No human genome has ever been completely sequenced • Hacker News Board

Re: No human genome has ever been completely sequenced

#11

Post by El_Montanero » Mon, Oct 23, 2017, 5:04 PM UTC

eggie wrote: post #8

IBM wrote: post #5

Earlier quoted context omitted.

As someone who's only casually interested in this field, what are the prospects of any of these upstarts actually unseating Illumina from the throne?

I expect us to use the long reads from ONT and PacBio to discover that structural variation is even more important and common than previously appreciated. If that's the case, you'd be silly to use the Illumina technology for anything more complex than population genetics, and this will probably trickle into many parts of the market as the medically-relevant parts of the field realize what the basic science is demonst…

This is so cool. I'd been taught in high school that the human genome was no longer a mystery, and that science had fully decoded the entire thing. It seems pretty obvious now that the subtleties would be even more complex than we could have imagined.

Re: No human genome has ever been completely sequenced

#12

Post by shpx » Mon, Oct 23, 2017, 5:06 PM UTC

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…

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 random.choices() was added in Python 3.6

[1] http://www.biology-pages.info/B/BasePairing.html source for `weights`

[2] 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 illumina is the most popular producer of genome sequencers

[4] https://news.ycombinator.com/item?id=5123377

Re: No human genome has ever been completely sequenced

#13

Post by slavik81 » Mon, Oct 23, 2017, 5:07 PM UTC

hprotagonist wrote: post #2

what do you mean, "the" human genome?

The was flag killed. I vouched for this because I had the same question. What does it mean to have sequenced the human genome? If different individuals have a different genome, what is the human genome?

Re: No human genome has ever been completely sequenced

#14

Post by phyzome » Mon, Oct 23, 2017, 5:18 PM UTC

coldtea wrote: post #4

In other words they don't know what they're doing and they're making it up as they go along -- "yeah, that part there is probably unused", "oh, wait, it's important after all".

As the article says, we know there's important stuff in those repetitive regions, it's just really hard to read.

Re: No human genome has ever been completely sequenced

#15

Post by chrisamiller » Mon, Oct 23, 2017, 5:21 PM UTC

slavik81 wrote: post #13

hprotagonist wrote: post #2

what do you mean, "the" human genome?

The was flag killed. I vouched for this because I had the same question. What does it mean to have sequenced the human genome? If different individuals have a different genome, what is the human genome?

You're right, and the next frontier in genome assembly and mapping algorithms is using graph-based genomes, where differences between individuals or populations can represented as different paths through a sequence graph. (There are lots of better explanations with pretty pictures out there with a little searching)

Re: No human genome has ever been completely sequenced

#16

Post by grzm » Mon, Oct 23, 2017, 5:21 PM UTC

slavik81 wrote: post #13

hprotagonist wrote: post #2

what do you mean, "the" human genome?

The was flag killed. I vouched for this because I had the same question. What does it mean to have sequenced the human genome? If different individuals have a different genome, what is the human genome?

The article acknowledges this, though perhaps obliquely:

> “As a matter of truth in advertising, the ‘finished’ sequence isn’t finished,” said Eric Lander, who led the lab at the Whitehead Institute that deciphered more of the genome for the government-funded Human Genome Project than any other. “I always say ‘finished’ is a term of art.”

The phrasing of your parent is arguably dismissive and does little to further substantive discussion. Can one meaningfully discuss "the human genome"? As you point out, each human (with the exception of identical twins) has a unique genome. I think it's reasonable and useful to be able to say "the human genome" as opposed to "the chimpanzee genome" or "the drosophila genome".

If one would rather insist on using the indefinite article, i.e., "a human genome", one can present it without resorting to a rhetorical question replete with scare quotes.

Re: No human genome has ever been completely sequenced

#17

Post by jashephe » Mon, Oct 23, 2017, 5:22 PM UTC

eggie wrote: post #8

IBM wrote: post #5

Earlier quoted context omitted.

As someone who's only casually interested in this field, what are the prospects of any of these upstarts actually unseating Illumina from the throne?

I expect us to use the long reads from ONT and PacBio to discover that structural variation is even more important and common than previously appreciated. If that's the case, you'd be silly to use the Illumina technology for anything more complex than population genetics, and this will probably trickle into many parts of the market as the medically-relevant parts of the field realize what the basic science is demonst…

The fact is, unfortunately, that Nanopore sequencing (and also, from what I’ve read, PacBio) has a dramatically higher error rate than Illumina sequencing-by-synthesis. In the near future, anyway, I would expect to see inaccurate PacBio/Nanopore long reads being used as scaffolds for accurate Illumina short reads (in fact, this is already happening). Illumina won’t be going anywhere any time soon.

Re: No human genome has ever been completely sequenced

#18

Post by jcvhaarst » Mon, Oct 23, 2017, 5:24 PM UTC

IBM wrote: post #5

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.

As someone who's only casually interested in this field, what are the prospects of any of these upstarts actually unseating Illumina from the throne?

PacBio and ONT are far from upstarts, they have both already invested millions and millions into their respective technologies. Pacific Biosciences has a Market Cap of 532.88M Oxford Nanopore is at least as big.

Re: No human genome has ever been completely sequenced

#19

Post by iskander » Mon, Oct 23, 2017, 5:27 PM UTC

IBM wrote: post #5

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.

As someone who's only casually interested in this field, what are the prospects of any of these upstarts actually unseating Illumina from the throne?

They currently specialize in different things. The larger Illumina instruments have a huge up-front cost (~$1M), tremendous throughput, low cost per base, short reads, 10% non-independent error rate and very long reads.

ONT will be much more useful for assembling reference genomes (which can then be polished with short reads), characterizing large scale structural variants, and real time applications like "what pathogen am I infected with?".

Re: No human genome has ever been completely sequenced

#20

Post by nonbel » Mon, Oct 23, 2017, 5:29 PM UTC

slavik81 wrote: post #13

hprotagonist wrote: post #2

what do you mean, "the" human genome?

The was flag killed. I vouched for this because I had the same question. What does it mean to have sequenced the human genome? If different individuals have a different genome, what is the human genome?

Not only do different individuals have different genomes, each cell from the same person will have different genomes. It is more like an "average" human genome, one that no actual cell has ever contained.