Search Explore

  • Aurornis · 1 days ago

    I wish this had some discussion of the results. The earlier reports about this sensor and process were very mixed. It’s a cool process either way, but I’d like to know how usable the real world output can be.

    • whatever1 · 1 days ago

      What is the accuracy in this ? Aka if I run the experiment 10 times how many differences will i get? I don’t have a physical sense on what would be a good number.

      • myhf · 1 days ago

        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)

        • Jules-Bertholet · 1 days ago

          > so 10x reads of every segment in the sample would give >99% accuracy for each base after aligning the reads with each other

          This assumes random errors, which IIRC isn't the case for Oxford Nanopore.

        • Jules-Bertholet · 1 days ago

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

          • Gethsemane · 1 days ago

            For most DNA it now sits at ~Q20 (1%) which is a big improvement - there was also some hacky stuff like HERRO and duplex sequencing which improved it substantially. For routine genome sequencing it's definitely suitable, and the long-read advantage helps resolve some of those trickier regions

            • mbeavitt · 1 days ago

              This is simply not true, advances in basecalling and using Duplex give you >Q25

            • drdaeman · 1 days ago

              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).

              • vibrio · 1 days ago

                I suspect there is a deep sequencing service that is non CLIA and cheap. True. they may not be trustworthy with the data. That said, there are steps here where the data is put into Claude. Do we trust that ?

                • tzumby · 1 days ago

                  I would never trust that. Instead I would use Claude to teach me genomics and build the tools to process and interpret data locally

                  • mylons · 1 days ago

                    haha. hubris thy name is tzumby.

                    look up what isaac asimov had to say about genomic analysis.

                    • sergey-a · 1 days ago

                      It's not impossible: Claude can take care of bioinformatics part. But to understand genetics and cellular biology you need a knowledge foundation first.

                      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.

                    • drdaeman · 1 days ago

                      That's another vector, and everyone considers separately. But at least here one can - hypothetically - have a BAA and zero-retention agreement with Anthropic. Which means they have moderately strong incentives to wipe your data after a fairly short while. CLIA, if I don't misremember, mandates a few years at minimum.

                  • j45 · 1 days ago

                    A service is not the same as the equipment

                  • bleepblap · 1 days ago

                    > This is intended to be read by AI

                    Fuck this

                    • asveikau · 1 days ago

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

                      • SuperSixFour · 1 days ago

                        Literally left the article to come here and say this.

                        • tclancy · 1 days ago

                          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.”

                          • fennec-posix · 1 days ago

                            Funniest thing I read today, thank you!

                          • hahahaa · 1 days ago

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

                            • bmwoolf · 1 days ago

                              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

                            • metalman · 1 days ago

                              I am very impressed with the, why wait? just do it now approach to the future. which while not here, IS there.

                              • dekhn · 1 days ago

                                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.

                                • ElenaDaibunny · 1 days ago

                                  just a hobby project for now,pretty wild that this can be done at home.

                                  • fragmede · 1 days ago

                                    Knowing exactly why I have high LDL because of a specific mutation on my DNA is very much the future, imo.

                                    • dekhn · 21 hours ago

                                      .... which does not need or really want home sequencing. That's clinical-grade with QC and high quality instruments, along with professional genetic analysis.

                                    • ngsevers · 1 days ago

                                      I disagree, I sequenced with nebula genomics years ago.. you can understand risk factors for various problems so that you can start interventions that make sense way in advance.

                                      • dekhn · 21 hours ago

                                        Did you actually find any actionable results? When I had my genome sequenced professionally they told me I literally had no SNPs in my genome that were associated with deleterious mutations. And even if you do, there are only some treatments- and those treatments usually have clinically validated tests that are accurate.

                                      • dtj1123 · 1 days ago

                                        I don't wasn't someone else to have a copy of my genome, whilst wanting to analyse my genome. The only way to do that is with affordable home sequencing.

                                    • dwa3592 · 1 days ago

                                      This is so cool. Thanks for doing this. The fact that we have this in a palm sized object is just crazy. Also, if/when we have a similar sized device for doing CRISPR .... umm i should stop here - it's becoming the plot of Gattaca

                                      • munib_ca · 1 days ago

                                        > This is intended to be read by AI- please just copy and paste the URL of this and have ChatGPT walk you through it. If you have AR glasses, even better, since the AI can walk you through the whole protocol.

