> 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)

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.

> 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? :)

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.

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.

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

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

Sequencing dot com.

TellmeGen

DNA Complete.

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

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

YSeq, TellMeGen - or reaching out to local sequencing labs

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.

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).

I suspect the intention is to give specific but dense notes with minimal explanation, on the theory that the LLM will fill in the appropriate hand-holding along the way

Hi, author here- I intended it to be hands-free so you can upload to ChatGPT/Claude and talk to it. I found it easier to follow the protocol each time by talking to AI rather than having to read from the computer every time I had to check something, reducing context-switching

You can still read it, though it is pretty dense

I feel it's actually kind of smart. Most people won't be reading the blog post themselves, they'd ask GPT to understand the text and fetch the summary or whatever is relevant to them. The author has directly made the resource such that it is optimised for the output after that mostly-everyone-would-do-this step.

https://www.envirodna.com/

https://www.naturemetrics.com/species-detection

https://www.ednacollab.org/industry/

https://wilderlab.co/

These companies focus on environmental DNA - some are more on the level of local government monitoring, some are for private customers.

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?

That’s a really clever idea, I would definitely pay for that in the right circumstances.

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?

How will you reach out to enough people so they are aware and can order the service? I'm thinking about the minimum viable business opportunity here.

Hard to get a plumber to knock on my door for under $100. Maybe you mean $500? Or is it $100 for the lab bit only?

Do it!

If it's an US-based lab, aren't they subject to CLIA with all its retention requirements?

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).

A service is not the same as the equipment

Nanopore data is a lot easier to analyze than short read sequencing data. You just don’t get the same alignment/assembly issues: these things sequence incredibly long reads.

(also a biochemist, MSc)

> this stuff is hard, you will fail a lot, and you will fail a lot more if you don't have an extremely clean environment to do this in

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.

Untrue in the cases of VEP, ClinVar, gnomAD. These are either offline, open-source tools or databases. You can download or query these and no one would be the wiser.

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.

At a quick glance, they all seem to have published their source code and they do run locally.

via comparison to other nucleotide sequences. This is called sequence alignment: https://en.wikipedia.org/wiki/Sequence_alignment

Run it multiple times, and then get professionals in on it as well, and then compare.

Not really. It is to learn.

I watched wall-e in theater, and when that scene came on, i remember muttering 'what bs'; since then, i recall that scene every time i see a situation of 'convenience at all costs'; metaphorically they were pretty accurate even after discounting ozempic influence;

It's been around for a decade and was $1k in early access, so don't hold your breath.

Per the article, ONT sells tiny sequencers that all this genre of "Omg I just sequenced my genome" posts use. They've been around for a decade or so. A commercial lab will give you 30x illumina sequencing for maybe 5% of the cost of this post.

As an 'at home' science project? Totally do-able, but very expensive. I did it as part of epidemiological field with a backpack of materials, so you can definitly do it at home.

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.

I think cameras or even just a reporting hotline would be easier. The problem is lack of motivation I think rather than a money thing.

It's quite a bit more difficult with poop. A rather large proportion of the DNA in poop isn't from the creature that pooped it. (mostly bacteria)

You would get a lot of differences, but the errors would cancel each other out with enough depth of coverage.

This technology's baseline accuracy is around 95% per base, so 10x reads of every segment in the sample would give >99% accuracy for each base after aligning the reads with each other.

https://en.wikipedia.org/wiki/Coverage_(genetics)

Oxford Nanopore unfortunately has a high error rate (3-5%) compared to other sequencing technologies. And the errors are non-random

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 the solo-founder of Gene Inspector Pro, mentioned in the blog post). AMA. :)

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.

Unfortunately you’d have no power to correct it. Even if such a thing were possible. I hope that changes.

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

Nothing about this is the future. Sequencing at home will not solve any major problems. It's mainly a fun exercise to demonstrate that sequencing has been commodified.

yes https://www.the-odin.com/blog/how-to-do-crispr-at-home-begin...

True story, I found a god damn tick in my navel yesterday. Sometimes a bit of navel gazing can be healthy, figuratively and literally.

On a reasonable level, navel gazing (the figurative kind) is maybe better called self-reflection. I use DNA for genealogy, and it seems to me from the people I meet, that many get a healthier approach to our identity once we learn more about our genetic background. Identity politics, collective identity building around ancestry - identity building of all kinds really - needs simple stories. And the stories DNA tell are never simple.

That’s quite judgmental and shows an impressive lack of scientific curiosity.

When you are taking care of your health, and need to learn more about your built-in limitations is it still narcissistic?

At the bottom of the page there is a link to Sid Sijbrandij's cancer journey. He is one of the cofounders of GitLab. This is one of the coverages of his story: https://centuryofbio.com/p/sid

I don't get you at all.

Is going to your doctor or eating better food "navel gazing"? Predispositions to some diseases can be read from your DNA. Remember Angelina Jolie undergoing preventive mastectomy because she had a high genetic risk for breast cancer? Well, so do many non-celebrities.

Then there is the specific case of people who may suspect that their bio-parents are someone else, and there is nothing weird about wanting to know where you actually come from.

Man, doctors thought they had it bad before. For just a six yards I can play Peter Thiel at home! $6k invested so I can set an AI in YOLO mode to tell me I have some hyper-specific version of kennel cough?

“But that occurs in dogs?”

“You’re right. Let me look into actual gene sequencing instead of just guessing. I think the N is the load bearing letter.”

Hi, author here- you can read it too, though it is dense. I have updated that specific sentence.

I found it easier to upload the protocol to ChatGPT and have audio walk you through it. This allows you to swap between pipettes, measurements, etc without having to look at the screen, reducing context-switching

Yeah that's weird. The instructions are not even hard to read. I don't understand what an LLM would add to this.

As long as the AI doesn't brush its teeth all good.

Literally left the article to come here and say this.