<p>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:</p>
<p><a href="https://doi.org/10.1038/s41587-019-0156-5" rel="nofollow noreferrer">https://doi.org/10.1038/s41587-019-0156-5</a></p>

CC BY-SA 4.0
2020-10-24T10:32:57.610Z
2022-07-31T21:39:00.057Z
2022-07-31T21:39:00.057Z
gringer
<p>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:</p>
<p><a href="https://journals.plos.org/plosone/article/comments?id=10.1371/journal.pone.0076096" rel="nofollow noreferrer">https://journals.plos.org/plosone/article/comments?id=10.1371/journal.pone.0076096</a></p>
<p>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.</p>

CC BY-SA 4.0
2022-12-28T23:38:38.270Z
2022-12-28T23:38:38.270Z
Supertech
<p>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.</p>
<p>Has anyone found a good reference (or anecdotal evidence) for a range of human to pathogen DNA ratios typically found in sputum samples?</p>
<p>Does this depend on whether the patient is infected by a virus or bacteria, and the species that is infecting the patient?</p>
<p>I am seeking a ballpark estimate. Can I expect to find 10x as much human DNA as pathogen DNA, or 100x-1000x?</p>

<nanopore><covid-19><bacteria><virus>
What is the typical host-to-bug DNA ratio found in nanopore sequencing without amplification?
# What is the typical host-to-bug DNA ratio found in nanopore sequencing without amplification?

(Asked by: username_0 on 2020-10-23)

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?

**Tags:** nanopore, covid-19, bacteria, virus

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## 2 answers

### Answer by username_1 on 2020-10-24. Score: 1

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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### Answer by username_2 on 2022-12-28. Score: 0

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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