1
$\begingroup$

I'm interested in sequencing a sputum sample using an ONT MinION without performing any type of DNA amplification. Has anyone found a good reference (or anecdotal evidence) for a range of human to pathogen DNA ratios typically found in sputum samples? Does this depend on whether the patient is infected by a virus or bacteria, and the bacterial species? Can I expect to find 10x as much human DNA as pathogen DNA, or 100x-1000x? I would really just like a ballpark estimate.

$\endgroup$
0
$\begingroup$

My recollection of a conversation I had with Justin O'Grady is that it's about 99% host DNA for unfiltered samples. There are a few ways to reduce that portion prior to sequencing; he has written a paper that mentions a saponin-based host depletion method that is quite effective:

https://doi.org/10.1038/s41587-019-0156-5

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.