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The complete sequence of a human Y chromosome

nature.com

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Re: The complete sequence of a human Y chromosome

#121

Post by jfoutz »

jacquesm wrote: post #105
jfoutz wrote: post #68

Earlier quoted context omitted.

I know hn isn't the place for memes, but, I'm obligated. Imagine what they could do with a beowulf cluster of pentium pros?

They weren't using pentium pros, they were using Alpha's because the memory interconnect between a beowulf cluster of pentium pros would be orders of magnitude slower. So likely 'the same, but much slower'.

oh, ha. yeah, that was sort of the root of the joke. companies like Celera, or whoever had the money would write a (large) check for big iron.

smaller organizations were realizing they could get slower computers power pretty cheap, and they could get a whole lot of them. There was a little flurry of activity with flocking algorithms, objective-c had a little renaissance due to swarm computing. probably the most famous and lasting was map-reduce, from alphabet, but they were called google back then.

there were a bunch of clever little tricks, like channel bonded network cards to make multiple cards look like one fast card, so you could double or triple bandwidth.

The beowulf cluster joke was kind of the spirit of the scrappy, make something cool out of junk approach while calling companies like sun, hp, compaq dinosaurs. and it continued for a while with people building stuff like this - https://ncsa30.ncsa.illinois.edu/2003/05/ncsa-creates-sony-p... I think there was some weirdness with export controls of ps2's for this kind of stuff.

I don't remember what pc chip was the new hotness back then, it was a good 20 years ago and my memory is dim.

but that, I think, captures the gist of the meme.

Re: The complete sequence of a human Y chromosome

#122

Post by pmoriarty »

borissk wrote: post #37
cvoss wrote: post #33

Earlier quoted context omitted.

It's a slight exaggeration of the information content to report the data size using an ASCII encoding. Since there are 4 bases, each can be encoded using 2 bits, rather than 8. So we're really talking 750 megabytes. But still mind-blowing.

I'm curious if these 750MB + the DNA of mitochondria + the protein metagenomics contain all the information needed to build a human, or if there's extra info stored in the machinery of the first cell. That is if we transfer the DNA to an advanced alien civilization - would they be able to make a human.

"if we transfer the DNA to an advanced alien civilization - would they be able to make a human."

I'm really surprised that in all these responses to your question no one's mentioned the womb or the mother, who (at least with current technology) is still necessary for making a human.

That's not to mention the necessity of the egg.

We're not just DNA.

Re: The complete sequence of a human Y chromosome

#123

Post by udkl »

kazinator wrote: post #116
jhbadger wrote: post #75

Earlier quoted context omitted.

As noted, the shotgun sequencing wasn't any worse than the traditional chromosome walking method used by the other human genome project, and neither created a truly complete sequence, which is only possible today with improvements in technology. And it is worth noting that despite all the critiques of shotgun sequencing at the time as "cheating", chromosome walking sequencing is dead, and shotgun is what we use today…

I feel a joke coming on. Mother: "Amy, dear, you hardly touched any of your vegetables. Most of them are still on your plate." Amy: "That's not true, Mom; I completely sequenced them into my tummy using the shotgun method."

Someone submit this to smbc comics !

Re: The complete sequence of a human Y chromosome

#124

Post by jakobnissen »

space_fountain wrote: post #18

As I understand it this was hard because most mechanisms we have for sequencing genes work by first splitting large sequences of genes into random chunks and sequencing each chunk individually. These chunks then need arranged properly to form the entire genome. This is possible at all because we can get overlap between the chunks, but when a sequence has repeating sections overlap still isn’t enough to stitch everyth…

They relied mainly on PacBio HiFi reads (which I think is a truly understated revolutionary technology in genomics), then used Nanopore sequencing to link together the HiFi contigs to cover the truly gnarly regions of the chromosome.

And yeah, you're right: All modern large-scale sequencing is shotgun sequencing where the DNA is randomly broken up, each fragment is sequenced, and then the individual segments (reads) are assembled using a genome assembler.

Re: The complete sequence of a human Y chromosome

#125

Post by jakobnissen »

xwdv wrote: post #50

Could we in theory just build up any kind of creature from scratch if we write out its genome? How would we compile it into organic matter?

