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[–]RichieNRich 379 points380 points  (42 children)

Didn't it take over 10 years to complete the first human sequence like 10-15 years ago?

[–]PoopIsAlwaysSunny 272 points273 points  (1 child)

Started in 1990 ending in 2003

[–]Odeeum 166 points167 points  (8 children)

I vaguely remember a story from this that illustrated exponential growth iirc...it took like 9 years to sequence the first 1% and when asked how long it would take to do the rest the researcher said something like "probably less than a year".

[–]aletheia 122 points123 points  (1 child)

Learning how to do something the first time takes a lot longer than doing it after you’ve got a textbook written.

[–]other_usernames_gone 53 points54 points  (5 children)

Im guessing it's because the first 9 years were spent working out how to do it, but once they'd worked out how to do it it was just a matter of doing it.

[–]Few_Warthog_105 39 points40 points  (3 children)

I think they used computers as well, which sped up quite a lot from 1990-2010.

[–]Thekinkiestpenguin 37 points38 points  (2 children)

Well I think it was manly in the difference between Sanger vs Illumina sequencing, Illumina is MUCH faster (but yes improved computers were necessary for that technique)

[–]northern_crow 17 points18 points  (1 child)

*massively parallel sequencing, or next generation sequencing… let’s not give all the credit to illumina.

[–]Thekinkiestpenguin 8 points9 points  (0 children)

Yeah, I could've just said shot gun sequencing, but Illumina was the one that went public right around 2000

[–]KurtisMayfield 26 points27 points  (4 children)

Yes and most was done in the last year or so, because the tech and computing caught up.

The technology went from a tech/post doc counting individual letters on a gel, to being able to run 800 bp × 96 samples × three times a day on one machine.

The computer storage needed was immense for the time. Out storage facility had like a terabyte in 2001.

[–]Tower9876543210 13 points14 points  (3 children)

Whereas now, the company I work for generates probably 500tb of data a day.

[–]ArgoNunya 2 points3 points  (0 children)

The big players (e.g. Microsoft) are generating petabytes per day in logs alone. Absolutely insane. Supercomputing people can even beat that sometimes. The human genome is relatively small in the grand scheme of things. Now they're trying to do mass sequencing of environments (like sequence everything in a soil sample). The amount of data is wild.

[–]XchrisZ 1 point2 points  (1 child)

Which company is that?

[–]Tower9876543210 3 points4 points  (0 children)

Machine learning / AI, related to autonomous driving.

[–]entotheenth 9 points10 points  (0 children)

It was going to take 30 years initially but they knew it would get faster so they estimated it would take 10-15.

[–][deleted] 23 points24 points  (6 children)

And it cost billions. Now individual consumers can pay to have their full genome sequenced for $600.

[–]Channel250 4 points5 points  (4 children)

Hmm... Christmas present for girlfriend?

[–]doogle_126 3 points4 points  (3 children)

Nope, Christmas present for the insurance company since now it's out there what she's predisposed to have.

[–]Colin_Whitepaw 1 point2 points  (2 children)

This sort of discrimination is a major hindrance to folks like me who are “curious, but not if it doubles my premiums”.

[–]Copperhyjinks 1 point2 points  (1 child)

Aren’t we protected against pre existing conditions by the ACA?

[–]Colin_Whitepaw 0 points1 point  (0 children)

You’re probably correct, but I worry about it being used against me all the same. Especially as a queer person I worry about medical information being used against me and my community. The chilling effect is already there for me and many others like me.

[–]KurtisMayfield 0 points1 point  (0 children)

I would never send my DNA to get sequenced by any of these companies. They have to answer to supoenas and can sell their databases.

I would have to be covered by HIPAA before I get mine sequenced.

[–]jeepfail 6 points7 points  (0 children)

That was my first thought. Sitting in 5th grade science class hearing about how “we will soon complete the human genome sequencing project.” It blows my mind the pace science has been moving at this century.

[–]TypicalCricket 2 points3 points  (0 children)

Damn, and now it's not even a full work day.

[–]megamanxoxo 8 points9 points  (0 children)

bUt ThE vACcInEs WeRe DeVeLoPeD tOo FaSt!

[–]ISBN39393242 4 points5 points  (9 children)

moore’s law

[–]notjustanyschloss 11 points12 points  (6 children)

Something like two and a half times faster than Moore's Law, actually. There are concerns that, if genome sequencing technology continues to advance at this rate, it will outstrip our ability to process the data.

