Study

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

Study ID Alternative Stable ID Type
EGAS00001002602 Other

Study Description

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. ... (Show More)

Study Datasets 1 dataset.

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Dataset ID Description Technology Samples
EGAD00001005076
The TrypanoGEN project was designed in two phases: this dataset is for Phase 1: Variant discovery, and includes 233 samples sequenced to approximately 10X coverage on an Illumina 2500.
Illumina HiSeq 2500 233

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