Sequencing your DNA with a USB dongle and open source code

Re:Sequencing your DNA with a USB dongle and open source code by dekhn on Wednesday February 03, 2021 @05:16PM (#26019900)

it didn't turn out to be harder than I thought it was going to be. I came into this in the 90s fully prepared for the idea of polygenic risk. In my opinion, most people who did molecular biology first think that way, while most people who learned mendelian genetics don't.

I had my genome sequenced a few years ago by Illumina. They had a big slick presentation, blah blah blah, ApoE1, etc. When the genetic counsellors came to my genome they said "huh. you don't have any risk factors". I checked and each of their risks was from an existing gene panel, so the WGS wasn't valuable (it's on PGP, if you want to work with it https://my.pgp-hms.org/profile/hu80855C).

I talked in more detail with the counsellors. Turns out, whenever they saw a novel variant that wasn't covered by a gene panel they were googling the variant and skimming the abstracts of papers.

It was at that point I realized the difference between research, PR, and actionable medical data.

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Re:Sequencing your DNA with a USB dongle and open source code by searine on Wednesday February 03, 2021 @08:46PM (#26021618)

>it didn't turn out to be harder than I thought it was going to be.

Fair.

I've done my as well. Most of the "company" sites don't tell you much, which I think is a legal thing. They aren't cleared to release clinical predictions from genotypes, so they just... don't. I ended up running my through promethease (which mines SNPepedia) and found quite a bit more than what was reported.

I work with some certified clinical geneticists and yeah they do take a much closer look, but at the end of the day its all just sequencing and interpretation. I think its mostly just safeguards to keep bad actors at bay.

PGP looks interesting. I see that you submitted phenotype data. I didn't know they had a questionnaire with that. That's actually really interesting. I need to see what kind of questions they ask.

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