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 :)
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.
Of course if you just go tell everyone you are or are at high risk of being schizoaffective, you've done it to yourself. Not having a bad outcome yet doesn't mean that a bad outcome is not now more likely.
My nephew died by suicide, I tried my mother and my brother tried. A whole family of pretty evident genes.
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.
- 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
Or even more likely: “your insurance premium has now increased”, “your credit score is now degraded”.
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? :)
The main factor for using myheritage was that they have this cheap 30€ offering at the moment.
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.
"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.
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).
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.