                                        What kind of magic is going on here, am I missing something?

                                        • alwa · 1 days ago

                                          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

                                          • shresthjain · 1 days ago

                                            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.

                                            • mschuster91 · 1 days ago

                                              > 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.

                                              What a sad reality we live in. Or to quote C3PO from Star Wars 2... "Machines building machines. How perverse.".

                                            • bmwoolf · 1 days ago

                                              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

                                              • abhaynayar · 1 days ago

                                                But where does AR fit in? Doesn't this just need voice mode?

                                                • lachlan_gray · 1 days ago

                                                  Funny, I was really impressed with how concise and goal oriented the directions are!

                                                  I would have done better in uni if the lab manuals were written like this

                                                  • munib_ca · 1 days ago

                                                    If you wanna take it a step further you can just embed a chat/llm icon at the start of your article, give it a header like "summarize this article using:", that leads to this query:

                                                    > 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...

                                                • TurdF3rguson · 1 days ago

                                                  I'm too afraid I would learn something awful about myself.

                                                  • peyton · 1 days ago

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

                                                    • TurdF3rguson · 1 days ago

                                                      Are you talking about time travel? I don't think that would help.

                                                      • ggirelli · 1 days ago

                                                        More like genome editing.

                                                      • vintermann · 1 days ago

                                                        You have no power to correct something with gene editing, true, but there may potentially be preventive action you can take. It's all largely hypothetical today anyway, most things you care about (e.g. cancer, Alzheimer's) you can't usually tell very reliably if you're going to get from a DNA test.

                                                      • vintermann · 1 days ago

                                                        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.

                                                        • sergey-a · 8 hours ago

                                                          Everybody is a carrier of several genetic disorders, I haven't not seen a single person without that. If somebody doesn't like to know, let them be.

                                                      • __MatrixMan__ · 1 days ago

                                                        I've bee thinking about starting a company where I fish roots out of your sewer and identify the plant (by sequence if necessary) that you have to kill so your sewer doesn't collapse as soon as it otherwise would.

                                                        $100 to stave off that $10000 sewer replacement for a few years would be worth it to a lot of people

                                                        • fragmede · 1 days ago

                                                          Do it!

                                                          • hahahaa · 1 days ago

                                                            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?

                                                            • __MatrixMan__ · 1 days ago

                                                              Well if you have this problem, then having the plumber over is a sunk cost. You're paying them regularly to clear the sewer, and their snake will come back with root matter in the bit. Put that sample in a zip-lock bag and call me. I'll come over, take the sample, and identify the plants near your sewer line. If I get a match, I'll sell that info to you for $100.

                                                              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.

                                                              • Gethsemane · 1 days ago

                                                                Fastest/cheapest sequencing based method would likely be to collect samples in DNA preserving agent (zymo DNA shield is decent for this), then have an automated platform for extracting DNA and preparing amplicon sequencing libraries (rbcL + matK probably?). Worth having a look at how Plasmidsaurus did this, they did have a similar service for microbiome analysis (https://plasmidsaurus.com/sample-prep/microbiome#16S-extract... - looks like they don't accept raw samples anymore though...). Oxford nanopore sequencing is a decent technology for this as it's fairly straightforward to get working and easy to scale :) As an added bonus, you could perhaps also carry out 16S sequencing in parallel from the sample to get an idea of the microbiome of the sewer.

                                                            • cowthulhu · 1 days ago

                                                              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?

                                                              • eks391 · 1 days ago

                                                                This is precisely what I do each year with a product designed for this exact purpose. $8+shipping gets me enough for my annual pipe maintenance. It's even the special kind because I have clay pipes.

                                                                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

                                                                • __MatrixMan__ · 1 days ago

                                                                  I hope yours keeps working for you. I flushed a lot of blue crystals, but the plant was not deterred.

                                                                  • Lvl999Noob · 1 days ago

                                                                    Isn't this a problematic idea? If you flush down herbicide without checking the results, you would risk breeding herbicide resistance in the weeds.

                                                                  • mschuster91 · 1 days ago

                                                                    > could you just pour some sort of biodegradable broad-spectrum herbicide down the drain to get the same effect for cheaper?

                                                                    It will not degrade anywhere near fast enough to not cause serious issues in the biological treatment stage of the wastewater plant.

                                                                  • randogp · 1 days ago

                                                                    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.

