[jdmoreira]

I don't want to sequence at home.

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.

[stymaar]

> But I do want to sequence it using a third-party

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)

[vintermann]

They did not leak their database, the attacker guessed some user passwords and scraped those people's match lists.

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.

[jefftk]

I know you put an asterisk, but to make it clear: these locations are very far from random. They're the most informative positions, which is why we check them.

[vintermann]

Well, they're what 23andMe thinks are most informative, for the things they think their customers care about. Or thought; for compatibility reasons they can't change their SNP panels very often or too much.

And the interesting positions are still reasonably randomly distributed by nature :)

[bonsai_spool]

I don't do SNP design but I don't think 23andMe made their own chips at first (if they have ever). SNPs are chosen based on being informative for population discrimination, with traits being overlaid afterwards

[vintermann]

I could be wrong, but I do believe they get to choose. What I do know is that none of the big testing companies test exactly the same SNPs, there is some overlap but every test is different. They also change their SNP sets from time to time, 23andMe has changed at least 5 times, and interestingly, their current test isn't the biggest (it tests fewer SNPs than some of their earlier ones).

[doctorpangloss]

well SNPs aren't useful for drug development, commercialization, medicine, etc. you want whole genome or whole exome sequencing for stuff that is future-looking. they use a process for the present day (quickly becoming the past) of okayish drugs instead of sequencing for a future of cures.

[neoden]

what is the attack vector btw?

[saxonww]

Finding yourself in a genetically-determined out group, and being treated differently / discriminated against because of it.

[Noaidi]

Honestly, you don't need someone's genetics for this to happen. They will find out more about you by scraping your socials and spending habits and driving habits.

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.

[saxonww]

It's overblown _right now_ because this information is not broadly available. The fear is that pervasive access to this data would lead to e.g. you or your partner not getting insurance to pay for anything fertility-related, or you not getting hired for a job you want despite being otherwise qualified, or even that <insert authority> is less inclined to take you seriously because their perception of what schizoaffective means makes them think your perception of reality can't be trusted.

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.

[Noaidi]

I am homeless currently living with schizoaffective disorder (and OCD) by myself because no one wants to take care of people with mental illness so I have zero to lose.

My nephew died by suicide, I tried my mother and my brother tried. A whole family of pretty evident genes.

[graemep]

You have control over your habits, and what you reveal on your "socials". I post very little personal.

You have no control over your genes.

[vintermann]

23andMe bet big that genetic big data would be super valuable. That really didn't work out for them.

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...

[Noaidi]

> You have control over your habits

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.

[Self-Perfection]

That gives some probabilistic info to scraper. Like person might have genes that are: - susceptible to drugs abuse - or game addiction Bam - you get target ads

- 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

[stymaar]

> That gives some probabilistic info to scraper. Like person might have genes that are: - susceptible to drugs abuse - or game addiction Bam - you get target ads

Or even more likely: “your insurance premium has now increased”, “your credit score is now degraded”.

[vintermann]

YSEQ is basically a mom- and pop shop, two German scientists who helped set up Family Tree DNA's labs in Texas then went home to start a small competitor (I think there was some sort of disagreement or conflict) in the space of high-resolution Y DNA sequencing for genealogists.

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.

[balfirevic]

> But be warned, it takes a long time

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?

[cydodon]

From their website yseq.net:

- 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."

[_zoltan_]

700 EUR doesn't seem like expensive for what it is.

[embedding-shape]

> 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?

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? :)

[super256]

I used myheritage and simply exported all my data and then requested an account closure and data deletion.

The main factor for using myheritage was that they have this cheap 30€ offering at the moment.

[weinzierl]

I want long-read raw data. Also Europe (Germany) and simple consumer. Is there any third-party service that offers this? How much will it cost me?

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.

[sergey-a]

Sequencing dot com.

TellmeGen

DNA Complete.

Unless you live in Germany (in Germany it seems to be illegal to send saliva to other countries).

[eps]

Can you get raw data from Tellmegen?

Can't seem to find any info on this on their website.

[fph]

Yes, it is in profile/settings.

[croes]

TellMeGen has a lifelong update, I guess they store your data to do that.

[RossBencina]

What does "lifelong update" mean in this context? are they not doing whole genome sequencing to begin with?

[croes]

Seems like if new studies find a link between genes and diseases they would update the result of your gene based health risks.

[shevy-java]

Many companies offer that. In the local area they have e. g. mail-like stations where you give out your order and they give you what you need (e. g. if it is a plasmid, it is mailed into storage boxes often on the same day or next day).

"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).

[crote]

Files aren't magically stored forever.

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.

[anoneng]

Much like many cameras process and discard the RAW sensor data after processing to pixel data if not further compressing and discarding the processed pixel data to a lossy image format, even more so the raw BAM sequencing read data is vastly larger than processed VCF files. Even many companies that retain that data are liable to archive it offline rather than keep the raw reads permanently accessible online. There are real costs involved and a business case is needed for keeping that data. Especially with a decent privacy policy or regulations storing 100G or multiples of that online for free and downloading on demand is a significant compared to the entire cost of sequencing.

[lukan]

"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"

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.

[inferniac]

I used Macromo, think theyre a czech company, they give you the data

[mfld]

YSeq, TellMeGen - or reaching out to local sequencing labs

[croes]

TellMeGen says something about a lifelong update of the result.

So they store your data

[BiraIgnacio]

GeneDx _might_ do it https://www.genedx.com/

[RobotToaster]

If a service doesn't give you the raw data for some reason you should be able to get it with a GDPR subject access request.

[vintermann]

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 want you uploading your raw data to competing trees (in particular YFull).

[sergey-a]

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

[vintermann]

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.

[jjtheblunt]

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

[sergey-a]

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

[jjtheblunt]

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.