No, this is not technically possible. Cells are simply to complex to just build using humanity's current level of technology. The closest thing we have done is to fully synthesize a bacterium's genome, remove the genome from a bacterial cell, then transplant the synthetic genome into the cell and have the cell survive: https://en.wikipedia.org/wiki/Mycoplasma_laboratorium

That's insanely cool, but very far from what you are asking. An analogy: We have re-installed the operating system of an existing computer, when you are asking whether we can manufacture a computer.

Re: The complete sequence of a human Y chromosome

#126

Post by globular-toast »

chihuahua wrote: post #9
jshorty wrote: post #6

Could someone explain exactly what it means to be "completely sequence" the human genome when all humans have distinct genetic makeup (ie, different sequences of nucleobases in their DNA/RNA)?

I've never understood this either. I assume the genome is many megabytes of [ATCG]+. If we have that sequence, what does it tell us? Do we look at it and say "Ah, yes, ...ATGCTACGACTACGACTAGCG... very interesting?"

The genetic code maps nucleotide sequences (DNA) to amino acid sequences (proteins). Every three bases (say AGT) maps to one amino acid. So you can literally read a sequence of ACGTs and decode it into a protein. A sequence that encodes a protein is called a gene.

Almost all variations that humans have in their genomes (compared to each other or a reference genome) are tiny, mostly one base differences called single nucleotide polymorphisms (SNPs). These tiny changes encode who you are. The rest of it just makes you carbon-based organism, a eukaryote, an animal, a mammal etc, just like a whole load of other organisms.

Re: The complete sequence of a human Y chromosome

#127

Post by bux93 »

tobinfricke wrote: post #70
brayman30 wrote: post #3

This is actually kind of a huge deal since it means that all 24 chromosomes have now been fully sequenced. As it says in the abstract, up until now the Y chromosome proved difficult to sequence due to its nature.

What makes the Y chromosome more difficult?

It's on line 1 of the linked article: "The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications" and comes with 3 citations.

Re: The complete sequence of a human Y chromosome

#128

Post by goodcanadian »

msuvakov wrote: post #82

This news should be dated back in December, not now. The T2T team published a preprint [1] last December and released the data [2] in March. However, due to the peer review process, the findings have only just been formally published in Nature. The publication timeline can indeed be slow, and in cases like this one, the question is: what's the point when all scientists interested in the topic already know about it an…

what's the point when all scientists interested in the topic already know about it and working with this assembly?

In this context, I would say the point of a press release is getting the news out generally to non-scientists.

Re: The complete sequence of a human Y chromosome

#129

Post by aastronaut »

dekhn wrote: post #38
chihuahua wrote: post #9

Earlier quoted context omitted.

I've never understood this either. I assume the genome is many megabytes of [ATCG]+. If we have that sequence, what does it tell us? Do we look at it and say "Ah, yes, ...ATGCTACGACTACGACTAGCG... very interesting?"

If you think like an ML engineer, the genome is a feature vector 3B bases (or 6B binary bits) long that is highly redundant (many sections contain repeats and other regions that are correlated to other regions), and the mapping between that feature vector and an individual's specific properties (their "phenotype", which could be their height at full maturity, or their eye color, or hair properties, or propensity to d…

> If you had a list of all the genomes of all the people in the world, and all their phenotypes (height, eye color, hair type, etc), you could take all their genomes as input variables and treat all their phenotypes as output variables, and make embeddings or other models that mapped from genomes to phenotypes. The result would be a predictive model that could take a human genome, and spit out a prediction of what that person looks like and other details around them (up to the limits of heritability).

Would such a predictive model really be possible? As far as I'm aware there is contradicting research whether a specific phenotype distinctly originates from a SNP/genotype.

Re: The complete sequence of a human Y chromosome

#130

Post by 2dvisio »

dekhn wrote: post #54
alexchantavy wrote: post #43

Earlier quoted context omitted.

Fascinating, are there lots of people looking at genetics with this ML kind of lens?

Sure, although I'm not aware of anybody who is contemplating quite the level I believe is necessary to really nail the problem into the ground. When I worked at Google, I proposed that Google build a datacenter-sized sequencing center in Iowa or Nebraska near its data centers, buy thousands of sequencers, and run industrial-scale sequencing, push the data straight to the cloud over fat fiber, followed by machine lear…

Guys at Verily are working on Terra.bio with the Broad institute and others. Genomics England in the UK is also experiencing with multimodal and machine learning applied to whole genome sequences [1].

[1] https://www.genomicsengland.co.uk/blog/data-representations-...

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