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$200 retail whole genome sequencing now available
- ydnaclementine 8y agoCan anyone comment on privacy for this company? I know that's an issue around 23&me
- craftyguy 8y agoIt's a serious issue for any service that offers to sequence any/all of your genome. AFAIK, none of them get it right. I hope to be corrected here, but I doubt it.
- jghn 8y agoI believe you can opt out of them storing your data once you retrieve it.
- dsfyu404ed 8y agoWhich is useless unless we can get someone on the inside to vouch for the fact that it's actually not stored
- stochastic_monk 8y agoMost companies at least track frequencies. We used to think that deidentified was enough, but apparently it’s not that hard to figure out who a person is if you know that much about them. (Especially if you have relatives.) There’s been a lot of work with homeomorphic encryption, but I think that the new avenue of research using sketches to provide a sense of anonymity while preserving comparability.
- jghn 8y agoThe storage of the data is a not inconsequential portion of the total cost. A lot of work is done to cut costs on genomic data storage. No better way than not storing it in the first place
- tempestn 8y agoThey explicitly state they're GDPR compliant, so at the very least if they keep customer data after saying they've deleted it and are discovered they would probably be looking at huge fines. Doesn't make much sense from a business perspective, especially given that most customers probably won't bother to have their data deleted.
- striking 8y agoLink to privacy policy: https://us.dantelabs.com/pages/privacy-policy https://us.dantelabs.com/pages/privacy-policy
- FriedPickles 8y agoI believe in the future it will be basically free to sequence the genome from a strand of hair. Given that, is it reasonable to try protecting your genome data?
- mattnewton 8y agoImo yes; the ability to match dna to individuals without their consent should belong to law enforcement only. I am holding out hope for legislation that makes this work.
- conception 8y agoThe ability to match dna to individuals is sadly pretty easy and even the idea that you can "de-identify" dna is the elephant in the room for things like HIPPA since dna is the most identifiable thing a person has. Looking at things like this - https://phys.org/news/2013-03-easy-identity-cell.html https://phys.org/news/2013-03-easy-identity-cell.html https://33bits.wordpress.com/about/ https://33bits.wordpress.com/about/ etc Having DNA and just looking at the traits that person has will reduce the population down to a pretty manageable number. Any other bits - location, gender, etc will be enough to make an educated guess to an almost certain one. This will not become more difficult to do in the future.
- echelon 8y agoI wouldn't be surprised if we trained ML models to map DNA to adult faces. It doesn't seem out of the realm of possibility.
- m1573rp34130dy 8y agothere is a thing called developmental noise, thats the outcome of phenotype after post expressional events further modify the expression products [proteins, RNA, MeDNA etc.] the face you interpolate from genetic sequence will be an approximation.
- JProthero 8y ago
- klmr 8y ago> I know [privacy is] an issue around 23&me In what regard? I’ve not heard of any privacy related issue with 23andme, and I follow the field quite closely (professional interest). On the contrary, 23andme has been known to uphold customer privacy in the face of government requests [1]. The FTC is investigating 23andme and other companies (which is a good thing), but there is no indication that they’ve found any violation. [1] https://www.23andme.com/transparency-report/ https://www.23andme.com/transparency-report/
- cjbprime 8y agoIf I recall, some friends signed up with Dante and sent in their sample more than six months ago and never heard anything more..
- akvadrako 8y agoThis should really be the top comment, and it's amazing that after 6 hours it isn't. Who cares about privacy if the whole thing is a simple scam?
- mnw21cam 8y agoWhile I agree that this is slightly worrying, in mitigation they are using BGI for the sequencing, and BGI are known to be extraordinarily busy right now. Our lab sent off 150 genomes to be sequenced by them, and they delayed by quite a few months. Hopefully that should be sorted out soon. The data we got back was very good quality.
- ololobus 8y agoThere is also some feedback in the Reddit thread [1] and it is mixed, though someone claims, that got full refund. [1] https://www.reddit.com/r/promethease/comments/9866da/dante_labs_took_my_havent_received_any_data_back/ https://www.reddit.com/r/promethease/comments/9866da/dante_l...
