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The complete sequence of a human Y chromosome

nature.com

111–120 of 232 posts

Re: The complete sequence of a human Y chromosome

#111

Earlier quoted context omitted.

Many genes are highly conserved or consistent enough. E.g.: if there's a 1% difference between two people, then it's a bit like two very unique sentences that have a couple of small typos. They're sill recognisable, and it's also still pretty obvious that they're the "same". A gene sequence allows researchers to determine the amino acids that are coded for, and from those, which proteins match which genes. This can b…

But you can only know that by having a large sample of very “stable” (have few genetic irregularities) gene samples compared to a large pool of samples from people with very narrow and pronounced gene irregularities, right? Is this why it’s so hard? This feels more like a healthcare records keeping people and less like an “actually reading the data problem”. I can’t help but feel like some form of single payer health…

Single payer healthcare here (UK) is still subject to privacy controls in a way which would make it very difficult to do that.

(Also our health system's IT is a hellscape, but one reason for that is that people would literally rather not have a working system at all, than one with less than impeccable privacy controls.

Personally I'd gladly sacrifice a fair bit of medical privacy in return for giving scientists greater insight into disease processes, but the average citizen here wants advanced healthcare without giving their data to research scientists. /facepalm )

Re: The complete sequence of a human Y chromosome

#112
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…

What do you mean by "LR"? I queried an LLM but no results there either.

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Re: The complete sequence of a human Y chromosome

#113
post #41
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.

And since the data is highly redundant the 750MB can be compressed down even further using standard approaches (DEFLATE works well, it uses both huffman coding and dictionary backreferences). Or, you could build an embedding with far fewer parameters that could explain the vast majority of phenotypic differences. the genome is a hierarchical palimpsest of low entropy. My standard interview question- because I hate le…

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Re: The complete sequence of a human Y chromosome

#114

So I have my whole genome sequenced by Nebula. What do I have to do to match it up?

You could download the raw sequence reads (FASTQ files) and map them to the new T2T-Y. Probably it makes more sense to wait for a new release of the T2T human genome reference, as mapping to a subset of the genome increases false positives. It helps to have some genome bioinformatics knowledge to correctly handle those T2T references.

Re: The complete sequence of a human Y chromosome

#115
post #37
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.

Yes, there is extra information in the first cells, in particular regulatory elements such as miRNAs. The headline here is epigenetics.

Re: The complete sequence of a human Y chromosome

#116
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…

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."

Re: The complete sequence of a human Y chromosome

#117
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)?

We really should say "a human genome". Reference genomes serve as a Rosetta Stone of genomics. So we can take DNA/RNA sequences from other individuals and align (pattern match) them to the reference as a way of understanding and comparing individuals.

It is not perfect, as a references can be missing or have large variability in DNA regions. The goal of the Human Pangenome Reference Consortium (HPRC) https://humanpangenome.org/ is to sequence individuals from different populations to address this issue. We are also working to develop new computation models to support analysis of data across populations.

Re: The complete sequence of a human Y chromosome

#118
post #97

Earlier quoted context omitted.

Given code written for unknown hardware... can you execute it?

Given that the code contains the instructions how to make the hardware - if one is very smart than yes.

It would not necessary be possible, because it's incremental instructions on how to make the hardware, but based on already existing, unspecified and very complex, hardware. So the first instruction would be something like "take the stuff you have on your left and fuse it with the stuff you have on your right", both stuff being unspecified very complex protein assumed to be present.

Re: The complete sequence of a human Y chromosome

#119
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)?

It means that they are trying to find a baseline from which they can eventually clone a human being.

Let's not pretend that this is not an end goal. It always was.

Re: The complete sequence of a human Y chromosome

#120
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)?

While you are correct, the differences between different people's DNA is tiny, less 1% at best. So this information is still very valuable. This article is talking about the first time in finishing sequencing one person's Y chromosome's DNA.
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