3 ms·

I think the currenntly more interesting application in sequencing is pathogen detection. These have smaller and simpler genomes (mostly), and tracking them and

I think the currenntly more interesting application in sequencing is pathogen detection. These have smaller and simpler genomes (mostly), and tracking them and their features improves epidemiology and the choice of treatments.

noname123 11y ago
nextflu.org and wwarn.org and ebola.nextfu.org NextFlu takes global samples uploaded to a global flu genomic sample database and construct a phylogeny tree to monitor how influenza evolve and I think the authors behind the project wants to make predictions as to which cohort of influenza variation will become dominant. Wwarn.org I believes tracks the emergence of Artesminin resistance (front-line drug in malaria treatment) in malaria in SE Asia and tries to map it out on GIS to inform public health officials further from SE Asia how it is spreading to their region (India, Africa where current Artesminin resistance gene is only 5% while Artesminin resistance is already the dominant wild type in SE Asia) and whether to modify front-line treatment protocol.
damurdock 11y ago
Pathogen identification is indeed a very exciting application for NGS. In case you're interested, here[0] is a paper about a tool called SURPI (Sequence-based Ultra-Rapid Pathogen Identification) which was designed for that purpose. Also, here[1] is a case report from the NEJM where SURPI was used to diagnose a patient with Neuroleptospirosis, which allowed him to be treated quickly and eventually recover. SURPI isn't the only horse in this game, of course, but I've worked with it before so it immediately came to mind. [0]: "A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples" http://genome.cshlp.org/content/24/7/1180.long http://genome.cshlp.org/content/24/7/1180.long [1]: "Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing" http://www.nejm.org/doi/full/10.1056/NEJMoa1401268 http://www.nejm.org/doi/full/10.1056/NEJMoa1401268
- tridint 11y ago
  The clinical work they're doing is great, but the code is problematic. Its a bunch of Perl and Python duct taped together with shell scripts. From the github repo: Shell 84.3% Perl 8.9% Python 6.3% C 0.5% Check out the source https://github.com/chiulab/surpi https://github.com/chiulab/surpi

noname123 11y ago

nextflu.org and wwarn.org and ebola.nextfu.org NextFlu takes global samples uploaded to a global flu genomic sample database and construct a phylogeny tree to monitor how influenza evolve and I think the authors behind the project wants to make predictions as to which cohort of influenza variation will become dominant. Wwarn.org I believes tracks the emergence of Artesminin resistance (front-line drug in malaria treatment) in malaria in SE Asia and tries to map it out on GIS to inform public health officials further from SE Asia how it is spreading to their region (India, Africa where current Artesminin resistance gene is only 5% while Artesminin resistance is already the dominant wild type in SE Asia) and whether to modify front-line treatment protocol.

damurdock 11y ago

Pathogen identification is indeed a very exciting application for NGS. In case you're interested, here[0] is a paper about a tool called SURPI (Sequence-based Ultra-Rapid Pathogen Identification) which was designed for that purpose. Also, here[1] is a case report from the NEJM where SURPI was used to diagnose a patient with Neuroleptospirosis, which allowed him to be treated quickly and eventually recover. SURPI isn't the only horse in this game, of course, but I've worked with it before so it immediately came to mind. [0]: "A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples" http://genome.cshlp.org/content/24/7/1180.long http://genome.cshlp.org/content/24/7/1180.long [1]: "Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing" http://www.nejm.org/doi/full/10.1056/NEJMoa1401268 http://www.nejm.org/doi/full/10.1056/NEJMoa1401268

tridint 11y ago
The clinical work they're doing is great, but the code is problematic. Its a bunch of Perl and Python duct taped together with shell scripts. From the github repo: Shell 84.3% Perl 8.9% Python 6.3% C 0.5% Check out the source https://github.com/chiulab/surpi https://github.com/chiulab/surpi