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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

#161

Post by alexvitkov »

wslh wrote: post #156
10g1k wrote: post #5

For those who don't recall: Back in the Dark Ages, there was a race to decode the human genome. The leading competitiors (wealthiest) were Celera Genomics and the Human Genome Project. After some time, Celera (headed by Craig Venter), announced they had done the deed. However, what Celera had actually done was used what they called a "shotgun method", which meant they took small samples here and there, then built a m…

TIL that. I was 100% sure the DNA was completely sequenced. Even have a friend with a sequencing company. It is incredible how ignorant one can be. Thank you 10g1k and HN.

Thought so too, turns out we're right now

Re: The complete sequence of a human Y chromosome

#162

Post by AlecSchueler »

wslh wrote: post #156
10g1k wrote: post #5

For those who don't recall: Back in the Dark Ages, there was a race to decode the human genome. The leading competitiors (wealthiest) were Celera Genomics and the Human Genome Project. After some time, Celera (headed by Craig Venter), announced they had done the deed. However, what Celera had actually done was used what they called a "shotgun method", which meant they took small samples here and there, then built a m…

TIL that. I was 100% sure the DNA was completely sequenced. Even have a friend with a sequencing company. It is incredible how ignorant one can be. Thank you 10g1k and HN.

Found out you were wrong on the day you became right!

Re: The complete sequence of a human Y chromosome

#164

Post by cowsandmilk »

comboy wrote: post #157
10g1k wrote: post #5

For those who don't recall: Back in the Dark Ages, there was a race to decode the human genome. The leading competitiors (wealthiest) were Celera Genomics and the Human Genome Project. After some time, Celera (headed by Craig Venter), announced they had done the deed. However, what Celera had actually done was used what they called a "shotgun method", which meant they took small samples here and there, then built a m…

Anybody familiar with news sources which questioned Celera accomplishment before they admitted how they did it?

Parent is weird in claiming celera was hiding things. The second half of the 90s was a very vocal spat between Celera and the HGP about sequencing methods and Celera saying shotgun sequencing was superior. And the HGP was publishing updates to their genome every 24 hours while Celera published their sequence on completion of the initial draft, which showed their coverage. The fact that there wasn’t 100% coverage wasn’t hidden to anyone who read the published papers. (The abstract for the Celera paper even states “reduced the size and number of gaps”, which plainly indicates there were still gaps…)

Re: The complete sequence of a human Y chromosome

#165

Post by checkyoursudo »

dotancohen wrote: post #144
dekhn wrote: post #30

Earlier quoted context omitted.

Yes, but the HGP didn't make a full sequence either, using their scaffold-based contig assembly. Both groups declared a truce and announced they were "finished with the first draft" 35 years ago: https://www.nytimes.com/1987/12/13/magazine/the-genome-proje... 33 years ago: https://www.nytimes.com/1990/06/05/science/great-15-year-pro... 29 years ago: the competition gets fierce https://www.nytimes.com/1994/02/22/scien…

> The primary author of the shotgun assembly was Gene Myers No conflict of interest there!

His wife, Chromosome, was an uncredited contributor.

Re: The complete sequence of a human Y chromosome

#166

Post by brookst »

Angostura wrote: post #139
dekhn wrote: post #47

Earlier quoted context omitted.

This is a complex question. The cocktail soup in a gamete (sperm or egg) and the resulting zygote contains an awful lot of stuff that would be extremely hard to replace. I could imagine that if the receiving civilization was sufficiently advanced and had a model of what those cells contained (beyond the genomic information) they could build some sort of artificial cell that could bootstrap the genome to the point of…

I’m just pondering this, and it’s not clear to me that there is anything intrinsic in the genome itself that explicitly’says’ “this sequence of DNA bases encodes a protein” or even “these three base-pairs equate to this amino acid”. I wonder if that information could ever really be untangled by a civilisation starting entirely from scratch without access to a cell

It’s an interesting question. Naively, I would expect it to be about like reverse engineering a CPU from a binary program. Which sounds daunting but maybe not impossible if you understand the fundamentals of registers, memory, opcodes, etc.

But… doing so from first principles without a mental model of how all (human) CPUs work? I guess it comes down to whether the recipients had enough context to know what they’re looking at.

Re: The complete sequence of a human Y chromosome

#167

Post by VeninVidiaVicii »

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?"

I always make this mistake too as a computational biologist; when talking about DNA it’s megabases not megabytes.

Re: The complete sequence of a human Y chromosome

#168

Post by oldgradstudent »

coldtea wrote: post #77

Is this like: "we have a working keyboard driver" or more like "we identified all 104 keys on a standard 104-key US QWERTY layout"?

They now have the raw data for the CAD files used for manufacturing the keyboard.

We understand some CNC instructions, but there's no good understanding of the control mechanisms or sequencing.

One day we'll identify the keys, but we are very far from the driver, and more importantly, from identifying what each key does.

Oh, we did discover that changing specific bits in the raw data causes the keyboard to fail in interesting ways.

Re: The complete sequence of a human Y chromosome

#169

Post by comboy »

cowsandmilk wrote: post #164
comboy wrote: post #157

Earlier quoted context omitted.

Anybody familiar with news sources which questioned Celera accomplishment before they admitted how they did it?

Parent is weird in claiming celera was hiding things. The second half of the 90s was a very vocal spat between Celera and the HGP about sequencing methods and Celera saying shotgun sequencing was superior. And the HGP was publishing updates to their genome every 24 hours while Celera published their sequence on completion of the initial draft, which showed their coverage. The fact that there wasn’t 100% coverage wasn…

Huh, narration matters. Thanks.

Re: The complete sequence of a human Y chromosome

#170

Post by dopylitty »

bglazer wrote: post #22
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?"

It’s actually about 3 gigabases (ATCG). There are some recurrent features of the genome whose function we’ve worked out. For example the TATA box is a classic sequence that typically indicates the start of a part of the genome that codes for a protein. The vast majority of the genome doesn’t code for proteins. The function of these genome regions are much more murky. Some of these regions function like scaffolds for…

Also interesting are HERVs - human endogenous retroviruses which integrated into the human or our ancestor species’ genomes. They have degraded over time so none of the human hervs seem to be capable of activating but there are some in other mammals that can fully reactivate.

In humans even though hervs don’t reactivate into infectious viruses they have been implicated in both harmful (senescence during aging[0]) and beneficial (protection from modern retroviruses)[1] activities in the body.

They might be up to 8% of the human genome.

0: https://www.cell.com/cell/pdf/S0092-8674(22)01530-6.pdf

1:https://www.microbe.tv/twiv/twiv-956/

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