

One Codex (YC S14) Wins the CDC's “No-Petri Dish” Challenge - LukeB_UK
http://blog.ycombinator.com/one-codex-yc-s14-wins-the-cdcs-no-petri-dish-challenge

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boyd
Hi everyone - co-founder of One Codex here. Happy to answer any questions
folks have!

~~~
srunni
1\. What bodily sample types can you start from? The CDC page gives stool as
an example, but can you work from blood or mucus as well? What sorts of
preparation/purification steps (if any) are required in those cases?

2\. How long does it take with your system to get a positive ID?

3\. How often do you get false positives/negatives? How much does this matter
(from a clinical perspective)? Are the phenotypes similar enough that it's not
that important?

4\. Can you rapidly/correctly classify any _E. coli_ at the strain level, and
not just STEC? What about other bacteria?

5\. Have you considered taking this system to the clinic? Have you
investigated whether there's demand for it from clinicians? Bacterial
diagnostics haven't really benefited from the GAIN Act the way antibacterial
therapeutics have
([http://www.nature.com/scibx/journal/v7/n41/full/scibx.2014.1...](http://www.nature.com/scibx/journal/v7/n41/full/scibx.2014.1196.html)).
Do you think the path to market will be significantly eased/improved for IVDs
by the impending change from cost-based to market-based reimbursement
([http://www.analysisgroup.com/uploadedFiles/Publishing/Articl...](http://www.analysisgroup.com/uploadedFiles/Publishing/Articles/Advanced_Diagnosis_IV1410.pdf))?

6\. For clinical purposes, how would you compare/contrast a NGS-based
bacterial ID platform to an AST-based one (e.g., $AXDX's ID/AST system:
[http://acceleratediagnostics.com/our-science/culture-free-
mi...](http://acceleratediagnostics.com/our-science/culture-free-
microbiology/))? Do we really need the genotype, or is it just the phenotype
that matters?

~~~
boyd
1\. We're working from a variety of sample types (those you mentioned) as well
as cultured isolates.

2\. The technology demonstrated for the CDC prize takes ~20 minutes to process
an Illumina HiSeq run. And there's a lot of further optimization opportunity.
Put differently, the bioinformatics are sufficiently fast so as to be "real
time" (i.e., they could be stream processed off of a sequencer, and don't
require a substantial % of additional time over the hardware runtime).

3\. In general, the false positive and negative rates for our
(bioinformatic/in silico) approach are very good. But, ultimately these rates
also depend greatly on the underlying hardware and the sample collection,
preparation, etc. protocol.

4\. A) Yes, we can identify any strain across a reference library of several
thousand E. coli strains. B) Yes, and we're starting with, E. coli,
Salmonella, and several others.

5\. Yes - but this getting rather long, so pls. e-mail me (below) if you're
interested in discussing further.

6\. I'm not intimately familiar with the system in question, but in general
NGS offers greater "resolution" than other molecular approaches. And, as the
existence of this initiative at CDC hints, having this resolution is
particularly important for strain-typing and other public health functions.
Ultimately, we think many of these benefits will also carry over in the form
of better clinical (diagnostic) information and data collection.

Happy to chat about this further if it's of interest. My email is
nick@onecodex.com.

