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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 consu

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.

shevy-java 2mo ago
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).
- lukan 2mo ago
  "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.
- crote 2mo ago
  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 2mo ago
  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.
sergey-a 2mo ago
Sequencing dot com. TellmeGen DNA Complete. Unless you live in Germany (in Germany it seems to be illegal to send saliva to other countries).
- croes 2mo ago
  TellMeGen has a lifelong update, I guess they store your data to do that.
  - RossBencina 2mo ago
    What does "lifelong update" mean in this context? are they not doing whole genome sequencing to begin with?
    - croes 2mo ago
      Seems like if new studies find a link between genes and diseases they would update the result of your gene based health risks.
- eps 2mo ago
  Can you get raw data from Tellmegen? Can't seem to find any info on this on their website.
  - fph 2mo ago
    Yes, it is in profile/settings.
stymaar 2mo ago
> 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 https://en.wikipedia.org/wiki/23andMe_data_leak)
- vintermann 2mo ago
  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 2mo ago
    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 2mo ago
      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 2mo ago
        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
        2mo ago
inferniac 2mo ago
I used Macromo, think theyre a czech company, they give you the data
embedding-shape 2mo ago
> 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? :)
mfld 2mo ago
YSeq, TellMeGen - or reaching out to local sequencing labs
- croes 2mo ago
  TellMeGen says something about a lifelong update of the result. So they store your data
vintermann 2mo ago
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 2mo ago
  > 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 2mo ago
    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_ 2mo ago
      700 EUR doesn't seem like expensive for what it is.
RobotToaster 2mo ago
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 2mo ago
  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 2mo ago
    Storing genetic data is not against GDPR. It matters where they store it and who else has access to the data.
    - vintermann 2mo ago
      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.
weinzierl 2mo ago
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.
BiraIgnacio 2mo ago
GeneDx _might_ do it https://www.genedx.com/ https://www.genedx.com/
super256 2mo ago
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.
jjtheblunt 2mo ago
In Europe Dante (an Italian company) is excellent at this.
- sergey-a 2mo ago
  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 2mo 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.

shevy-java 2mo ago

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).

lukan 2mo ago
"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.
crote 2mo ago
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 2mo ago
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.

sergey-a 2mo ago

Sequencing dot com. TellmeGen DNA Complete. Unless you live in Germany (in Germany it seems to be illegal to send saliva to other countries).

croes 2mo ago
TellMeGen has a lifelong update, I guess they store your data to do that.
- RossBencina 2mo ago
  What does "lifelong update" mean in this context? are they not doing whole genome sequencing to begin with?
  - croes 2mo ago
    Seems like if new studies find a link between genes and diseases they would update the result of your gene based health risks.
eps 2mo ago
Can you get raw data from Tellmegen? Can't seem to find any info on this on their website.
- fph 2mo ago
  Yes, it is in profile/settings.

stymaar 2mo ago

> 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 https://en.wikipedia.org/wiki/23andMe_data_leak)

vintermann 2mo ago
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 2mo ago
  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 2mo ago
    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 2mo ago
      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
      - 2mo ago

inferniac 2mo ago

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

embedding-shape 2mo ago

> 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? :)

mfld 2mo ago

YSeq, TellMeGen - or reaching out to local sequencing labs

croes 2mo ago
TellMeGen says something about a lifelong update of the result. So they store your data

vintermann 2mo ago

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 2mo ago
> 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 2mo ago
  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_ 2mo ago
    700 EUR doesn't seem like expensive for what it is.

RobotToaster 2mo ago

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 2mo ago
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 2mo ago
  Storing genetic data is not against GDPR. It matters where they store it and who else has access to the data.
  - vintermann 2mo ago
    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.

weinzierl 2mo ago

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.

BiraIgnacio 2mo ago

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

super256 2mo ago

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.

jjtheblunt 2mo ago

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

sergey-a 2mo ago
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 2mo 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.