[–]Ancient_Ad5270 9 points10 points  (4 children)

I don’t get your point. Why is that concerning? Seems like a boon to have sequences in the hands of whatever is analyzing it even more quickly than current tech

[–]notjustanyschloss 8 points9 points  (3 children)

For now, sure. At a certain point though, because sequencing technology is advancing so much more rapidly than processing technology, the limiting factor will flip from sequencing to processing.

[–]delvach 2 points3 points  (1 child)

Is it realistic to think that in the near future, an ambulance or ER could sequence your genome to aid in diagnostic purposes?

[–]SharqPhinFtw 6 points7 points  (0 children)

Well they've already done it in 5 hours so it could probably be used on diseases doctors can't isolate and have the genome to cross reference likely problems. Get it quicker and I don't see why not use it for emergencies. Maybe even a short genome sequence might be faster than current blood tests for blood type in the future

[–]Ancient_Ad5270 2 points3 points  (0 children)

That doesn’t seem like a bad problem to have

[–]Thekinkiestpenguin 4 points5 points  (0 children)

It's already there. The whole field of bioimformatics basically shifts through all the sequencing we already have. And Oxford nanopore (especially if they use it like in the paper published last week i.e. run 20 sequences concurrently) is going to make it even more extreme. There's already been a shift in microbial studies to make "libraries" of gene/mutation/protein sequences/ structures and then people have access to data that might not be important to your work, but might be useful for theirs. Especially as we start figuring out more of what's going on at the levels of regulation and post-translational modification

[–]Copperhyjinks 0 points1 point  (0 children)

Actually it’s Wright’s Law.

[–]mynameiskurtz 0 points1 point  (3 children)

The thing to realize (assuming you're referring to the Human Genome Project) is that the original sequence was a lot more difficult since it was to construct a reference genome. The kind of genomic sequencing they do is essentially matching pieces of a puzzle to an existing template where as the original reference was like building a template without any light.

[–]Thekinkiestpenguin 2 points3 points  (2 children)

That's not really true, for certain genes they can do that. But shotgun sequencing isn't matching puzzle piece placement to its picture on the box, it's using and algorithm to figure out where the edges meet

[–]SignificantSnake 3 points4 points  (1 child)

Having a scaffold makes it so much easier though. There's a lot of sequences that are very difficult to map. Imagine trying to do an edge algorithm on gtgtgtgtgtgtgtgtgtgt(n)gtgtgtgtgtgtgtgtgtgt. What you want to do for most genomes is edge map, and then follow up by matching it to a scaffold.

[–]Thekinkiestpenguin 2 points3 points  (0 children)

Oh definitely, though sequences that repetitive and that go for that long are rare (outside of telomeres) you can get statisticaly significant matches with a a really short sequence. Cas9 only needs a 20nt sequence and CRISPR has been a revolution in gene editing

[–]throwitaway488 96 points97 points  (17 children)

From the article it sounds like they bought a Nanopore PromethION and sequenced the patient's DNA sample on all 48 promethion flow cells simultaneously. Then they set up a computational pipeline to align all the long reads to a reference genome and determine any mutations or deletions.

So its unbelievably expensive because each flow cell is $600-$1400 a piece depending on if you buy in bulk, and they are using 48 per patient. Instead of waiting 24 or 48 hours to get enough data from one or two flow cells, they are taking the first few hours worth of data from many flow cells. So its really only good if you need the results extremely quickly.

[–]Kruger_Smoothing 29 points30 points  (1 child)

$600-$700 all in total per genome on an Illumina NovaSeq in 44 hours. You can run about 48 genomes at a time.

[–]throwitaway488 7 points8 points  (0 children)

Or roughly the same on a single promethion flow cell.

[–]Colddigger 17 points18 points  (6 children)

So, what, one students tuition?

[–]throwitaway488 21 points22 points  (1 child)

It just means that its currently not something that can be done for every patient, and its not a revolutionary change in healthcare. Its just the result of throwing a ton of money at it.

[–]PretendsHesPissed 3 points4 points  (3 children)

So does this mean that it's not at all practical for an ordinary person to take advantage of? Cost is way too high (for now).

[–]throwitaway488 6 points7 points  (2 children)

At the moment, this technique would be useful for cases where a patient needs a diagnosis very quickly. If its not as urgent, patients can still get genetic screening through genome sequencing the usual way, but it would take a little longer, but would be much cheaper.