                                                                      • culi · 21 hours ago

                                                                        Isn't this one of the primary techniques with which covid levels are being monitored?

                                                                        • a_bonobo · 18 hours ago

                                                                          They are pretty much the same, yes! Those eDNA providers usually use a wider range of primers (12S, 16S, COI etc.) to capture a range of invertebrates, vertebrates, plants etc. For Covid, since it's only that one virus, you can target only the one gene so it's a bit easier.

                                                                      • mhb · 1 days ago

                                                                        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?

                                                                        • __MatrixMan__ · 1 hours ago

                                                                          Well if you've got two trees and two bushes, and you know one of them is destroying your sewer line but you don't know which one, then you might not want to kill them all just to be sure.

                                                                          Or in some cases you might not even need to kill the whole plant, just dig a targeted hole and hack off the problematic root. It'll probably take years for a different root to find the same crack in your sewer line and start wedging it open.

                                                                          • mhb · 1 hours ago

                                                                            OK. I was thinking you would be applying the chemicals in the pipe, but what you're saying makes sense.

                                                                      • armanj · 1 days ago

                                                                        one main marketing leverage of 23andMe, AncestryDNA, etc are fulfilling the curiosity of people who want to know which part of the world their genes are from. I guess that dataset should be preparatory.

                                                                        • sergey-a · 1 days ago

                                                                          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. :)

                                                                          • vintermann · 1 days ago

                                                                            It's a bit ironic, since FTDNA and MyHeritage (which uses FTDNA's lab) have switched to NGS now, so they presumably could deliver those notorious "health insights", at least better than 23andMe. But they aren't in that market, and 23andMe shows no inclination to switch. They're probably licking their wounds after the user hack and buyout fiasco.

                                                                            • sergey-a · 8 hours ago

                                                                              Need to check if they do 30x read depth or much less - ancestry doesn't need 30x, so companies may just do 2-3x reading, which is not enough for anything health-related due to high chance of errors.

                                                                        • joel_liu · 1 days ago

                                                                          The "non-random errors" point buried a few replies down deserves to be the headline, not a footnote. With Illumina, 10x coverage genuinely washes out errors because they're closer to independent per-read noise. With Nanopore, errors cluster at specific motifs (homopolymers, certain k-mers) due to how the pore physically reads the strand — so the same systematic mistake shows up across most of your reads at that position, and naive majority-vote consensus won't fix it. You need a basecaller/consensus model trained to correct for those specific failure modes (which is exactly what the current-gen Guppy/Dorado models try to do), not just "more depth." That distinction matters a lot for a home setup: coverage is cheap, but knowing where your specific errors are systematic vs. random is what determines whether "buy more reads" actually gets you to clinical-grade accuracy or just gives you a very confident wrong answer.

                                                                          • SilentM68 · 1 days ago

                                                                            Reminds me of the Gloing Plant Project. I never got my glowing flower but would have settled for the instruction manual, also never created :(

                                                                            https://en.wikipedia.org/wiki/Glowing_Plant_project

                                                                            By the by, can't seen to bring up the actual site linked on this post.

                                                                            • shellfishgene · 1 days ago

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

                                                                            • purpleidea · 1 days ago

                                                                              I like the privacy conscious aspects. Apart from the obvious issue of "run it through Claude" how many of those referenced analysis tools are entirely open source or at least run locally? Would have liked to see that in the article.

                                                                              • ggirelli · 1 days ago

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

                                                                              • KashifNY · 1 days ago

                                                                                Bringing everything to your doorstep and everything at your feet and everything near your fingertips is just what all industries are trying to accomplice. The cartoon Animation Wall-E has scenes in it where they show obese humans doing everything through a screen though notice their legs and feet and it's as if they've mutated to a point where they aren't able to walk anymore and all their transport is through a hovering chair cum bed.

                                                                                • mirmor23 · 1 days ago

                                                                                  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;

                                                                                • thomasfromcdnjs · 1 days ago

                                                                                  I'm waiting for someone to make an open source gene sharing platform to rival ancestry etc in the future.

                                                                                  There must be some cool way to share enough structure with some cryptography to share parts of your dna to find relatives etc

                                                                                  • brikym · 1 days ago

                                                                                    With such cheap costs every city should be sequencing dog turds and sending out big fines. The pay back would be very quick.

