10 ms·
The genomic era arrives, and this time is probably real
- patates 10y agoIt feels like many of us were so excited about the automation scenarios, we may have missed what the significance of the latest developments in machine-learning (both algorithmic and hardware-based) would have in other fields - or maybe it's just me.
- melling 10y agoI disagree but it's a digression. How about we discuss the article? Update: Please ignore my comment. The original post was changed and my upvotes have turned to downvotes. Now I can't delete this comment.
- patates 10y agoArticle starts with discussing how recent improvements in computing led to the start of the expected discoveries in genetics. I don't understand how my comment is unrelated?
- melling 10y agoYou changed your comment. Where is the remark about the singularity? The entire meaning of your comment has changed.
- patates 10y agoI changed "path to singularity" to "automation scenarios" and "IT people and target audience of HN" to "many of us" to make it more clear. I'm very sorry if you think it meant something else with those words, I'm not a native English speaker.
- melling 10y agoWhat are "automation scenarios"? Saying people on HN discuss the singularity too often vs "automation scenarios" is going from a specific idea to a vague idea. English is my first language and I would never say "automation scenarios"
- patates 10y agoProgramming is mainly about automation and I mean "automation scenarios" as the general concepts we work on. Improving automation is a path towards "singularity" (in this case that meaning not AI world domination, but nothing to do left for humanity as everything is being done automatically) with a nice feedback loop. Many people here, including me, naturally obsess over the parts that are directly relevant to our jobs and not think too much about the possible effect on other industries. Hope it is clear now :)
- tosseraccount 10y agoThe National Human Genome Research Institute keeps an up to date website on the costs of sequencing: https://www.genome.gov/27541954/dna-sequencing-costs/ https://www.genome.gov/27541954/dna-sequencing-costs/ Their "cost per genome" image suggests the $1000 genome : https://www.genome.gov/images/content/costpergenome2015_4.jpg https://www.genome.gov/images/content/costpergenome2015_4.jp... . The costs of assaying a genome has dropped from $100 million to $1 thousand. Identifying correlations with clinical metadata, understanding the post translational interactions and understanding the full roles of proteins and other molecules remains an intimidating and difficult job.
- grey-area 10y agoPeople are working hard on using the data now though. This sort of thing takes time but we now have the tools to do it. http://www.genomicsengland.co.uk/the-100000-genomes-project/ http://www.genomicsengland.co.uk/the-100000-genomes-project/
- themartorana 10y ago$1000 is a drop in the bucket of a normal hospital bill or lifelong drug prescription for advanced/debilitating/catastrophic diseases. Edit: I realize it's a small part, but it's the first step, and it's already relatively inexpensive, which is a good sign.
- mbreese 10y agoThe $1000 is also minor compared to the computational and personnel costs required to interpret a clinical genome. It's almost cheaper to re-sequence a genome than store the raw data long term. And the interpretation of the genome usually requires a multi-disciplinary team with advanced degrees (MS/PhD/MD). That part of the problem is still largely a manual process, and will be for the foreseeable future. I'm not saying that it's not worth it in some cases, but the sequencing is only a small part of the overall costs.
- tosseraccount 10y ago
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- bognition 10y agoI kind of hate articles like this. They feed into the myth that single event cause revolutionary changes in the way the world works, when it reality its thousands of evolutionary events that cause change. I'm not trying to belittle recent advances in genomics, on the contrary I believe that cheap sequencing and technologies like CRISPR are going to change the world. However, its the insinuation that the last 20+ years of hard work were a fraud that upsets me. We wouldn't be were we are now without the last 20 years of genomics research. /rant
- swalsh 10y agoThe article kind of says that though, the very beginning of the article explains how it was assumed that after we sequenced a genome, we'd make fast progress. However what's actually starting to make a difference is the sequencing of greater number of genomes (more data), and the improvement of our filtering (identification and algorithms). Basically, the big difference is a lot of hardwork, and refinement. There's not actually any mention of a single breakthrough discovery.
- ThePaco 10y agoI think I get where the rant is coming from though. Even though the article isn't talking about a single discovery, it's more the idea that the world will turn one day and it will suddenly be the age of
- nextos 10y agoI think it's not only about genomes. Actually, cells have a lot of state. See [1] for a basic, slightly old, CS-biased explanation. That's how a single genome yields an incredibly varied repertoire of cell types. We need to work a lot on understanding those epigenomes to then get a chance to pinpoint genetic causes of disease. [1] http://ds9a.nl/amazing-dna/ http://ds9a.nl/amazing-dna/
- dipnuggetron 10y agoSick Theranos burn.
