Hacker News Board Hacker News, browsed like a classic message board
Live data from Hacker News

No human genome has ever been completely sequenced

statnews.com

Post reply on HN
Print view View original

71–80 of 96 posts

Re: No human genome has ever been completely sequenced

#71

Post by daemonk »

iskander wrote: post #3

It's strange that this article ends as an advertisement for PacBio sequencing (which can ~50k-60k base reads) but makes no mention of Oxford Nanopore (which has gotten megabase reads and keeps improving). Single molecule nanopore sequencing is on track to sequence across the centromeres of human chromosomes in the next few years.

I've personally prep libraries and used nanopore. While there is a lot of promise to the technology, I found it to be too inconsistent. Nanopore claims they can get 10gigs of data, while power users claim they get 2-5gig on average. I consider myself lucky if I get 2gigs of data.

The non-random nature of their error profile is also a problem.

Re: No human genome has ever been completely sequenced

#72

Post by [deleted] »

Bromskloss wrote: post #46
nether wrote: post #27

Earlier quoted context omitted.

Side note: your comment is one of the few times I've seen the code tag used for actual code on HN, rather than quotations or just indentation.

Yeah, why does Hacker News not have a real way to indent things? It wouldn't make loading the page any less light-weight.

[deleted]

Re: No human genome has ever been completely sequenced

#74

Post by eradicatethots »

jessriedel wrote: post #6

As usual, the journalist spends many paragraphs painting a picture of human conflict before actually getting on to the interesting claim. > The reason for these gaps is that DNA sequencing machines don’t read genomes like humans read books, from the first word to the last. Instead, they first randomly chop up copies of the 23 pairs of chromosomes, which total some 3 billion “letters,” so the machines aren’t overwhelm…

They do that for the rest of their audience, for whom that is important motivating context, or just informational context. I think It’s a good approach to writing, and it’s he really awkward to their main readership otherwise.

There’s even evidence that this is true, for who knows their audience better than them? You, while making up a a portion of the audience, are not the main portion, or so it seems, unless they don’t understand their audience that well after all... although that seems pretty unlikely

Re: No human genome has ever been completely sequenced

#75

Post by x0x0 »

jessriedel wrote: post #6

As usual, the journalist spends many paragraphs painting a picture of human conflict before actually getting on to the interesting claim. > The reason for these gaps is that DNA sequencing machines don’t read genomes like humans read books, from the first word to the last. Instead, they first randomly chop up copies of the 23 pairs of chromosomes, which total some 3 billion “letters,” so the machines aren’t overwhelm…

I worked on a slab gell dna sequencer contemporaneous to the humane genome project. It's actually worse than described, because the dna isn't cut randomly. Instead, restriction nucleases cut the dna at certain fixed sequences. Of course you can use multiple restriction nucleases, either in the same (subject to their chemistry being compatible) run or over multiple runs. When everything went well, our tech allowed you to read 800-ish bp with good quality and perhaps up to 1.1k if you were willing to to get dodgy quality at the ends.

So you have two problems. The first is, you never read anything longer than say 1k bp ever. The second is say your nuclease cuts at GAATTC. You will have great difficulty counting runs of that sequence.

this is the technique https://en.wikipedia.org/wiki/Polyacrylamide_gel_electrophor...

Re: No human genome has ever been completely sequenced

#76

Post by epistasis »

x0x0 wrote: post #75
jessriedel wrote: post #6

As usual, the journalist spends many paragraphs painting a picture of human conflict before actually getting on to the interesting claim. > The reason for these gaps is that DNA sequencing machines don’t read genomes like humans read books, from the first word to the last. Instead, they first randomly chop up copies of the 23 pairs of chromosomes, which total some 3 billion “letters,” so the machines aren’t overwhelm…

I worked on a slab gell dna sequencer contemporaneous to the humane genome project. It's actually worse than described, because the dna isn't cut randomly. Instead, restriction nucleases cut the dna at certain fixed sequences. Of course you can use multiple restriction nucleases, either in the same (subject to their chemistry being compatible) run or over multiple runs. When everything went well, our tech allowed you…

For modern Illumina sequencing the shearing process is typically sonication, or some other method that's far more random than a restriction enzyme.

Re: No human genome has ever been completely sequenced

#77

Post by x0x0 »

epistasis wrote: post #76
x0x0 wrote: post #75

Earlier quoted context omitted.

I worked on a slab gell dna sequencer contemporaneous to the humane genome project. It's actually worse than described, because the dna isn't cut randomly. Instead, restriction nucleases cut the dna at certain fixed sequences. Of course you can use multiple restriction nucleases, either in the same (subject to their chemistry being compatible) run or over multiple runs. When everything went well, our tech allowed you…

For modern Illumina sequencing the shearing process is typically sonication, or some other method that's far more random than a restriction enzyme.

I think the entire tech that I worked on has been superseded by better technologies. However, I (think?) the limitations are still of interest because they influenced the original sequencing and probably a lot of the early data.

The other takeaway I had, as someone who came to this with a CS and stats background, is that chemistry sucks. None of it is deterministic, and when people say some chemistry does X, what they really mean is it generally does that. Most of the time. Subject to conditions and a reasonable amount of stochasticity. We're built on a pile of random muck hacked together.

Re: No human genome has ever been completely sequenced

#78

Post by et2o »

pishpash wrote: post #66

Haven't paid attention to this area in a while but back in the day I've wondered about the garbage-in garbage-out problem in genome databases. A lot of subsequent sequence assemblies were made on the basis of approximate matching to certain results in the database that have no quality information, and conclusions made on the basis of further approximate matching across datasets. Has anyone seriously worked out how re…

I don't think anyone knows.

Re: No human genome has ever been completely sequenced

#79

Post by epistasis »

x0x0 wrote: post #77
epistasis wrote: post #76

Earlier quoted context omitted.

For modern Illumina sequencing the shearing process is typically sonication, or some other method that's far more random than a restriction enzyme.

I think the entire tech that I worked on has been superseded by better technologies. However, I (think?) the limitations are still of interest because they influenced the original sequencing and probably a lot of the early data. The other takeaway I had, as someone who came to this with a CS and stats background, is that chemistry sucks. None of it is deterministic, and when people say some chemistry does X, what the…

Older tech stays around quite a while! No sequencing technology is perfect, so even Sanger sequencing is still used quite a bit for various tasks from clinical sequencing to validation studies to anywhere you just want to phase something that's longer than 300bp, etc.

And yes, the chemistry that biology takes advantage of means embracing uncertainty in the world. It's all thermodynamic chances, with lots of non-linearity added on top of it all.

Re: No human genome has ever been completely sequenced

#80

Post by nether »

labster wrote: post #52
Bromskloss wrote: post #46

Earlier quoted context omitted.

Yeah, why does Hacker News not have a real way to indent things? It wouldn't make loading the page any less light-weight.

Seriously. I can't go a week in HN without reading someone's complaint about not being able to read a quote, probably on mobile. If users keep complaining regularly, it's a problem with the software interface, not the users.

I emailed dang about it a while (years) ago. He said he's added it to the fix list, after initially saying that having a quote tag would mess up the site's "character." You may want to email him too.
Post reply on HN