Methods
Summary
ActiWGS TB will combine established DNA extraction, whole-genome sequencing and bioinformatic analysis methods in a laboratory study using a TB model. Appropriate controls and repeat testing will help us assess genome completeness and the consistency of results.
Baobab Biotechnology will coordinate the project with a specialist laboratory partner, drawing on expertise in molecular biology, TB research and genomics. The findings will guide future evaluation using patient samples.
Challenges
The main challenge is whether the recovered DNA will provide enough usable information for reliable whole-genome sequencing, particularly when bacterial DNA is scarce. We will assess this using appropriate controls, repeat testing and predefined quality criteria. Limited consumables or supply delays could affect progress, so we will prioritise essential experiments and order materials early. This laboratory study may identify limitations as well as promising results; performance in patient samples will require separate evaluation.
Pre Analysis Plan
Our hypothesis is that ActiWGS TB can generate usable whole-genome data from laboratory-prepared blood samples using a TB model. Before analysing results, we will define success criteria based on genome completeness and data quality. The primary outcome will be the proportion of samples meeting these criteria.
We will also assess consistency across repeat measurements and variation between planned sample groups. Results will be summarised using descriptive statistics, with repeat measurements accounted for rather than treated as independent samples. Secondary outcomes will be considered exploratory.
All attempted samples, unsuccessful runs and any exclusions will be documented, with reasons provided. Conclusions will be limited to laboratory feasibility and used to guide future evaluation with patient samples.
Protocols
Browse the protocols that are part of the experimental methods.
