adaptation. Mulindwa J, Noyes H, Ilboudo H, Pagani L, Nyangiri O, Kimuda MP, Ahouty B, Asina OF, Ofon E, Kamoto K, Kabore JW, Koffi M, Ngoyi DM, Simo G, Chisi J, Sidibe I, Enyaru J, Simuunza M, Alibu P, Jamonneau V, Camara M, Tait A, Hall N, Bucheton B, MacLeod A, Hertz-Fowler C, Matovu E, TrypanoGEN Research Group of the H3Africa Consortium. Am J Hum Genet 107: 2020 473-486	7
SNPs in IL4 and IFNG show no protective associations with human African trypanosomiasis in the Democratic Republic of the Congo: a case-control study. Fataki Asina O, Noyes H, Bucheton B, Ilboudo H, MacLeod A, Mumba Ngoyi D, TrypanoGEN Group, as members of The H3Africa Consortium. AAS Open Res 3: 2020 35	1
Analysis of Structural Variants Previously Associated With ALS in Europeans Highlights Genomic Architectural Differences in Africans. Monnakgotla NR, Mahungu AC, Heckmann JM, Botha G, Mulder NJ, Wu G, Rampersaud E, Myers J, Van Blitterswijk M, Rademakers R, Taylor JP, Wuu J, Benatar M, Nel M. Neurol Genet 9: 2023 e200077	1
Polygenic risk scores for disease risk prediction in Africa: current challenges and future directions. Fatumo S, Sathan D, Samtal C, Isewon I, Tamuhla T, Soremekun C, Jafali J, Panji S, Tiffin N, Fakim YJ. Genome Med 15: 2023 87	14
The genetic legacy of the expansion of Bantu-speaking peoples in Africa. Fortes-Lima CA, Burgarella C, Hammarén R, Eriksson A, Vicente M, Jolly C, Semo A, Gunnink H, Pacchiarotti S, Mundeke L, Matonda I, Muluwa JK, Coutros P, Nyambe TS, Cikomola JC, Coetzee V, de Castro M, Ebbesen P, Delanghe J, Stoneking M, Barham L, Lombard M, Meyer A, Steyn M, Malmström H, Rocha J, Soodyall H, Pakendorf B, Bostoen K, Schlebusch CM. Nature 625: 2024 540-547	13