- nikolay 8y agoI passed the 10-week mark and still nothing. If I don't get my data in 2 more weeks, I'm contacting Amazon and FTC.
- Sgt_Apone 8y agoTheir ad copy is also riddled with errors. It's not exactly confidence inspiring. >Receive actionable insights based on solid genetic and clinical evidence for your and your doctor.
- sparkzilla 8y agoAs long as the A, C, G and Ts are in the right order.
- relyks 8y agoHas anyone used this service? The only reliable service I know of is Veritas. I never heard of this before its mention on HN right now
- toomuchtodo 8y agoI cannot speak for Dante, but I have used Veritas for whole genome sequencing and only have good things to say about them.
- eudora 8y agoDid you learn anything useful? (I'm not asking the specifics of what you learnt, but say... Is it helpful to know disease related info? Ancestry? Etc)
- toomuchtodo 8y agoI didn't dive into the data. I provided it to researchers, along with my medical records, as part of Harvard's Personal Genome Project.
- kelleyk 8y agoThere may be nice things to say about Veritas, but they charge an extra $99 for VCF files, and the actual raw data (FASTQ/BAM) is not available at any price (to you; Veritas has it). This is after you've paid $1,000 for sequencing.
- berberous 8y agoWhat does VCF lack vs FASTQ/BAM?
- klmr 8y agoVCF only contains variant information; FASTQ and BAM contain the “raw” sequencing information (in reality that data is already heavily processed but it’s the starting point for all usual analysis). Depending on how you do the analysis, the variant data will be slightly different. There are some current baselines (so-called “best practice” workflows) for performing the analysis but many of the details are variable, and subject to much current research. To be fair, for most things the VCF is completely sufficient (and in fact most people won’t care even about that). It just feels cooler to be in control of the raw data (and personally if I end up using a sequencing service, I would want to perform my analysis; but this is obviously irrelevant for 99.99% of users).
- totololo 8y agoTempting, no shipping fee from Singapore. Anyone recommends?
- 14 8y agoI would have thought this day and age a DNA sequencing company would have a big splash about privacy on their main page. I didn't see it.
- Joakal 8y agoIf they have a copy of your data, no matter how many privacy promises, your data could still end up sold/leaked/etc or even stored accidentally and still leaked. What we need is independent devices that don't call home. But that's not profitable.
- tempestn 8y agoYeah, it's probably wise to have them delete your data after you download it.
- Joakal 8y agoWise, how? Even if they promised that they deleted it, it might show in logs somewhere, out of your control.
- tempestn 8y agoWhat might show in logs, your full VCF file? Regardless, it wouldn't be out of your control. Their FAQ states they're GDPR compliant, which means they're obligated to completely remove your data on request, including from things like logs and backups. Sure, you could say they might make a mistake and keep it anyway, but they would be opening themselves up to large fines. And given that they explicitly mention their GDPR compliance, presumably they have given it some thought.
- CptFribble 8y agoAs others have said, the real issue is how they get all the way down to $200. Sale of personal info? Maybe when we get a clear answer, I'll consider checking my genome. But not before.
- 88e282102ae2e5b 8y agoThis is a huge red flag for me. Maybe if you made your own bootleg flow cells and reagents? But even that seems like a stretch.
- CptFribble 8y agoDIY microfluidics is possible with shrinky-dinks circa 2014; but for-real genomics is a little harder TBH
- 88e282102ae2e5b 8y agoIs there anything more to it than carving a piece of silica and ligating the adapters to the surface? I mean, I know the process is a bit more involved than that but the patents make it seem relatively straightforward.
- CptFribble 8y agoIt's straightforward in a conceptual sense, but as with most things there are a ton of gotchas and fiddly implementation details, especially if you're doing it in your kitchen/garage. A lot of the difficulty comes with the tedium of maintaining sterile conditions and lots and lots of pipetting. If you're really interested in DIYBIO there are subreddits and many tuts out there, but fair warning: getting started is easy, but the devil is in the details a heck of a lot more than learning to code.
