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As usual, the journalist spends many paragraphs painting a picture of human conflict before actually getting on to the interesting claim. > The reason for thes

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 overwhelmed. The resulting chunks contain from 1,000 letters (during the Human Genome Project) to a few hundred (in today’s more advanced sequencing machines). The chunks overlap. Computers match up the overlaps, assembling the chunks into the correct sequence. > That’s between difficult and impossible to do if the chunks contain lots of repetitive segments, such as TTAATATTAATATTAATA, or TTAATA three times. “The problem is, when you have the same exact words, it’s hard to assemble,” said Lander, just as if jigsaw puzzle pieces show the same exact blue sky. > In 2004, the genome project reported that there were 341 gaps in the sequence. Most of the gaps — 250 — are in the main part of each chromosome, where genes make the proteins that life runs on. These gaps are tiny. Only a few gaps — 33 at last count — lie in or near each chromosome’s centromere (where the two parts of a chromosome connect) and telomeres (the caps at the end of chromosomes), but these 33 are 10 times as long in total as the 250 gaps. I recommend reading HN user eggie's comments on this from last week. https://news.ycombinator.com/item?id=15482439 https://news.ycombinator.com/item?id=15482439 https://news.ycombinator.com/item?id=15483462 https://news.ycombinator.com/item?id=15483462

shpx 9y ago
https://youtu.be/fCd6B5HRaZ8 https://youtu.be/fCd6B5HRaZ8 is the best visualization of how the most popular type of DNA sequencer works (that I've found). Imagine you have a string of length 3 billion made by randomly choosing from 4 characters. Like this dna = ''.join(random.choices('atgc', weights=[30.9, 29.4, 19.9, 19.8], k=3_234_830_000)) you get to randomly sample 1 billion[3, page 7] overlapping substrings of length 200[3, page 7] with .1% of the characters randomly changed[3, page 8]. Trying to find the original string from this is technically an undecidable problem. If there's a sequence 400 characters long that repeats multiple times, how could you know if it repeats 5 times or 50 times? (this would be unlikely to happen with random.choices() but DNA isn't random). This is called sequence alignment and it's one of the hard problems in bioinformatics[4]. [0] https://docs.python.org/3/library/random.html https://docs.python.org/3/library/random.html random.choices() was added in Python 3.6 [1] http://www.biology-pages.info/B/BasePairing.html http://www.biology-pages.info/B/BasePairing.html source for `weights` [2] https://en.wikipedia.org/wiki/Human_genome https://en.wikipedia.org/wiki/Human_genome source for 3_234_830_000 (python ignores underscores in numbers) [3] http://sci-hub.io/10.1111/j.1755-0998.2011.03024.x http://sci-hub.io/10.1111/j.1755-0998.2011.03024.x illumina is the most popular producer of genome sequencers [4] https://news.ycombinator.com/item?id=5123377 https://news.ycombinator.com/item?id=5123377
- nether 9y ago
  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.
  - Bromskloss 9y ago
    Yeah, why does Hacker News not have a real way to indent things? It wouldn't make loading the page any less light-weight.
    - labster 9y ago
      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.
      - nether 9y ago
        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.
        lolreally1 9y ago
        I fail to see how a quote tag would drive away the throngs of Silicon Valley elites, people who begin sentences with “I’m not an expert, but...”, hardcore Randians, and Paul Graham sycophants.
        sspiff 9y ago
        And yet here you are, on the site whose users you are attacking, commenting on an off-topic comment thread. Perhaps you should rethink your life choices?
        9y ago
latj 9y ago
This person also forgot to mention that the original human genome project was not even the sequence of a single individual- it was several people. The other thing this article doesnt mention is the idea of coverage. Its not like a jigsaw puzzle with one copy of each tile-- every time a whole genome is sequenced it is done so 30 times over to ensure that the pieces are correct. Finally, Read length varies from technology to technology. This one claims average 10k base pairs. http://www.pacb.com/smrt-science/smrt-sequencing/read-lengths/ http://www.pacb.com/smrt-science/smrt-sequencing/read-length...
wahern 9y ago
My biologist friend isn't patient enough to ELI5, but AFAIU don't genes realign through the natural course of replication? That is, there is no specific, canonical sequence at large scales, neither between two individuals nor even two cells, even if the complete set of base pairs[1] is otherwise identical (i.e. no mutations). I realize that the magnitude of this natural shuffling, even during meiosis, is nowhere near like what happens when sequencing DNA[2], but (assuming I'm correct) it's helpful to realize that this problem of deciphering the "correct" sequence reflects something intrinsic to the operation of the machinery; that this applies even when the relevant macro sequences are all genes that directly code for phenotypes as traditionally understood; and that gene sequencing works precisely because many (most?) genes are relatively tolerant to being spliced in at random locations in the strand. (Which is different than saying all locations--or even any two locations--produce identical results.) [1] I refrain from saying "complete set of genes" because I imagine for some genes location at both the micro- and macro-scale is everything. AFAIU the term gene is sometimes better understood as more a description of the result of possibly non-local sequences which maintain reproductive affinity than an identification of a specifically adjoining sequence of base pairs. [2] Or is it?
- jdale27 9y ago
  there is no specific, canonical sequence at large scales, neither between two individuals nor even two cells This is correct, and is a reason why genome informatics has been moving away from representing the genome as a single linear "reference" sequence of 3 billion nucleotides, and towards a graph-based model: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411762/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411762/.
eradicatethots 9y ago
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
x0x0 9y ago
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_electrophoresis https://en.wikipedia.org/wiki/Polyacrylamide_gel_electrophor...
- epistasis 9y ago
  For modern Illumina sequencing the shearing process is typically sonication, or some other method that's far more random than a restriction enzyme.
  - x0x0 9y ago
    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.
    - epistasis 9y ago
      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.