- fitzwatermellow 10y agoI'd like to see the cost of bioinformatics cloud computing come down by several orders of magnitude as well. The ideal scenario seems to be a global network of in-field mobile clinical units that can collect samples, run diagnostic tests and sequence genome data. Then upload that collected real time data to public data stores on AWS S3 or Google Cloud Genomics. Which a team of researchers can then access from their own labs around the world.
- jackcosgrove 10y agoGenomic data needs very strong privacy controls. HIPAA would probably prohibit making entire genomes public without patient consent, even if they have been de-identified. Just sequencing a fraction of the patient's genome subsequently could make identifying the entire public genome easy.
- tosseraccount 10y agoNot all countries have HIPAA style privacy restrictions. Public whole genomes are available.
- gumberculese 10y agoHere are 1000 whole genomes: http://www.1000genomes.org/ http://www.1000genomes.org/ The VCF files are reasonably formatted, the raw sequencing data is in the FASTQs, which are huge and hard to deal with. Go nuts!
- jackcosgrove 10y agoThe About page says, "The 1000 Genomes Project developed guidelines on ethical considerations for investigators doing sampling, outlined in the Informed Consent Background Document and the Informed Consent Form Template. All collections included in the Project followed these ethical guidelines and model informed consent language." Here is the consent template: http://www.1000genomes.org/sites/1000genomes.org/files/docs/Informed%20Consent%20Form%20Template.pdf http://www.1000genomes.org/sites/1000genomes.org/files/docs/... The post I responded to sounded like the genomic data would be uploaded without consent to a giant public database. Even with consent the greater concern is that employers, medical providers, national health services, and health insurance companies could, by sequencing part of your genome, match it to a public database identifying you and your entire genome. This could then be used to raise prices, deny health care, or deny employment. De-identification is not enough if the material is indicative enough that efforts to re-identify it can succeed. Kudos to those advancing science by making their genomes public, but it's a risk I would not take.
- astazangasta 10y agoIt's laughable that they led with the genetic cause for schizophrenia which (a) probably doesn't exist and (b) wasn't found a few months ago; they found a weak statistical association across a large number of variants that explains < 3.5% of the variability in disease susceptibility. What this demonstrates is what we've learned over and over across the past decade with association studies: yes, we're a product of our genes, and variation affects us, but no, common diseases are probably not mostly driven by genetics. For me, the big story in genomics over the past few years is one of massive failure. We spent a lot of time and effort sequencing tumors in the hopes that the genetics would tell us something interesting and lead to cures. It did not. We now have a relatively complete cabinet of the major variants that drive tumors. Most of these variants we already knew about before we did these genomics studies (through older sequencing methods from decades prior), and most of what we learned tells us nothing new. Genetics is at this point mostly garbage information. Why? Because we don't know what it means. We still don't understand gene expression, we don't understand signal transduction, and we can't understand the effects of mutations without painstaking characterization. All of these things mean our sudden wealth of knowledge of genetic variation tells us fuck-all about biology.
- toufka 10y agoWhat? This is so very wrongheaded. We learned quickly that 'cancer' is to the twentieth century 'the fevers'. We learned there are many reasons and causes for the catch-all, 'cancer'. Some we now know how to cure effectively. Some we now now how to prevent, effectively. Some we now know what to do to cure, but don't have good tools yet. And many we still do not understand. That is a significant improvement in a very short time span. But there's a LOT more to learn than 'how to cure cancer'. We very clearly understand gene expression and signal transaction to a first order, and have bits of the second order down too. There might be more - but that doesn't make that first order inneffective or wrong. There's lots you can do with a first order understanding - see what Newtonian physics did for the world - it was correct only to the first order. The idea that we know 'fuck-all' about biology because of dna sequencing is just ridiculous. The ability to read and write dna is fueling one of the fastest growing segments of human progress today.
- sickbeard 10y agoif you don't know if it's real how can you claimed it has arrived?
- amelius 10y agoI'm still looking for a way to have my genome sequenced (SNP analysis), while staying anonymous.
- kyberias 10y agoWhile 23andme's terms dictate that you should use your own identity, in practice you could circumvent that by asking your friend to provide the info and credit card payment. Preferably same sex.
