TB Genomics Service Pilot Project
TB Genomics Service: Pilot project to start next month
PHE Birmingham are launching our TB Genomics Service pilot project next month.
- In the last 10-months we have participated in an eight-centre international collaboration study on TB Whole Genome Sequencing (WGS) led by Oxford which has used DNA extracted from MGIT.
- The Oxford led project is a feasibility study on the use of WGS in TB diagnosis, resistance profiling and epidemiological mapping of outbreaks. During this Feasibility study, working with our colleagues at Oxford, DNA extraction and MiSeq sequencing methodologies have been established at Heartlands. Raw sequence data has been shared with Oxford through a cloud setup and analysis reports (on mycobacterial species identity, drug resistance predictions and strain typing) received within 48 hours of the raw data being uploaded.
- A total 13 MiSeq runs have been carried out at Heartlands, all of which successful. Consequently the Birmingham lab has been a major contributor to the project, submitting the highest number of sequences and achieving the best sequence quality of all the contributors.
- The results from this feasibility study were presented at this year’s ECCMID in a joint report with our colleagues from Oxford.
- The Birmingham lab has now been selected to set up a pilot for a TB Genomic Service (TBGS).
TBGS Pilot project plan
- This TBGS pilot has been identified as a top priority for PHE. It has been fully funded with the aim of introducing WGS into the mainstream of the NHS TB patient care pathway.
- We are required to deliver this project within 12 months (July 2014-Jun 2015).
- Workload: The pilot will involve WGS based analysis of all mycobacterial isolates submitted to the Reference Centre from NHS laboratories across the Midlands, and parts of South Yorkshire and Humberside (up to 80 isolates per week).
- A local TBGS group meeting is scheduled to occur on a weekly basis and we will provide regular feedback on progress at both local management meetings and by e-mail to the wider group of stakeholders.
Further information about the project can be found here