- klmr 8y agoThey’re not. They are using BGI’s MGISEQ2000 machines. They simply sell the sequencing at a price that doesn’t cover its cost. Both because this is a promotion and because they retain the rights to using your genomic data in research: it’s simply a cheap way for them to get samples.
- throwaway487548 8y agoAnd the rate of errors is..? The same genome sequenced two times - how many differences between two sequences? Please, don't tell me it is none.
- heartles 8y agoThe sample file they provide lists 12 errors, so likely at least that. https://s3.amazonaws.com/dantelabswebsite/Dante+Labs+Genome+Overview+Sample+Report.zip https://s3.amazonaws.com/dantelabswebsite/Dante+Labs+Genome+... EDIT: Unless I'm reading the results wrong
- gravelc 8y agoHas anyone ever claimed it's none? There's no simple answer to your question as it depends on many things - sequencing technology used, library prep and coverage to name a few. Generally, it's not far from none when aligning short reads to a high-quality reference genome. Provided there's sufficient coverage and a majority of reads covering a particular nucleotide don't have a error at that position, than the correct answer will be given. Errors creep in due to things like systemic errors in library prep (such as a PCR error), and very low coverage over particular loci due to weird AT/GC content, meaning errors are harder to correct for. Repetitive regions can cause issues for short read alignment too, but coding regions generally aren't that repetitive. $200 is very cheap for WGS - guessing it would be at the low end of the accuracy range, as they can't be sequencing to great depth (presumably).
- klmr 8y agoThey sequence at 30x using BGI technology. Meaning: They provide the current offer at a loss.
- legulere 8y agoThe genes don’t even have to be the same when you have two samples from a person: https://www.sciencedaily.com/releases/2009/07/090715131449.htm https://www.sciencedaily.com/releases/2009/07/090715131449.h...
- tonyoconnell 8y agoNebula Genomics https://nebula.org https://nebula.org analyses your whole genome for $99 or free. They store your DNA in a blockchain and you can decide and track who you share your data with.
- berberous 8y agoNebula only offers 1x coverage. As a comparison, most other companies (such as Veritas), offer 30x coverage. I do not know what that means practically, but if anyone has expertise, would love to hear if that matters. The reason I don’t just assume 1x is much worse is George Church is involved in both Nebula and Veritas, and I get the sense he wouldn’t be involved in something if it was worthless.
- gravelc 8y agoIt matters a lot - any error in a read cannot be corrected for if it's the only read covering a loci. Coverage is also uneven; an average of 1x would mean a significant portion of the genome has no coverage. Even 30x would leave gaps (not sure how many as don't work with humans).
- cure 8y ago> Even 30x would leave gaps Correct - the coverage number is an average across the sequenced parts of the genome. In some areas the coverage will be much higher, in others much lower. Importantly, what is commonly called 'whole genome sequencing' is not really that. There remains ~5-8% of the genome that is (almost) impossible to sequence with current technology, and as such has no coverage. Areas with lots of repeats, centromeres, etc.
- tonyoconnell 8y agoNebula uses 30X coverage for the free-with-sharing service. However, the $99 sequencing is about 0.4X.
- esyir 8y ago
- thedailymail 8y agoSave $200. Keep your genome to yourself. You won't regret it.
- busterarm 8y agoIn the future you're (rightfully) afraid of, people will either collect your DNA from you without consent or as a condition of service. It's most unfortunate.
- davchana 8y agoSome countries like Bahrain or others collect it for residents, & few others might be thinking about the same for tourists too.
- whatshisface 8y agoThat happens in one of the futures we're trying to avoid. In the rest it's just a bunch of opportunistic bad actors. Today there are a few heavy-handed government issues but the vast majority of the problems we face day to day are a result of smaller players who behave badly. So while it's always nice to secure against a joint CIA/NSA attack, if you can't then it's still OK to secure against identity theft.
