Posted by bilsbie 17 hours ago
But I do want to sequence it using a third-party that gives me all the raw data. I live in Europe and I'm just a simple consumer. Does anyone know how I can do this? What service would I use / you can recommend?
Them not keeping it on their side would be a huge bonus of course but not sure I can ask for that much.
Don't forget to change your DNA when the third party's database will eventually leak. (see the 21andMe's data leak: https://en.wikipedia.org/wiki/23andMe_data_leak)
I don't think they even got their hacked user's test results - you can download those from 23andMe, as GDPR requires, but it's a "request your data" process which isn't so easy to do at scale without people noticing.
23andMe is also not NGS sequencing, so you get only a couple of 100000 letters randomly* distributed across your whole genome.
And the interesting positions are still reasonably randomly distributed by nature :)
- Indicate that any common substance is especially dangerous/harmful for him (think of allergies). So attacker might plan assassination or severe inconvenience by exposure to the substance and then claim he did not know
I think this whole fear is over blown anyway. I am in a genetic out group (schizoaffective disorder and yes my risk is genetic) and the benefits of getting my genetics run twice out weighed any risk that might have befallen me.
You have no control over your genes.
It turns out that it's more valuable for advertisers to learn if you actually smoke, than that you have a genetic propensity for smoking. Your genotype is just useful for figuring out your phenotype, and in the vast majority of cases, your genetics (especially not at the resolution offered by 23andMe) are not a shortcut to learn your behavior, which is what they're really after.
You're probably already classed as some variety of paranoid/dissident for your careful social media preferences...
If you have to change your habits because a secret system is watching over you it means they are already controlling you.
You cannot hide your bank account, where you drive, what you buy, and on and on and on.
And all I need to get your DNA is pick up a cup you drank from or go through your garbage.
They also do high resolution full genome sequencing on request. But be warned, it takes a long time, and they reserve the right to cancel your order if you complain about how long it takes!
They're not the cheapest option, but when it comes to privacy for Europeans, I think they're as good as they come. You want a bit of "difficult to work with" when it comes to privacy.
What's a "long time"? A month, a year, 10 years?
> They're not the cheapest option
Whats "not the cheapest"? 100 EUR, 1000 EUR, 10000 EUR, more?
- Whole genome sequencing ultra plus (150 Gbases raw data) is €699,- incl. shipping for the sampling kit
- "The turnaround time is approx. 5-7 months at the moment."
At one point I randomly bumped into a cancer researcher as he were in town for some conference. I posed exactly the same question to him, and he told me to reach out to local labs, specifically to the individuals posted on the websites, and ask them directly to help me out or point me in the right direction. He said he've done it himself in multiple countries before, but I'm not sure yet people helped him because of his title, but he assured me I'd find someone willing to help me even if I was just a lowly software engineer. I have yet to actually try it myself, but maybe you could try if there is any nearby? :)
Why must it be long-read? The info I want is from nearly identical duplicated genes. I have FASTQ and BAM files from Dante Labs, but wasn't able to get the info I want out of them.
TellmeGen
DNA Complete.
Unless you live in Germany (in Germany it seems to be illegal to send saliva to other countries).
Can't seem to find any info on this on their website.
So they store your data
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 want you uploading your raw data to competing trees (in particular YFull).
"Not keeping it on their side" ... well. If they sequenced it, they have data in their computer, right? How could you avoid that? I don't see this as possible, it depends on trust (and whether you really care about that).
> What service would I use / you can recommend?
I won't recommend anything as I do not want to be an ad-amplifier, but my personal rule of thumb is that those companies that are affiliated with science clusters, are often chosen because they offer high quality (and to some extent because of corruption e. g. xyz knows abc, but this is IMO the smaller part, usually it is quality/speed/ease of use).
They could have the sampling machine write to an SD card and mail that back, or store it with a one-time-use link like pwpush.com, or have it expire & self-delete after N days like WeTransfer.
You of course have to trust that they aren't secretly keeping their own copy on S3 forever, but that'll always be a risk, and it can probably be contractually enforced and audited.
First it depends on the contract, if it states they have the right, then they can and will legally use it.
If the contract would say no - then they would have a much harder time making use of that data, as it would be illegal.
