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How to sequence your own DNA at home

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Re: How to sequence your own DNA at home

#151

Post by sergey-a »

vintermann wrote: post #89
sergey-a wrote: post #38

Earlier quoted context omitted.

Problem with those providers - they only check 700K positions out of 3 billion and there is no mapping quality or allelic depth data in those dataset and this is critical for assessing whether the detected variant is a false positive or real. It's not suitable for health investigations since most of DNA is not sequenced and genotyping technology is known to produce high rate of false positive for rare mutations. (I'm…

It's a bit ironic, since FTDNA and MyHeritage (which uses FTDNA's lab) have switched to NGS now, so they presumably could deliver those notorious "health insights", at least better than 23andMe. But they aren't in that market, and 23andMe shows no inclination to switch. They're probably licking their wounds after the user hack and buyout fiasco.

Need to check if they do 30x read depth or much less - ancestry doesn't need 30x, so companies may just do 2-3x reading, which is not enough for anything health-related due to high chance of errors.

Re: How to sequence your own DNA at home

#152

Post by sergey-a »

vintermann wrote: post #91
TurdF3rguson wrote: post #19

I'm too afraid I would learn something awful about myself.

That's unlikely, but I do think that the health benefits of full sequence testing yourself are largely hypothetical at this point anyway. Unless you're a competitive athlete maybe? It's genealogy it's useful for. But genealogy, it's really useful for.

Everybody is a carrier of several genetic disorders, I haven't not seen a single person without that. If somebody doesn't like to know, let them be.

Re: How to sequence your own DNA at home

#153

Post by vintermann »

sergey-a wrote: post #150
vintermann wrote: post #115

Earlier quoted context omitted.

Some DNA companies (FTDNA for one) play fast and loose with this. FTDNA gives you a vcf file, which contains the variant calls, but not the raw reads which those calls are made from (as in the BAM file). They do keep that data, because they charge extra for a BAM file download. It's almost certainly against the GDPR. Worse, I think they do it for anticompetitive reasons - they own the largest Y-DNA tree, and don't wa…

Storing genetic data is not against GDPR. It matters where they store it and who else has access to the data.

That's not the issue. If you store PII, which genetic data certainly is, you have to delete it on request, and you have to allow the user to download all of it, everything they have on you, in standard formats. That's the reason all DNA services have data download options in the first place, but FTDNA's is incomplete.

FTDNA should either offer the BAM file for free on request, or offer the same information in a standard format - such as a fasta file with the reads, or a reference-compressed BAM file - so that the user should be able to reconstruct it on their own, or with a competing service (this is actually a service YSEQ offers). They currently don't do this, which means they're withholding PII.

Re: How to sequence your own DNA at home

#154

Post by jjtheblunt »

sergey-a wrote: post #149
jjtheblunt wrote: post #141

Earlier quoted context omitted.

In Europe Dante (an Italian company) is excellent at this.

Uhm, no no. DanteLabs has a very bad reputation because it hasn't delivered results for many customers who sent their kits years ago.

That's interesting. They work ok in the US, but they also do mention that their major contracts are with hospital pathology groups and the consumer services are lower priority. Good to know the European customer experience, except that lower priority is lower than ever produces results. that's ridiculously bad.

Re: How to sequence your own DNA at home

#155

Post by __MatrixMan__ »

mhb wrote: post #133
__MatrixMan__ wrote: post #20

I've bee thinking about starting a company where I fish roots out of your sewer and identify the plant (by sequence if necessary) that you have to kill so your sewer doesn't collapse as soon as it otherwise would. $100 to stave off that $10000 sewer replacement for a few years would be worth it to a lot of people

I don't really understand this. How much better are things for killing a specific plant than whatever you would use to kill a superset of the plants that might be there? Or treating with a few different plant species killers. And wouldn't those options cost less than the cost of this service?

Well if you've got two trees and two bushes, and you know one of them is destroying your sewer line but you don't know which one, then you might not want to kill them all just to be sure.

Or in some cases you might not even need to kill the whole plant, just dig a targeted hole and hack off the problematic root. It'll probably take years for a different root to find the same crack in your sewer line and start wedging it open.

Re: How to sequence your own DNA at home

#156

Post by mhb »

__MatrixMan__ wrote: post #155
mhb wrote: post #133

Earlier quoted context omitted.

I don't really understand this. How much better are things for killing a specific plant than whatever you would use to kill a superset of the plants that might be there? Or treating with a few different plant species killers. And wouldn't those options cost less than the cost of this service?

Well if you've got two trees and two bushes, and you know one of them is destroying your sewer line but you don't know which one, then you might not want to kill them all just to be sure. Or in some cases you might not even need to kill the whole plant, just dig a targeted hole and hack off the problematic root. It'll probably take years for a different root to find the same crack in your sewer line and start wedging…

OK. I was thinking you would be applying the chemicals in the pipe, but what you're saying makes sense.

Re: How to sequence your own DNA at home

#157

Post by ngsevers »

dekhn wrote: post #143
ngsevers wrote: post #30

Earlier quoted context omitted.

I disagree, I sequenced with nebula genomics years ago.. you can understand risk factors for various problems so that you can start interventions that make sense way in advance.

Did you actually find any actionable results? When I had my genome sequenced professionally they told me I literally had no SNPs in my genome that were associated with deleterious mutations. And even if you do, there are only some treatments- and those treatments usually have clinically validated tests that are accurate.

Yes, mostly preventative. Like it caused me to have my cholesterol checked and realized my triglycerides were a dumpster fire. Also good to know about certain cancer risks that I never would have checked up on regularly.

But if you had your entire genome sequenced and not just a check for specific risk factors then 100% there is all sorts of interesting information you can find on yourself. There are tons of correlative studies out there.

Re: How to sequence your own DNA at home

#158

Post by SilentM68 »

shellfishgene wrote: post #45
SilentM68 wrote: post #27

Reminds me of the Gloing Plant Project. I never got my glowing flower but would have settled for the instruction manual, also never created :( https://en.wikipedia.org/wiki/Glowing_Plant_project By the by, can't seen to bring up the actual site linked on this post.

You can get one here, you'll have to wait until next year though: https://light.bio/

Thank you :)

Re: How to sequence your own DNA at home

#159

Post by vintermann »

sergey-a wrote: post #151
vintermann wrote: post #89

Earlier quoted context omitted.

It's a bit ironic, since FTDNA and MyHeritage (which uses FTDNA's lab) have switched to NGS now, so they presumably could deliver those notorious "health insights", at least better than 23andMe. But they aren't in that market, and 23andMe shows no inclination to switch. They're probably licking their wounds after the user hack and buyout fiasco.

Need to check if they do 30x read depth or much less - ancestry doesn't need 30x, so companies may just do 2-3x reading, which is not enough for anything health-related due to high chance of errors.

MyHeritage uses 2x. FTDNA uses a custom targeted enrichment panel, so high accuracy in selected regions important for genealogy.

Re: How to sequence your own DNA at home

#160

Post by __MatrixMan__ »

mhb wrote: post #156
__MatrixMan__ wrote: post #155

Earlier quoted context omitted.

Well if you've got two trees and two bushes, and you know one of them is destroying your sewer line but you don't know which one, then you might not want to kill them all just to be sure. Or in some cases you might not even need to kill the whole plant, just dig a targeted hole and hack off the problematic root. It'll probably take years for a different root to find the same crack in your sewer line and start wedging…

OK. I was thinking you would be applying the chemicals in the pipe, but what you're saying makes sense.

Yeah, the cause of death is a shovel or a saw.
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