Hi, believe it or not, I have actually done what the authors were attempting. I used saliva rather than blood as a source of DNA and extracted it using a Qiagen kit.

My Nanopore flow cell had nearly every pore working from the start. So I would say that is not normal. Maybe it was stored incorrectly.

Do you have a write up somewhere? If not, it would be amazing if you wrote one!

I was planning on doing a similar thing (also with saliva) once I finished moving in and had a bit more time after conferences. (But, of course, I’d have to go through and actually figure out all of the mechanics and so on.)

Thanks for the kind words! I have not written it up but would like to. A word of warning: by trying to get into sequencing, I eventually burned through ~20k USD of student loans (still unpaid) with little to show. Nanopore sequencing also requires some specialized equipment (at least a micro centrifuge and micropipette and possibly more) which is not cheap.

For sure, I think it’d be fun to show it can be done under 5k or so, which would be close ish. Can probably get older equipment from university surplus, but yeah, these are the “things that need to get figured out” :)

I suspect the authors read the number of active pores during sequencing and then wrongly assumed that the non-active ones had a manufacturing defect.

In my experience, most inactive pores are due to a poorly prepared sample. I don't know why, but maybe it blocks or jams the pores.

When I analyzed Oxford nano pore data a few years ago, I found it to be very sensitive to skilled sample preparation. The data quality varied so much that I could tell which of my laborant co-workers (the experienced one or the new one) had prepared the sample by analyzing the data. So I expect that the authors garage sample prep maybe wasn't great.

Coincidentally, I had a colleague who worked on building a portable sequencing lab powered by a car battery. The purpose was to be able to identify viruses by DNA from a van in rural Central Africa or wherever. Last I talked to her, the technical bottleneck was sample prep - the computational part of the van lab wasn't too hard.

> Is this normal for the machine?

No, it's not "normal," but it is fairly common. When I worked in NGS, nearly 1/4 of flow cells were duds. ONT used to have a policy where you could return the cell and get a new one if it failed its self-test.

it depends of the sample. usually you have at least 1200, with a guaranteed of at least 800, so maybe he could ask for a refund.

Like most analytical methods, the preparation of the sample is key. High quality output comes with careful sample prep so that the analytical process can run optimally.

I think it was pretty interesting in a "what would likely happen if you tried this" way. Negative results are good. A lot of technical problems is what I'd expected though, from my little experience in genetic genealogy.