TBDB Sequencing Interest Group
Tuberculosis Genome Sequencing Interest Group
Current sequencing technologies provide the capability to go beyond the generation of individual TB genomes to the generation of comprehensive groups of TB genomes in order to identify the genetic basis of drug resistance, pathogenesis, persistence and latency, and transmissibility.
Moreover, these technologies are not limited to simply the generation of sequence. Functional applications using sequencing are being developed and include expression analysis, chip-seq to map promoter regions, and immunosequencing. The use of sequencing as a functional assay may also contribute to efforts to develop TB diagnostics and drugs.
The purpose of the Tuberculosis Genome Sequencing Interest Group is to provide a forum for TB scientists discuss and propose applications of high-throughput sequencing to TB, and to accelerate the dissemination of new whole genome data. If you would like to be added to the TB Sequencing Interest Group mailing list and receive information about sequence releases, please email tbdb-curator@lists.stanford.edu
For information about submitting a ?white paper? proposal for a sequencing project, please see http://www.niaid.nih.gov/dmid/genomes/mscs/
For information about ongoing TB sequencing at the Broad Institute MSC please email James Galagan or Bruce Birren
Other URLs of interest are:
Sanger Center: http://www.sanger.ac.uk/Projects/Microbes/
TIGR: http://cmr.tigr.org/tigr-scripts/CMR/CmrHomePage.cgi
NCBI: http://www.ncbi.nlm.nih.gov/genomes/MICROBES/microbial_taxtree.html
Pasteur Institute:
http://genolist.pasteur.fr/TubercuList/
http://genolist.pasteur.fr/BoviList/
http://genolist.pasteur.fr/BCGList/
Mycobacterial Genome Sequencing Projects
| Project | # genomes | Summary | Status | Contact | Center |
|---|---|---|---|---|---|
| Mycobacterium africanum | 1 | link | Finishing/gap closure | Julian Parkhill parkhill@sanger.ac.uk | Sanger Institute |
| Mycobacterium canetti | 1 | link | Shotgun in progress | Julian Parkhill parkhill@sanger.ac.uk | Sanger Institute |
| Mycobacterium marinum | 1 | link | Finished | Julian Parkhill parkhill@sanger.ac.uk | Sanger Institute |
| Mycobacterium microti | 1 | link | Shotgun in progress | Julian Parkhill parkhill@sanger.ac.uk | Sanger Institute |
| Mycobacterium abscessus | 1 | link | - | Valérie Barbe vbarbe@genoscope.cns.fr | Genoscope |
| Mycobacterium bovis BCG str. Moreau RDJ | 1 | link | - | Plataforma De Sequenciamento De DNA PDTIS/FIOCRUZ | Fiocruz |
| Mycobacterium chelonae | 1 | link | - | Valérie Barbe vbarbe@genoscope.cns.fr | Genoscope |
| Mycobacterium liflandii 128FXT | 1 | link | In development | Tim Stinear tim.stinear@med.monash.edu.au | Monash University |
| Mycobacterium marinum DL240490 | 1 | link | - | Tim Stinear tim.stinear@med.monash.edu.au | Monash University |
| Mycobacterium microti | 1 | link | - | Julian Parkhill parkhill@sanger.ac.uk | Sanger Institute |
| Mycobacterium tuberculosis 210 | 1 | link | - | TIGR | TIGR |
| XDR microevolution | 93 | Approved | Megan Murray mmurray@hsph.harvard.edu | Broad Institute | |
| MDR | 7 | In sequencing | Megan Murray mmurray@hsph.harvard.edu | Broad Institute | |
| KZN strains | 3 | In sequencing | Megan Murray mmurray@hsph.harvard.edu | Broad Institute | |
| Persistence | 20 | Approved | Kim Lewis k.lewis@neu.edu | Broad Institute | |
| Global Diversity | 31 | Approved | Peter Small peter.small@gatesfoundation.org, Sebastien Gagneux sgagneux@systemsbiology.org |
Broad Institute |