                                                                                    • colechristensen · 1 days ago

                                                                                      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)

                                                                                      • kriro · 1 days ago

                                                                                        And you'd need the DNA of all dogs to boot (unless they are already somehow stored when a dog is registered). But generally speaking, I do like the idea. Also for horse poop which is pretty common on roads here in the countryside.

                                                                                      • podocarp · 1 days ago

                                                                                        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.

                                                                                      • bambax · 1 days ago

                                                                                        This feels like the acme of narcissism. How much time and money are people willing to spend on navel gazing?

                                                                                        • rtodea · 1 days ago

                                                                                          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

                                                                                          • bambax · 10 hours ago

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

                                                                                            Well, yes, if done in excess. Hypochondria is a narcissistic trait.

                                                                                          • inglor_cz · 1 days ago

                                                                                            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.

                                                                                            • epgui · 1 days ago

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

                                                                                              • vintermann · 1 days ago

                                                                                                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.

                                                                                              • jdmoreira · 1 days ago

                                                                                                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 · 1 days 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 · 1 days 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 · 1 days 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 · 1 days 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 · 1 days 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 · 1 days ago

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

                                                                                                          • RossBencina · 1 days ago

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

                                                                                                            • croes · 1 days 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 · 1 days ago

                                                                                                            Can you get raw data from Tellmegen?

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

                                                                                                            • fph · 1 days ago

                                                                                                              Yes, it is in profile/settings.

                                                                                                          • stymaar · 1 days 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)

                                                                                                            • vintermann · 1 days 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 · 1 days 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 · 1 days 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 · 1 days 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

                                                                                                                    • vintermann · 1 days ago

                                                                                                                      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 · 1 days ago

                                                                                                                      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 · 1 days ago

                                                                                                                  what is the attack vector btw?

                                                                                                                  • saxonww · 1 days ago

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

                                                                                                                    • Noaidi · 1 days ago

                                                                                                                      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.

                                                                                                                      • graemep · 1 days ago

                                                                                                                        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.

                                                                                                                        • Noaidi · 1 days ago

                                                                                                                          > 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.

                                                                                                                          • vintermann · 1 days ago

                                                                                                                            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...

                                                                                                                          • saxonww · 23 hours ago

                                                                                                                            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 · 18 hours ago

                                                                                                                              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.

                                                                                                                        • Self-Perfection · 1 days ago

                                                                                                                          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 · 10 hours ago

                                                                                                                            > 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”.

                                                                                                                      • inferniac · 1 days ago

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

                                                                                                                        • embedding-shape · 1 days 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 · 1 days ago

                                                                                                                            YSeq, TellMeGen - or reaching out to local sequencing labs

                                                                                                                            • croes · 1 days ago

                                                                                                                              TellMeGen says something about a lifelong update of the result.

                                                                                                                              So they store your data

                                                                                                                            • vintermann · 1 days 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 · 1 days 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 · 1 days 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_ · 1 days ago

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

                                                                                                                              • RobotToaster · 1 days 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 · 1 days 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 · 9 hours ago

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

                                                                                                                                    • vintermann · 7 hours 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 · 1 days 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.

                                                                                                                                    • super256 · 23 hours 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 · 21 hours ago

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

                                                                                                                                        • sergey-a · 9 hours 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 · 3 hours 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 · 1 days ago

                                                                                                                                        > The near-term value is turning a static genome into something queryable

                                                                                                                                        Ok. So ... how exactly is this valuable?

                                                                                                                                        If you realise "hey, I gots Huntington disease", this is going to make you feel better? Or any other incurable disease? I am not disputing that knowing the sequence is useless in general, mind you. I am specifically asking WHY it is necessary to know your genome sequence. This seems to be a simplification or just a "having reached a milestone". But then they don't really explain WHY it is useful. None of the bulletin points he listed is really useful:

                                                                                                                                        > Which variants do I have?

                                                                                                                                        And this is useful ... how exactly?

                                                                                                                                        > Which genes and pathways are affected?

                                                                                                                                        And ... this matters why?

                                                                                                                                        > Which medicines might I metabolize differently?

                                                                                                                                        Ok, so this has a potential use case here, since he can choose to avoid specific drugs. How useful that really is in practice is unclear. (Don't confuse drug companies trying to convince YOU that personalized medicine is important on THEIR use case.)

                                                                                                                                        > What rare variants should I take seriously?

                                                                                                                                        Seriously ... how? Ok, you avoid some compounds. Now what.