shpx 9y ago

https://youtu.be/fCd6B5HRaZ8 https://youtu.be/fCd6B5HRaZ8 is the best visualization of how the most popular type of DNA sequencer works (that I've found). Imagine you have a string of length 3 billion made by randomly choosing from 4 characters. Like this dna = ''.join(random.choices('atgc', weights=[30.9, 29.4, 19.9, 19.8], k=3_234_830_000)) you get to randomly sample 1 billion[3, page 7] overlapping substrings of length 200[3, page 7] with .1% of the characters randomly changed[3, page 8]. Trying to find the original string from this is technically an undecidable problem. If there's a sequence 400 characters long that repeats multiple times, how could you know if it repeats 5 times or 50 times? (this would be unlikely to happen with random.choices() but DNA isn't random). This is called sequence alignment and it's one of the hard problems in bioinformatics[4]. [0] https://docs.python.org/3/library/random.html https://docs.python.org/3/library/random.html random.choices() was added in Python 3.6 [1] http://www.biology-pages.info/B/BasePairing.html http://www.biology-pages.info/B/BasePairing.html source for `weights` [2] https://en.wikipedia.org/wiki/Human_genome https://en.wikipedia.org/wiki/Human_genome source for 3_234_830_000 (python ignores underscores in numbers) [3] http://sci-hub.io/10.1111/j.1755-0998.2011.03024.x http://sci-hub.io/10.1111/j.1755-0998.2011.03024.x illumina is the most popular producer of genome sequencers [4] https://news.ycombinator.com/item?id=5123377 https://news.ycombinator.com/item?id=5123377

nether 9y ago
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.
- Bromskloss 9y ago
  Yeah, why does Hacker News not have a real way to indent things? It wouldn't make loading the page any less light-weight.
  - labster 9y ago
    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.
    - nether 9y ago
      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.
      - lolreally1 9y ago
        I fail to see how a quote tag would drive away the throngs of Silicon Valley elites, people who begin sentences with “I’m not an expert, but...”, hardcore Randians, and Paul Graham sycophants.
        sspiff 9y ago
        And yet here you are, on the site whose users you are attacking, commenting on an off-topic comment thread. Perhaps you should rethink your life choices?
        9y ago

latj 9y ago

This person also forgot to mention that the original human genome project was not even the sequence of a single individual- it was several people. The other thing this article doesnt mention is the idea of coverage. Its not like a jigsaw puzzle with one copy of each tile-- every time a whole genome is sequenced it is done so 30 times over to ensure that the pieces are correct. Finally, Read length varies from technology to technology. This one claims average 10k base pairs. http://www.pacb.com/smrt-science/smrt-sequencing/read-lengths/ http://www.pacb.com/smrt-science/smrt-sequencing/read-length...

wahern 9y ago

My biologist friend isn't patient enough to ELI5, but AFAIU don't genes realign through the natural course of replication? That is, there is no specific, canonical sequence at large scales, neither between two individuals nor even two cells, even if the complete set of base pairs[1] is otherwise identical (i.e. no mutations). I realize that the magnitude of this natural shuffling, even during meiosis, is nowhere near like what happens when sequencing DNA[2], but (assuming I'm correct) it's helpful to realize that this problem of deciphering the "correct" sequence reflects something intrinsic to the operation of the machinery; that this applies even when the relevant macro sequences are all genes that directly code for phenotypes as traditionally understood; and that gene sequencing works precisely because many (most?) genes are relatively tolerant to being spliced in at random locations in the strand. (Which is different than saying all locations--or even any two locations--produce identical results.) [1] I refrain from saying "complete set of genes" because I imagine for some genes location at both the micro- and macro-scale is everything. AFAIU the term gene is sometimes better understood as more a description of the result of possibly non-local sequences which maintain reproductive affinity than an identification of a specifically adjoining sequence of base pairs. [2] Or is it?

jdale27 9y ago
there is no specific, canonical sequence at large scales, neither between two individuals nor even two cells This is correct, and is a reason why genome informatics has been moving away from representing the genome as a single linear "reference" sequence of 3 billion nucleotides, and towards a graph-based model: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411762/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411762/.

eradicatethots 9y ago

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

x0x0 9y ago

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_electrophoresis https://en.wikipedia.org/wiki/Polyacrylamide_gel_electrophor...

epistasis 9y ago
For modern Illumina sequencing the shearing process is typically sonication, or some other method that's far more random than a restriction enzyme.
- x0x0 9y ago
  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.
  - epistasis 9y ago
    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.