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TB-DAR Whole Genome Sequencing Study

116 Whole Genome Sequencing (WGS) samples from the TB-DAR study, which consists of a cohort of adult pulmonary tuberculosis patients recruited in Dar es Salaam, Tanzania.

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

1 Dataset 2 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
EGAD00001008400	116 Whole Genome Sequencing (WGS) samples from the TB-DAR study, based on a cohort of adult pulmonary tuberculosis patients recruited in Dar es Salaam, Tanzania. WGS was performed at the Health2030 Genome Center in Geneva on the Illumina NovaSeq 6000 instrument (Illumina Inc, San Diego CA, USA), starting from1μg of whole blood genomic DNA and using Illumina TruSeq DNA PCR-Free reagents for library preparation and the 150nt paired-end sequencing configuration. Average coverage was above 30X for 75 samples, between 10X and 30Xfor 40 samples, and approximately 8X for a single sample. Sequencing reads were aligned to the GRCh38 (GCA_000001405.15) reference genome using bwa (Version 0.7.17).	Illumina NovaSeq 6000	116

Publications	Citations
Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations. Xu ZM, Rüeger S, Zwyer M, Brites D, Hiza H, Reinhard M, Rutaihwa L, Borrell S, Isihaka F, Temba H, Maroa T, Naftari R, Hella J, Sasamalo M, Reither K, Portevin D, Gagneux S, Fellay J. PLoS Comput Biol 18: 2022 e1009628	7
Genome-to-genome analysis reveals associations between human and mycobacterial genetic variation in tuberculosis patients from Tanzania. Xu ZM, Zwyer M, Hiza H, Schmidiger S, Sasamalo M, Reinhard M, Doetsch A, Borrell S, Naret O, Rüeger S, Lawless D, Tang S, Isihaka F, Temba H, Maroa T, Naftari R, Beisel C, Hella J, Reither K, Brites D, Portevin D, Gagneux S, Fellay J. BMC Med Genomics 18: 2025 99	0

Publications

Citations

Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations.
Xu ZM, Rüeger S, Zwyer M, Brites D, Hiza H, Reinhard M, Rutaihwa L, Borrell S, Isihaka F, Temba H, Maroa T, Naftari R, Hella J, Sasamalo M, Reither K, Portevin D, Gagneux S, Fellay J. PLoS Comput Biol 18: 2022 e1009628

Genome-to-genome analysis reveals associations between human and mycobacterial genetic variation in tuberculosis patients from Tanzania.
Xu ZM, Zwyer M, Hiza H, Schmidiger S, Sasamalo M, Reinhard M, Doetsch A, Borrell S, Naret O, Rüeger S, Lawless D, Tang S, Isihaka F, Temba H, Maroa T, Naftari R, Beisel C, Hella J, Reither K, Brites D, Portevin D, Gagneux S, Fellay J. BMC Med Genomics 18: 2025 99