                                                                                                                                        > Where does the model know nothing yet?

                                                                                                                                        Great, so a model that is limited, but now I need to burden myself with having to know where that limitations are. So my brain just has extra processing to do, without getting anything useful in return.

                                                                                                                                        > the “edit yourself with CRISPR” will most likely follow

                                                                                                                                        Except that they have not solved the off-target cleavage yet. Besides, they milk the prices anyway. DNA manipulation should be safe, secure, correct and affordable. None of that is the case right now. They publish papers where CRISPR has solved everything, but then fail to explain why it isn't already used by billions. And there are reasons as to why.

                                                                                                                                        > Give your genome to Claude Code

                                                                                                                                        Oh my god ... AI becomes your dependency here.

                                                                                                                                        Note that the step-by-step guide is actually not totally useless, as it can give a basis for real work. But I highly doubt that untrained people will easily be able to go through those steps. Everyone is a master in the lab now? RNA is easy to handle? Guess then one would have to explain why RNase A is used (ok ok it's not playing a huge role here since DNA is the target of isolation, but it is more of an example of how many things can go wrong, and there is not really an explanation of why xyz is used; this looks like an AI step-by-step guide. AI really makes people dumber).

                                                                                                                                        • felooboolooomba · 1 days ago

                                                                                                                                          How can I know if the the results I get are real or just some garbage?

                                                                                                                                            • fragmede · 1 days ago

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

                                                                                                                                            • mjg59 · 1 days ago

                                                                                                                                              As someone with experience (albeit almost 20 years out of date) experience of wet lab DNA collection and sequencing - 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. And once you have data, you should be asking yourself how accurate it is given the environment you collected it in, you should be looking at correlated sequence errors that are not taken into account[1].

                                                                                                                                              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

                                                                                                                                              • DrScientist · 1 days ago

                                                                                                                                                > 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.

                                                                                                                                                • epgui · 1 days ago

                                                                                                                                                  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)

                                                                                                                                                  • kriro · 1 days ago

                                                                                                                                                    It seems a bit odd to me to have a home lab for the sequencing and then feed it to a cloud LLM. I would have thought the point of the home lab is privacy.

                                                                                                                                                    • PunchTornado · 1 days ago

                                                                                                                                                      Not really. It is to learn.

                                                                                                                                                    • bluerooibos · 1 days ago

                                                                                                                                                      > Oxford Nanopore Technologies MinION ($7.5k)

                                                                                                                                                      Hmm, I'll come back in a few years when things have become cheaper.

                                                                                                                                                      • jebus989 · 1 days ago

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

                                                                                                                                                      • FrustratedMonky · 1 days ago

                                                                                                                                                        Can CRISPR also be done at home this cheaply?

                                                                                                                                                        Seems like maybe of the 3 dystopias: AI, Global Warming, Bio-warfare. That this is demonstrating that the home grown virus is closer than we think.

                                                                                                                                                      • sublimefire · 1 days ago

                                                                                                                                                        It might make even more sense once we get to the point of a wider use of encoding the data into dna. For now we have these few commercial players in the field that cad do it (eg look up dna microfactory for storage archiving), IIRC genomika was saying they can do an MB for a 100-200eur.

                                                                                                                                                        • NoSalt · 1 days ago

                                                                                                                                                          I want to sequence, but I absolutely do not want any company or government or church to have access to my data. When the author says:

                                                                                                                                                          > "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?

                                                                                                                                                          • mrzippipo · 1 days ago

                                                                                                                                                            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.

                                                                                                                                                            • NoSalt · 1 days ago

                                                                                                                                                              Very cool ... thank you!

                                                                                                                                                          • BorisMelnik · 1 days ago

                                                                                                                                                            I do want to sequence it at home but I'm gonna wait until it's under 500 bucks

                                                                                                                                                            • 1970-01-01 · 1 days ago

                                                                                                                                                              Has anyone succeeded in doing any of this? I always assumed if it were this simple, someone would be selling DNA kits on Amazon for a few thousand dollars.

                                                                                                                                                              • jebus989 · 1 days ago

                                                                                                                                                                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.

                                                                                                                                                                • searine · 1 days ago

                                                                                                                                                                  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.

                                                                                                                                                                • giantg2 · 1 days ago

                                                                                                                                                                  If the sequencer was 10x cheaper then I might do it.