[HN Gopher] 30 years since the Human Genome Project began - what...
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30 years since the Human Genome Project began - what's next?
Author : oedmarap
Score : 67 points
Date : 2021-01-04 12:12 UTC (10 hours ago)
(HTM) web link (www.wired.com)
(TXT) w3m dump (www.wired.com)
| suc_syn wrote:
| We need to leverage our current knowledge to deliver actionable
| results to regular people. Data generation is pretty reasonable
| from the standpoint of time and costs, data storage who owns it,
| has rights to it, and how to deliver incites from that data to
| regular providers (see family practitioners) that aren't deeply
| knowledgeable about genomics and their interpretation.
| bitwize wrote:
| > We need to leverage our current knowledge to deliver
| actionable results to regular people.
|
| Sure, Gavin Belson, what are our OKRs for that?
| cogman10 wrote:
| The problem to tackle, IMO, is medical privacy and intellectual
| property.
|
| We've created a system where the only sane way for a biomedical
| company to behave is to patent, copyright, and hide as much
| medical information as possible. Further, we've made it REALLY
| hard to share such medical data in the first place.
|
| Now, I get WHY we do this. There are a lot of good reasons
| (privacy and insurance issues come to the top of my mind).
| However, we should be working to eliminate those reasons as much
| as possible.
|
| What we need to advance human understanding of medicine is a
| national database of medical data that's publicly available.
|
| Ideally, We'd record every measurable aspect about a person in
| this database and update it throughout their lives (when did they
| get vaccinated? What allergies do they have? Did they get any
| cancers?)
|
| That sort of a database would make it really easy to start mining
| for treatments, correlations, etc. It'd even have some positive
| benefits like removing the need for every doctors visit giving
| you a form with 50000 questions you've answered a million times
| before.
|
| But I get why we don't do this. We don't do this for fear of
| police overly relying on genetic information to "prove" someone
| committed a crime (We found your DNA at the scene, you must be
| guilty). We don't do this out of fear of Insurance companies
| exploding their rates when any sort of marker comes up (Oh,
| you've got Gene XYZ that means you'll probably die sooner, so you
| get a higher rate or we won't insure you). We don't do this
| because of issues around discrimination (Oh, you have (had?) HIV?
| You must be gay and we hate gay people here).
|
| But, man, do I wish we could somehow shape society so some day we
| could do it. It'd have the potential for so much good.
| tejtm wrote:
| a glimmer.
|
| https://ncats.nih.gov/n3c/about
|
| As an optimist I like to think that this could be a wedge in a
| crack Covid exposed in our (US) collective medical/insurance
| dis-function.
|
| With dissimilar records harmonized across many institutions
| under the same roof and levels of access to the datasets for
| partners who did not "provide" records to the pool (you)
|
| we are testing the theory, my hope is before Covid is over the
| genie is out of the bottle and cant be stuffed back in for the
| profit of a few at the expense of many.
|
| But you folks reading this who are able to apply disparate
| strategies to reasoning over large complicated data sets...
| PLEASE DO !!!
| TedDoesntTalk wrote:
| Nice post, but what does that have to do with the Human Genome
| Project?
| tejtm wrote:
| The GP post highlights a "blocker" on where to go with the
| Human Genome Project ... integrating existing traditional
| data and "personalized medicine" i.e your genome at the scale
| of global statistical significance v.s entrenched interests
| and a history of bad behaviour by a few bad apples.
|
| fantastic rewards, fantastic risks, inevitable whether you
| work on it or not.
| cabaalis wrote:
| I know very little about this. Is it possible to get my sequence
| from one of the commercial groups doing this, and then "look it
| up" in a genome reference to verify my brown eyes, for example?
|
| I acknowledge the lack of knowledge leading to the question. But
| it would be neat if possible.
| emcq wrote:
| Shockingly the human genome itself has not been fully sequenced,
| despite the human genome project completing years ago [0]. There
| are difficult to map regions of the genome, some of which are
| interesting. Only recent advances in long read sequencers have
| helped to solve some of these issues [1].
|
| For the future to truly be amazing with one sequencing the lab
| prep, chemistry, and equipment required needs to advance. Oxford
| Nanopore has some advancements here [2] but it's still a ways to
| go before you could have a sample prepared as easily as an
| ultrasound or x-ray.