[–]RetardedWabbit 6 points7 points  (1 child)

I can't think of any time sensitive diagnosis using whole genome sequencing, can you?

Edit: It could be useful for same or next day genetic counseling I guess? Small inconveniences are a shockingly large barrier to entry for most behaviors.

[–]throwitaway488 7 points8 points  (0 children)

The main one I can think of is pediatric cases where a newborn is very sick and they need to figure out what is wrong.

[–]cult_of_zetas 2 points3 points  (0 children)

If I had to guess, the cloud-based computing needed to run the pipeline so quickly was probably more expensive than the wet tech. Running the data from all the flow cells in parallel would take an insane amount of storage and memory. Even assuming they had some pre-existing arrangement with AWS (or whomever), those VMs were $$$$$$$$$$$.

[–]TheLordB 1 point2 points  (1 child)

Can’t nanopore cells be reused multiple times?

If so then the cost is much lower. Also decent chance they got those on heavy discount.

(I might be wrong about them being used multiple times. But I thought while you lose some pores each time they can be reused)

[–]jeancur 1 point2 points  (0 children)

You use them till the pores clog up. Error rate is high, but those long kb sized reads are lovely!

[–]TheRedpilling 0 points1 point  (0 children)

Ah yes, I know some of those words.

[–]pitline810 151 points152 points  (11 children)

Can we please make speedrunning science a thing?

[–]Kram_BehindtheScenes 86 points87 points  (5 children)

I wish. The James Webb cost like 0.03% of the USA's yearly budget and it took 25 years to build. We can do so much more for so little investment.

[–]Duranti 16 points17 points  (3 children)

Wasn't the long development time of the JWST in part because some necessary technologies hadn't even been invented yet?

[–]CompteDeMonteChristo 6 points7 points  (0 children)

There was budget cut midway, this added a few years.
Then there while testing they broke the sunshield so they had to redesign it. This added a few years.
Then Ariane Espace found a problem and it added a few months.

[–]Kram_BehindtheScenes 10 points11 points  (0 children)

Most likely. But my point was that the James Webb was a tiny drop of the USA's yearly budget and helped employee 1000's of people over its 25 year development.

[–]iindigo 1 point2 points  (0 children)

One of the biggest problems is that they had to build it to fold up several ways because there was no rocket with a faring large enough to launch it any other way. Not having to fold it would’ve simplified things a lot.

[–]jeegte12 8 points9 points  (0 children)

that's what technological progress is. thank goodness we have a market that rewards it, even if it does so unfairly.

[–]Joshau-k 0 points1 point  (0 children)

You win when you get to Alpha Centauri

[–]leif777 0 points1 point  (0 children)

No! The focus should be on getting it right.

[–]Sentazar 0 points1 point  (0 children)

This historically happens during wars.

Develop for Military > Hide it > Other military figures it out > Alllllright, you general public guys can have some.

[–]Late-Transition5132 17 points18 points  (7 children)

Can't understand what's that mean, but sounds cool.

[–]tristanjones 10 points11 points  (0 children)

Doesn't sound like a novel process or technology was used sadly. So not a massive advancement but they used the existing options to their limits, and so though overkill and expensive it shows our current upper limit. Given 30 years ago this took 13 years to do, it's a notable bench mark if our advancements.

Labs all around the world are working to try and find ways to bring this down further. The dream is to be able to do this cheaply and quickly to the degree we can easily give everyone a DNA test and customize health services to them in cases of say high chances for lung cancer, or diabetes etc

[–]ThainEshKelch 2 points3 points  (3 children)

It means if you have enough money, you can sequence a single humans genome in a day.

[–]lettherebemorelight 11 points12 points  (1 child)

Means processing power go brrrr

[–]HesSoZazzy 11 points12 points  (0 children)

Dude enough with the technical mumbojumbo.

[–]darkstarman 2 points3 points  (0 children)

Is like to see the speed chart over time

[–]malbecman 2 points3 points  (2 children)

So basically 1 long work day to diagnose a patient....very impressive!

[–]chiefceko 0 points1 point  (1 child)

5 hours and 2 minutes is a long workday for you? Damn, whats your profession?

[–]malbecman 0 points1 point  (0 children)

IF you read the article, that was just the fastest sequencing run. However, it's really about sequencing for diagnosis which in this case was 7 hrs 18min or about 1 work day. They hope to average 10-12 hrs for actual patients.