- nosuchthing 8y agohttp://deweyhagborg.com/projects/stranger-visions http://deweyhagborg.com/projects/stranger-visions https://vimeo.com/257272785 https://vimeo.com/257272785 In Stranger Visions I collected hairs, chewed up gum, and cigarette butts from the streets, public bathrooms and waiting rooms of New York City. I extracted DNA from them and analyzed it to computationally generate 3d printed life size full color portraits representing what those individuals might look like, based on genomic research. Working with the traces strangers unwittingly left behind, the project was meant to call attention to the developing technology of forensic DNA phenotyping, the potential for a culture of biological surveillance, and the impulse towards genetic determinism. The forecast of Stranger Visions came true. Just 2 years later Parabon NanoLabs launched a service they called DNA "snapshot" to police around the US. For more examples see Identitas and read about their collaboration with the Toronto police. http://www.identitascorp.com/ http://www.identitascorp.com/ http://www.theverge.com/2014/7/20/5916661/the-most-advanced-police-sketch-ever-might-solve-cold-cases http://www.theverge.com/2014/7/20/5916661/the-most-advanced-...
- frankacter 8y agoCompared to services like 23andMe, how much more informational or actionable would a whole genome sequence be in comparison?
- aerodog 8y agoexactly - how is this news-worthy now?
- mnw21cam 8y agoThe genotyping technology used by 23andMe and similar efforts is a genotyping array chip. These are only capable of detecting common variants. This is great for calculating ethnicity and common traits, and even maybe some moderately rare conditions (such as the most common BRCA1 variants), but is completely incapable of detecting variants that cause rare conditions. Rare conditions can only be caused by rare variants. Whole genome sequencing can detect most of these rare variants.
- rdlecler1 8y agoThey cite hemochromatosis in the second user story— My father is homozygous, and 23andme told me I wasn’t. Is this going to be that much more helpful (at least in the next 5-10 years).
- crankylinuxuser 8y agoWith this in the works: https://www.forbes.com/sites/joshuacohen/2018/10/08/possible-removal-of-pre-existing-conditions-protections/#6b29946e50e8 https://www.forbes.com/sites/joshuacohen/2018/10/08/possible... Using any genomics is an 'admission' of preexisting condition as a genomic guilt. This $200 is proof you know what diseases you might contract, and this serves as information asymmetry that insurance companies have illegalized. If I could have this done, say, in Russia or China, and the results destroyed after completed, I'd consider it. I know that half of my genetic map has already been infiltrated with my mom using 23andme. I felt quite violated when my mom did that. I certainly had no choice. And yet, half of me is sitting in some database, where I have absolutely no say. And my dad's dead, so no non-degraded DNA there. I guess if my sister ever has the money and want, then more of my map will be known.
- nikolay 8y agoSorry to be so direct, but who cares about your DNA? People are so full of themselves thinking they are something unique and of great value. In fact, everything valuable in us is our brains - experiences and knowledge. Plus, don't worry so much about your mom and her 23andMe - that's not sequencing, it's just a test for a list of snips (SNPs).
- i_phish_cats 8y agoDo we get the FASTQ files?
- tempestn 8y agoFrom their faq: VCF files (the most effective and easy-to-use format) are easily downloadable from your account. FASTQ and BAM files are sent via a 500 GB Hard Disk. To order the Hard Disk, click here
- deleted 8y ago[deleted]
- Gatsky 8y agoInteresting to think about how you can ensure your anonymity and still take advantage of a cheap genome!! Some preliminary ideas: - misidentify yourself (eg get a few friends and submit each other's samples) - mix your DNA with a mammalian organism (something like a mouse). It will get flagged as a bad sample by them probably, due to poor alignment metrics and too many variants, but with the knowledge of which DNA you put in you can do a dual alignment to eg. the mouse and human genome and purify the reads that came from you (there are published methods to do this kind of thing). Not sure how you would get an equimolar mix of mouse and your own DNA, but for $200 you could submit multiple ratios I guess. - enzymatically modify your DNA. There are some enzymes which cause characteristic mutations. They will turn up as real variants in their pipeline, but you can use the sequence context to filter them out. Kind of like chemical code obfuscation. This would mean extracting your own DNA and treating it, probably not that feasible.