What kind of magic is going on here, am I missing something?
You can still read it, though it is pretty dense
> https://chatgpt.com/?q=summarize%20this%20article%20for%20me...
You make one for claude, perplexity etc.
The AR angle tho, still lost on me, maybe i'm missing something...
I would have done better in uni if the lab manuals were written like this
What a sad reality we live in. Or to quote C3PO from Star Wars 2... "Machines building machines. How perverse.".
$100 to stave off that $10000 sewer replacement for a few years would be worth it to a lot of people
https://www.naturemetrics.com/species-detection
https://www.ednacollab.org/industry/
These companies focus on environmental DNA - some are more on the level of local government monitoring, some are for private customers.
Now that I think about it - could you just pour some sort of biodegradable broad-spectrum herbicide down the drain to get the same effect for cheaper?
I don't wasn't to kill parents idea. It's neat, and Im sure there's use cases that my solution doesn't meet
It will not degrade anywhere near fast enough to not cause serious issues in the biological treatment stage of the wastewater plant.
Once I figure out how to make it work at all, I'll build a network of plant nerds and teach them to do the same in their cities, and pivot to providing lab services and training for them. Much of the time no sequencing will be required, just a microscope and knowledge of what's growing nearby. But if they have more than one plant of the same species, sequencing will be necessary.
Fingers crossed they're not clones, though I suppose I could do lab testing for that as well, and then I maybe you'd have to kill multiple just to be sure you got the one. In that case, hopefully I'd have at least narrowed it down for you. Probably would just deny the job if the odd of being helpful are low, like if you have 50 clones of the same tree all growing along your sewer line, then I can't help you, it's time to start saving for a liner or a replacement.
It's like uber, but for shit-covered roots.
> "I have a VCF, I can run it through tools like VEP, ClinVar, gnomAD, PharmGKB (highly recommend), Gene Inspector, or Claude"
I am assuming my data is now within the hands of some of the very entities I do not want to have access to my data ... true?
Claude on the other hand - yeah you are giving your data away. But that step really isn't necessary.
By running a standard pipeline you could get a VCF (File containing the Variants in your genome) and each variant would be annotated. You can check all the annotated genes and figure out if these variants are pathogenic, likely pathogenic, likely not pathogenic or benign.
If you want it quick and cheap(er) - 599.00
For $7.5k+ you get a guaranteed privacy (as other comments suggest, other properties may vary, but at least the data never leaves your home).
Unless you just want it on a level "Does this mutation leads to a genetic disorder X" - this is a simple way to put it, but not enough to actually understand genetics.
look up what isaac asimov had to say about genomic analysis.
As a useful genome? Marginal. ONT will need a couple runs to get complete human genome coverage and the substitution error rate is still high compared to short reads. For a fraction of the price and effort you can get your DNA resequenced at 10 times the quality.
I guess if you are super-ultra paranoid you can do it all yourself at home, but honestly. You're not that special, and if someone really actually wanted your genome that bad they'd just take it from a used coffee cup.
But also: genetic counselling is a real thing that real people study. Please don't ask an LLM questions about what your genes are going to do to you without having access to someone who has the ability to contexualise the data and put you in touch with relevant experts. I have a PhD in this and I would not trust myself to be able to interpret data about myself in a detached and rational way.
(And: why is the link to Molecular Biology of the Cell to the 6th edition, when the 7th came out 4 years ago? Random fact: the first three editions were co-authored by my supervisor during my first PhD attempt, who went on to demonstrate that Roger Penrose's ideas about the importance of microtubules in chemotaxis in E. coli were absolute bullshit. Great guy)
[1] I spent a while analysing very early (by commercial standards) Illumina data in 2007, and being able to align stuff to reference genomes made it possible to identify certain biases. Nanopore technology is likely to have more of those, and if you don't have the ability to take those into account you may have a very bad time
(also a biochemist, MSc)
The Oxford Nanopore sequencing technology is one of the most robust to use. You need to buy some kit - but defo doable. Nothing compared pouring your own gel and doing radioactively labelled Sanger reactions :-)
Though you could just go to an sequencing company that services labs ( that just does sequencing outsourcing - rather than a personal genome company ).
Totally agree on the dangers around interpretation.