|
| [0] https://www.statnews.com/2017/06/20/human-genome-not-
| fully-s... [1] https://www.ecseq.com/support/ngs/are-there-
| regions-in-the-g... [2] http://nanoporetech.com/products/voltrax
| aroch wrote:
| The Telomere-to-Telomere consortium has made fantastic progress
| on this in the last year or two:
| https://genomeinformatics.github.io/CHM13v1/
|
| Thanks to them we now have a nearly completed genome, only
| missing the deconvoluted rDNA array segments (~12mb or so, we
| know the sequences since they're basically identical but no one
| has accurately placed the individual array variants yet).
| cma wrote:
| No mention of computed protein folding?
| patall wrote:
| That is because the article is about genomics. Not molecular
| biology in general.
| alextheparrot wrote:
| There was an interesting comment made on the recent "Bio Eats
| World" episode [0] that genetic tests are not aligned with health
| care reimbursement cycles.
|
| Jorge Conda [0] cited two reasons that genome sequencing
| (Different from 23andMe's GWAS, for example). First he cited the
| high upfront cost to buy the machines (Usually meaning you need
| to be a big hospital). The second fact was a bit more
| interesting, which is that doing one expensive test (Genome
| sequencing) which then your health care provider could do cheap
| queries against ("Which other users have your symptoms and
| similar mutations in key genes" for example) does not align with
| the current billing model.
|
| I think that's the "What's next". Finding a way to effectively
| bring genomic care to the general population, to allow for better
| research into genetic conditions. If you're interested in how
| "big" this can be, here's a case where "This American Life"
| covered how just a few genetic differences was the difference
| between an olympic athlete and a muscular dystrophy patient [2].
|
| There's also the bio-terrorism and pandemic response angle, which
| is why the DoD is investing in third-generation sequencing
| systems where portability has finally become more of a priority.
|
| [0] https://en.wikipedia.org/wiki/Knome [1] https://a16z.com/bio-
| eats-world-podcast/ (About 13 minutes in) [2]
| https://www.propublica.org/article/muscular-dystrophy-patien...
| jdale27 wrote:
| There are a handful of sequencing-based genetic tests that have
| achieved fairly wide penetration; NIPT and cancer panels are
| probably the best examples.
|
| However, if the question is why whole-genome sequencing has not
| gained wider clinical usage, I think the answer is less about
| reimbursement, and more the fact that there are just very few
| clinically compelling reasons to sequence a whole human genome.
|
| Then there is the fact that although we have ostensibly
| achieved the fabled "$1000 whole genome" that was touted as the
| tipping point for clinical acceptance, that was really more of
| a publicity stunt by Illumina. In reality a clinical-grade WGS
| still costs a multiple of $1000 (see, e.g., https://bmchealthse
| rvres.biomedcentral.com/articles/10.1186/...). The Moore's Law-
| like cost reductions of genome sequencing are a bit of a myth
| at the present time; in practice Illumina has a monopoly on the
| technology used for clinical WGS, and therefore they have a
| great deal of influence over the effective cost of sequencing.
| ramraj07 wrote:
| If I want to sequence my own genome are there any services
| that do it already today with any reliability?
| dekhn wrote:
| It's really unclear what's next for the HGP. While HGP and many
| other sequencing projects have been invaluable to academic
| research, and it's truly useful for a number of diseases, the
| main result of the HGP, in my mind, is that it made clear to
| everybody how much harder the genotype->phenotype problem was
| than what the geneticists who set up the HGP anticipated.
|
| Medically speaking, there isn't enough evidence to support the
| cost of doing WGS for individuals in most circumstances, or even
| storing large amounts of WGSs to do large-scale population-level
| analysis.
| hardtke wrote:
| One thing that surprisingly hasn't happened in the 30 years since
| the Human Genome Project is a Nobel Prize for the work. There are
| examples from large physics projects where the leaders were
| awarded the prize. Surely Francis Collins and perhaps Craig
| Venter are deserving.
| jdale27 wrote:
| Francis Collins and Craig Venter certainly got a lot of the
| publicity, but arguably there are others who were more
| influential. E.g. Leroy Hood who developed the first automated
| DNA sequencer, and Mike Hunkapiller who led the commercial
| development of the technology at Applied Biosystems to the
| point where it was practical to sequence the whole genome.
| Hunkapiller was also the impetus behind the formation of
| Celera, though Venter was its leader.
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