Set up and optimize WGS workflows Determine the most cost-effective sequencing protocol for both dWGS and culture-based WGS in the sequencing center. Perform the required experiments to test, optimize, and complete the dWGS workflow in the sequencing center: DNA extraction, DNA quantification, library preparation, culture-based sequencing, and culture-free sequencing. The CRO will assist in obtaining sputum samples that can be used for these preliminary optimization experiments. Collaborate with Qaigen’s R&D team to determine the necessary optimizations to ensure high-quality and timely dWGS and culture-based WGS. Generate baseline RR-TB WGS data for the KZN province Generate WGS data for all culture-positive patients diagnosed with RR-TB in the KZN province during the 12-month pre-intervention period and during the 30-month intervention period. You will receive inactivated MGIT cultures from the laboratory in KZN and process these from DNA extraction to library preparation to sequencing. We estimate a total of 6,000 non-real-time samples that need to be processed in large batches. This includes samples generated during the entire Real-time sequencing during the intervention period of 18 months to generate real-time WGS data (turnaround time, i.e., from specimen collection to data delivery, of less than 14 days) for the intervention districts, utilizing samples from the non-intervention and the broader KZN province to efficiently fill the sequencing flow cells. You will receive decontaminated sputum samples and inactivated MGIT cultures from the laboratory in KZN and process these from DNA extraction to library preparation to sequencing. You are expected to regularly execute batches at a frequency of ±3 per month. We estimate that dWGS will be performed on 378 samples during the intervention period.

LOT-0001
1
Sequencing Center Appointment for TB Study in South Africa.
Set up and optimize WGS workflows Determine the most cost-effective sequencing protocol for both dWGS and culture-based WGS in the sequencing center. Perform the required experiments to test, optimize, and complete the dWGS workflow in the sequencing center: DNA extraction, DNA quantification, library preparation, culture-based sequencing, and culture-free sequencing. The CRO will assist in obtaining sputum samples that can be used for these preliminary optimization experiments. Collaborate with the R&D team of Qaigen to determine the necessary optimizations to ensure high-quality and timely dWGS and culture-based WGS. Generate baseline RR-TB WGS data for the KZN province Generate WGS data for all culture-positive patients diagnosed with RR-TB in the KZN province during the 12-month pre-intervention period and during the 30-month intervention period. You will receive inactivated MGIT cultures from the laboratory in KZN and process these from DNA extraction to library preparation to sequencing. We estimate a total of 6,000 non-real-time samples that need to be processed in large batches. This includes samples generated during the entire Real-time sequencing during the intervention period of 18 months to generate real-time WGS data (turnaround time, i.e., from specimen collection to data delivery, of less than 14 days) for the intervention districts, utilizing samples from the non-intervention and the broader KZN province to efficiently fill the sequencing flow cells. You will receive decontaminated sputum samples and inactivated MGIT cultures from the laboratory in KZN and process these from DNA extraction to library preparation to sequencing. You are expected to regularly execute batches at a frequency of ±3 per month. We estimate that dWGS will be performed on 378 samples during the intervention period.