- nosuchthing 8y agoThis project was made exactly for what you’re describing: http://biononymous.me/ http://biononymous.me/
- Gatsky 8y agoInteresting. To be honest, if someone is able to collect intact tissue from you without your knowledge, there is no way to hide. If you can control the donation then it is different.
- deytempo 8y ago1) yes 2) no 3) no The first one is the best because if enough people did it, it would create enough doubt in the accuracy of the stored datasets that they wouldn’t be worth anything to anyone except the person who owns the DNA. The problem is, as this becomes more popular more people related to you are going to get it done, meaning they will be able to automatically fit you into an identity based on who else had it done, their known identities and just the similarities between their DNA and yours. Trying to maintain anonymity only works if the data set is small. It looks like there is a market for a completely discrete secure dna sequencing company that doesn’t keep a copy of your genome after the fact and sends you a copy that is encrypted. Also it might be feasible to have some kind of kit that divides up the chromosomes into groups to be sent to different labs. It can’t be that difficult and expensive to do this. Why not just wait until there is a kit you can buy to do it directly from your PC if you are concerned with privacy?
- j7ake 8y agowill the sequence be availabe to the user so they can analyze it themselves? e.g. fastq format
- stormbrew 8y agoOut of curiosity, does "whole genome sequencing" include karyotyping?
- folli 8y agoYou can usually infer chromosome copy numbers from the median coverage rate.
- WhiteSage 8y agoFrom a saliva sample? How are they going to tell the bacterial DNA apart?
- ghkbrew 8y agoIt's pretty easy to tell human DNA from bacterial DNA. For one thing bacteria have small circular genomes versus huge linear chromosomes. More importantly individual sequencing for humans is heavily assisted by aligning reads to a known genome so any sequences which don't resemble known human DNA will probably be discarded. I cant speak to whether they are actually sequencing samples, but it'd be a pretty blatant lie if they're not.
- Sammi 8y agoYou basically take all the dna in the sample and chop it all into small pieces and all of these small pieces are read into computer memory, and then an algorithm goes through them all and merges the pieces that fit together back together into the original long form of the dna. Only pieces that have overlaps with each other will merge together, and there are many redundancies, so if any pieces accidentally fit together that aren't actually supposed to, then they are discarded, because this won't happen nearly as often as the real merge. So maybe a bunch of human dna gets mixed up with bacterial dna - I dunno really - but it really doesn't matter because of the way they put back together.
- puzzlingcaptcha 8y agoThe two basic ways to deal with bacterial contamination in NGS sequencing is to minimize it during extraction (e.g. extracting DNA from isolated nuclei, which bacteria do not have) and to clean up the raw reads by comparing them to known microbial sequences (e.g. with http://deconseq.sourceforge.net/ http://deconseq.sourceforge.net/ ) Considering they offer the raw data on a 500GB hard drive in a FASTAQ format (https://us.dantelabs.com/pages/faq https://us.dantelabs.com/pages/faq), I doubt it's just SNPs.
- WhiteSage 8y ago
- Kiro 8y agoIs this only for the US? Even if what people say is true I'm willing to sell my data if I get this large of a discount.
- mnw21cam 8y agoAccording to the web site, it is global. The price quoted for Europe is 169 euros.
- aj_g 8y agoI have been recently considering getting my genome sequenced. It seems like, if one of my main priorities in my life is longevity, this would be one of the most cost-effective ways to find out what factors are likely to influence that, and change my behavior based on the results. $1000 seems steep, but if you think about it over the course of a whole life, it's not so bad...thoughts?
- mikekchar 8y agoI think my biggest thought would be, assuming you had your genome sequenced, what could you do with it? I can think of a lot of theoretical things, but I think every inspection of that genome for something would cost money (possibly/probably more than the cost of sequencing). I may be wrong about that, though.