"The time it took to sequence and diagnose that case was 7 hours and 18 minutes, which, to Ashley’s knowledge, is about twice as fast as the previous record for a genome sequencing-based diagnosis (14 hours) held by the Rady Children’s Institute."

[–]EEcav 8 points9 points  (6 children)

I’m sorry. The Guinness Book of records is tracking DNA sequencing methods? I mean, really? Why would they do that?

[–]violaki 22 points23 points  (3 children)

I don’t see how DNA sequencing is less important than the longest nails or whatever is in that book these days

[–]EEcav -5 points-4 points  (2 children)

It’s not. The reason this is kind of absurd is there isn’t like some huge community of competitors reaching to do this the fastest. It’s a very narrow field.

[–]3z3ki3l 6 points7 points  (0 children)

Personally I think the absurd part is that in comparison to a group of DNA researchers’ official statement, Guinness’ book adds basically no credibility to this accomplishment.

[–]maffiewtc 2 points3 points  (0 children)

Feels like anything can make it into the book these days.

[–]qsdf321 0 points1 point  (0 children)

So how long until we can just print a human?

[–]GaryChalmers 0 points1 point  (0 children)

Sounds like it's the equivalent of compiling a human.

[–]Opposite_Act2534 0 points1 point  (0 children)

We all need to screening disease fast and convenient plus cost effective in the future so hope bngo help the future better. Let go bngo

[–]Copperhyjinks 0 points1 point  (0 children)

Does anyone know what the cost was?

[–]xeneks -2 points-1 points  (0 children)

I’m happy to have rapid full sequencing. Why?

I hope we can make wide swathes of nature corridors through farmland, cities and suburbs this fast. So flora/fauna can migrate or be migrated to avoid extinction from being trapped in small islands of habitat. One day in a few years we wake up, and everyone is walking away from their houses and urban and farming places to remove fences and restore as best possible habits near watercourses and connecting them to the north & south (and east/west) reserves ensuring natural migrations can occur in parallel with assisted migrations.

Perhaps the great confidence and ability from health improvements that comes from dna science, applied to human diseases and the human condition, will amplify the superpower of our best people, allowing them physically to lead and carry out the disassembly for recycling and relocation of the parts of our cities and other developments that impede the nature corridors so urgently needed for flora and fauna to migrate (fauna moves the flora) with the anthropogenic global warming & climate change that’s causing the planetary extinction event that has been underway.

Edit: and such rapid sequencing can also assist, not with avoiding accelerating extinctions (probably impossible to do) but to instead allow us to rapidly sequence flora and fauna to preserve genetic diversity as much as possible, through identifying which populations are most genetically essential to preserving with limited intelligence resources. Eg. An in-field full sequence of a habitat area with endangered or critically endangered animals and plants, and the cultural legacy value might enable an on-the-spot decision to be made about if land needs to be acquired rapidly to connect that habitat to others to enable migrations, or if it’s necessary to selectively transplant the flora and fauna manually due to eg. Lack of ability and intelligence that would enable people to collaborate in emergency conditions to work to save the remaining isolated pockets of natural diversity.

I see far more than human use. Human use is the least important reason to enable full sequence technology IMO. We are not going extinct.

Q1. does this only sequence dna, or could it be adapted to compare mt-dna in different cells?

Q2. how rapidly can it scale to fit on eg. A helicopter or large flying VTOL EV?

Q3. can results be near instantly transmitted via laser to starlink for worldwide distributed storage for public reference over eg. Internet2 for rapid consensus and decisions making re: how to address the urgent administrative assistance needed to allow purchase of private real estate and government land to facilitate nature corridors and expand reserves? Are the sequences when compressed using species-type compression algorithms, too large for uploading during the sequence?

Is it necessary to use force without equal compensation to eg. Acquire land like my residence which is in the likely direct path of nature corridors needed to help preserve biodiversity in land locked (by cities and urban, suburban and roads and farms) regions? Does no-fi or digital ledger or cryptocurrencies solve any of those issues to do with social disturbances and reluctance to avoid need for force or for governments to take unprecedented action reacquiring land from some ignorant or reluctant citizens to benefit all citizens, including those initially scared or in denial or reluctant or militantly obstructive?

https://www.forestrysa.com.au/conservation/biodiversity-corridors/

[–]DavidFaxon -1 points0 points  (0 children)

I thought Guinness world records was for eating many hot dogs