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 complete sequence of a human Y chromosome
171–180 of 232 posts
Re: The complete sequence of a human Y chromosome
#172Dumb question: what does it mean to sequence "the" X? I presume our DNA are not identical. So do they sequence a particular person's Y chromosome? Who's? How similar are two Y chromosomes from different persons?
Very similar. The difference between you and a chimp is only 4%, the largest difference between two individual humans is about a tenth of that. The person they picked is pseudonymously HG002, who is an Ashkenazi man who took part in the project and consented to commercial distribution of his genome.
Interesting they chose Ashkenazi, given this ancestry is fairly unique.
https://gnomad.broadinstitute.org/news/images/2018/10/gnomad...
Re: The complete sequence of a human Y chromosome
#173Earlier quoted context omitted.
Including code for the proteins that read DNA to produce proteins. You might hit similar problems trying to understand C given the source code for a C compiler - a non-standard environment could reproduce itself given the source code, meaning the code alone doesn't strictly determine the output.
I'll torture this DNA and C source code analogy a bit. Epigenetics is missing in this discussion about reproducing a human from just the DNA. These are superficial modifications (e.g. methylation, histone modification, repressor factors) to a strand of DNA that can drastically alter how specific regions get expressed into proteins. These mechanisms essentially work by either hiding or unhiding DNA from RNA polymerase…
There's also postprocessing: varying modification of the RNA, RNA interference, glycosylation and other post transcriptional modifications.
Re: The complete sequence of a human Y chromosome
#174For 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.
FWIW, the DNA was 100% sequenced. However, a proportion of that data that came back from the sequencing machine was too similar to each other, so it was impossible to assemble it into a coherent full set of contiguous chromosomes.
Imagine it like putting together a jigsaw puzzle, except that the picture on the front of the puzzle has lots of repeating motifs, so you end up with multiple pieces that look identical. You won't be able to tell how the whole thing fits together, but you can assemble the bits that are well-behaved and unique.
Modern technology gives us larger jigsaw pieces, which allows us to distinguish between almost-identical parts of the puzzle better. But I would note that the project linked did a huge amount of sequencing using very expensive methods to be able to resolve the whole thing.
Re: The complete sequence of a human Y chromosome
#175For 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…
Not true now with PacBio Revio and new Oxford Nanopore chemistry and flow cells. We still use a bit of older Illumina data for polishing, but long read methods now as accurate. HiC and Bionano more important as supplements than 150 nucleotide pair-end reads.
And the cost of a T2T using a combination of these technologies is already well under $10,000 in reagent costs. The assembly is still a complex art especially for a messy chromosome like Y.
Re: The complete sequence of a human Y chromosome
#176Earlier quoted context omitted.
Lincoln Stein is great, and perl was certainly critical to many processes, but it was and remains fairly niche in genomics, which used much more C++, Java, and later Python. IMHO the person who "saved the genome project" was WJ Kent, who developed the assembler, BLAT, that the public project needed. I strive to point out that he wasn't a sole hero, nor was Lincoln. What I really like about BLAT is that while Celera w…
Small correction: BLAT is a local alignment tool Jim Kent also wrote. I think his assembler you're referring to is GigAssembler ( https://www.ncbi.nlm.nih.gov/pmc/articles/PMC311095/ ).
I also love that all of their genomic tools are released as a virtualbox virtual machine and their entire site can basically be run locally with personal genomic data. I think it’s called genome in a box.
And if I remember correctly BLAT was so useful because it could be run on machines with less cpu power by loading more data into memory…or was it the other way around?
Re: The complete sequence of a human Y chromosome
#177Earlier quoted context omitted.
Lets not forget how Perl Saved The Human Genome Project [1], which I remember seeing in a print magazine at the time. As someone who is in the genomics world now as a software person, I find it amusing that I've gotten more into perl over the last year or so. It has its place, in the way that grep/sed/awk/etc does. [1] https://news.ycombinator.com/item?id=30327812
Lincoln Stein is great, and perl was certainly critical to many processes, but it was and remains fairly niche in genomics, which used much more C++, Java, and later Python. IMHO the person who "saved the genome project" was WJ Kent, who developed the assembler, BLAT, that the public project needed. I strive to point out that he wasn't a sole hero, nor was Lincoln. What I really like about BLAT is that while Celera w…
And Jim Kent!
Re: The complete sequence of a human Y chromosome
#178Earlier 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, who previously had written BLAST... So... um... BLAST processing?
I think blast is for mapping sequences on existing genomes, which uses similar algorithms but applied for a different purpose.
Re: The complete sequence of a human Y chromosome
#179As 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)…
And the PacBio system they used in this paper is already old news and has been replaced by PacBio Revio system. Higher throughput, cheaper per base and somewhat more accurate.
Re: The complete sequence of a human Y chromosome
#180For 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…
I don't think this was a secret. I remember reading an article (IIRC in Readers Digest) nearly ~20 years ago which specifically referred to it as a "shotgun method". I wasn't (and still am not) enough of an expert to have known that was a less authentic/accurate method, but at least at the time the tone was not that they were doing anything illicit.