- jonasmst 8y agoYou can quite easily do stuff like mutation calling and differential gene expression analysis with subsequent gene set enrichment analysis for free on a standard computer. You'd need to know what you're doing of course, but in terms of costs, it's definitely manageable. That's if they provide you the raw data, though, which doesn't seem to be the case with a lot of providers.
- rzr999 8y agoWhich one was the Finnish company doing sequencing?
- nikolay 8y agoThese guys seem and act like a pyramid as pretty much nobody has received their DNA data. They don't have much info about the company. Even if people get data, the huge delay justifies my suspicion - the new victims pay for the difference, and this will run until there are no more stupid people who are willing to pay Dante Labs despite all the negative reviews.
- new299 8y agoThere seem to be quite a few reviews showing people who received their data (with significant delay). More worry is that they sent out used kits to a number of customers! https://www.cnbc.com/2018/06/15/dante-labs-dna-testing-company-sent-used-kits-to-some-customers.html https://www.cnbc.com/2018/06/15/dante-labs-dna-testing-compa...
- yayana 8y agoNothing about many delayed reviews is inconsistent with a pyramid scheme.. The first 1/10 or 1/100 of customers might be a lot of people. But would reviewers detect if the results were not really theirs and just from someone that matched on a few data points either from their forms or from a cheaper test?
- deleted 8y ago[deleted]
- thecatspaw 8y agoI guess only if they were really neglectful, e.g. giving a asian guy the dna of a caucasian man
- nikolay 8y agoI posted a review on Amazon, which got removed. I said that I'm going to compare my Genos exome to what they give me.
- nikolay 8y ago
- amelius 8y agoNote that for $1000 you can buy a NanoPore DNA sequencing device [1]. [1] https://nanoporetech.com/applications/dna-nanopore-sequencing https://nanoporetech.com/applications/dna-nanopore-sequencin...
- fatboy93 8y agoWhile I agree with you on that, obtaining the required kits that the sequencer needs is another headache altogether. The reads lengths might be fascinating with Nick Loman's group reporting upto an Mb in size. But the error rates as well matter. Unfortunately nanopore errors are not easily mitigable, whereas PacBio's are. The one place where nanopore has them beat is the sheer portability and ready run time. Strains involved in 2015 ebola outbreak were being sequenced real time!
- graeme 8y agoWhat kind of competence is required to get a report out of this that the user or their doctor can understand?
- deleted 8y ago[deleted]
- new299 8y agoError rates are currently very high, and from a single run it doesn’t seem like you’d get a 1x coverage Genome, let alone 30x (which is what this service is claiming).
- sailfast 8y agoAnyone have an Explain like i’m Five version of why one would get their genome sequenced? What benefits to me as a consumer would I get in terms of things identified, etc. Maybe if I’m asking the question I’m not ready for the answer? Haha
- rossdavidh 8y agoTLDR is that there is no compelling reason, if you don't find the concept interesting from a scientific curiousity standpoint. It is likely that someday the information will be useful, but right now it is mostly more of a luxury/curiousity thing. Having your full genome would allow you to (in theory) look up if any upcoming discoveries about the impact of various genes, applies to you. But if you're not wanting to dive deeply into genetics out of personal curiousity, I don't think there's any reason to do this (right now).
- sailfast 8y agoThanks this is supremely helpful!
- sonofgod 8y agoIf some of your family have inheritable diseases, you could find out if you have them or if your children could have them. Finding out that you will suffer from a nasty disease in the future could be quite a shock, though. People also spend money on things like handwriting analysis, personality questionnaires and measuring people's skulls to try to work out what they are like; genomics is at least somewhat accurate and based on reality! In practice, you'll get told things like "You have endurance muscles, not fast muscles" and "You probably have blue eyes" (mirrors are more accurate!) and "You have twice the chance of getting this specific type of cancer" (twice a very small number is still a very small number).
- andreadantelabs 8y agoHello, Andrea from Dante Labs here. I am confused why you think it is a pyramid scheme. We have had delays in the past and even other issues and we have worked with every single user to solve issues, providing customized reports free of charge