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I'm interested in sequencing a human sputum sample using an ONT MinION without performing any type of whole genome DNA amplification or targeted PCR.

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 species that is infecting the patient?

I am seeking a ballpark estimate. Can I expect to find 10x as much human DNA as pathogen DNA, or 100x-1000x?

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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

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Anecdotally, I have been told that it varies from person to person, also might be affected by disease or hygiene in a particular environment. Here is an article dealing with that problem:

https://journals.plos.org/plosone/article/comments?id=10.1371/journal.pone.0076096

Not sure if they have references useful for you in their paper, but they describe a way of enriching microbial or human DNA. It might be helpful.

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