- adenadel 10y agoThis is nitpicky, but 23andme doesn't do whole genome sequencing. They use a genotyping SNP chip that interrogates about 500k individual bases (and imputes other positions) rather than sequencing the 2x3B base pairs in the whole genome.
- kyberias 10y agoWhy do you tell me this? Look what the OP asked.
- damurdock 10y agoI would recommend talking to a local genetic counselor. They may be able to find a genomics core that will fit your needs, and they will be able to help you interpret that data in a medically relevant way.
- iandanforth 10y agoI was under the impression that modern genomics had moved away from the "gender variants are what matters" mindset. Hasn't greater understanding of the proteom and the influence of the environment massively complicated this already daunting task?
- savemylife 10y agoI hope it brings with it some advances in diagnostics. I have some kind of autoimmune condition (I think) that has resisted a proper diagnosis for over 2 decades. Whatever it is, I lost my livelihood to it, and now I stand to lose my savings as well. Since I have no diagnosis I can't even apply for social security benefits, much less hope to return to work (I used to write code pretty successfully).
- berntb 10y agoI assume you have checked for allergies/intolerances (e.g. just vegetables for two weeks and changing the physical environment around)? I had effects for most of a week from my intolerances (nuts, peanuts and others), so I never really understood that I had them -- I got some allergen in me more often by pure chance. The biggest effect for me was relatively mild compared to you -- sugar/caffeine overuse to stay awake and depression. These days, my cheerful disposition would have really irritated the old me. :-)
- monknomo 10y agoI read that as the "The gnomic era arrives" which seemed pretty reasonable o me.
- aclimatt 10y agoIf you're interested in genomics, you should take a look at the pharmacogenomics knowledgebase from Stanford: http://www.pharmgkb.org/ http://www.pharmgkb.org/ It is a comprehensive database of dosing guidelines, drug labels, and annotations for thousands of combinations of genes, variants, drugs, and diseases. (We're actually helping them with a redesign, and if you'd like to be a beta tester, contact me.)
- sjg007 10y agoI think we are in the genomic platform era.
- krschultz 10y agoI would highly recommend the book 'The Emperor of All Maladies'. When you read a detailed account of the fight against cancer two things become clear. First, we had no idea what we were doing for a very long time. Second, the era of actually fighting some of these more complicated diseases is upon us. We have been trying to stop cancer for nearly 100 years but only in the last 15-20 have we actually been making any progress. It's a well written book and makes me quite hopeful for the future.
- dredmorbius 10y agoThere's very little meat to support the subhead's assertion. In Robert Gordon's The Rise and Fall of American Growth, a great deal of attention is focused profitably on the changes and progress in medicine and health outcomes from 1870 to present. Most notably, Gordon divides the period at 1950, noting that life expectencies improves 2x more before 1950 than afterward (and from my own explorations, far more prior to 1920 than after). There's been exceedingly little progress in medicine since 1970, at which point major cancer, heart disease, and virtually all infectuous disease treatments existed. We've seen many more treatments and more so imaging and diagnostic capabilities since ... but virtually no changes in outcomes. Healthcare is a land of very, very, very rapidly diminishing returns, and for which shoring up treatment and preventive care for the most under-served pays hugely greater dividends than highly invasive or heroic treatments at the top end. Much of the progress in health outcomes since 1970 appears to be in minority populations -- that is, the under-served. Gordon's book was published this year, its information is quite current. I see little reason to suspect massive improvements in actual outcomes -- impacts rather than change -- in the nine months or so since it was put to bed.
- hackuser 10y agoThis is broadly false; outcomes have in fact improved greatly in very many fields. Off the top of my head: Far more people surive heart disease and heart attacks; AIDS didn't even exist in 1970.
- dredmorbius 10y agoGordon's metric generally is QALYs. Yours?
- semi-extrinsic 10y agoI'm only half agreeing with you. Yes, improvements in medicine before 1920 were dramatic. Antibiotics and vaccines work wonders, making once-deadly diseases benign (e.g. pneumonia) or eradicated (e.g. smallpox). But more recent improvements in healtcare aren't just trivial stuff either. The five-year survival rates for childhood leukemia, for instance, have been on a steady increase from 40% to 80% since 1970. Recent monoclonal antibody therapies against inflammation/autoimmune diseases have provided actually revolutionary changes in the health situation of many. Going from chronic pain and having a hard time functioning at school/work, to living a relatively normal life, is a huge thing. But it's not captured by life expectancies.