People do talk about the genome and its elements using the location by chromosome number and range like you'd describe an index in a string. There has even been special notation developed to do so [1]. However, it depends on _how_ you're looking at biology.
I think an analogy would be: you can describe all code as machine code, but when there are higher level abstractions you wouldn't choose to do so.
The article doesn’t mention but now I’m curious what kind of read length and error rate they are achieving. This could have huge impacts across all sequencing.
It looks like they're using Oxford nanopore and PacBio sequencing technologies for the long reads. These are two up-and-coming sequencing technologies focused on extremely long reads. My understanding of both is that their error rates on individual base pairs are too high to reliably determine the actual sequence on their own (something like 15% error rates). Typically the long reads from these technologies are used…
Oxford error rates are up to 15%, they have optimized published runs that show 5% or even better, but in the real world the error rates are much closer to 15%. However, Oxford read lengths can be absolutely massive compared to even PacBio. PacBio's sequencing is actually much more accurate than Oxford, but read lengths top out at about 15,000 bases I think. Illumina read lengths are a bit less than 100 bases but the systems are massively parallel as compared to both PacBio and Oxford.
Step 1: the researchers use a diploid cell line where the entire diploid X chromosome is homozygous: both copies of the X chromosome in this cell line are identical. This is part of why the researchers chose to look at the X chromosome. > To circumvent the complexity of assembling both haplotypes of a diploid genome, we selected the effectively haploid CHM13hTERT cell line for sequencing (abbr. CHM13) Incidentally, t…
One minor correction - in step 2 the DNA is not amplified as this would reduce the fragment length and also lose the methylation information
Good point. Here they're starting from a cell line, so presumably just starting with as much DNA as they can get from the cells. Amplification is usually needed in other scenarios where the sample is more finite, though from what I've read, nanopore sequencing tech doesn't need much DNA.
In a simple English, could someone explain why is this good and what does it all mean?
From the article: "Repetitive DNA sequences are common throughout the genome and have always posed a challenge for sequencing because most technologies produce relatively short "reads" of the sequence, which then have to be pieced together like a jigsaw puzzle to assemble the genome. Repetitive sequences yield lots of short reads that look almost identical, like a large expanse of blue sky in a puzzle, with no clues…
It's crazy to me that we still haven't hacked RNA polymerase or some other such "obvious" method to just linearly read all of the strand. The machinery is all there, by definition!
From the article: "Repetitive DNA sequences are common throughout the genome and have always posed a challenge for sequencing because most technologies produce relatively short "reads" of the sequence, which then have to be pieced together like a jigsaw puzzle to assemble the genome. Repetitive sequences yield lots of short reads that look almost identical, like a large expanse of blue sky in a puzzle, with no clues…
It's crazy to me that we still haven't hacked RNA polymerase or some other such "obvious" method to just linearly read all of the strand. The machinery is all there, by definition!
Most sequencing methods do use DNA polymerase to effectively copy the DNA while reading out the bases that are being incorporated. However, even when the genome is being replicated in vivo, the polymerase doesn't just copy the entire chromosome in one go from end to end, for various reasons. For example, for larger genomes such as those of animals, it would just take too long to copy it that way. But even for small genomes such as bacteria, DNA replication is still naturally done in fragments. One simple reason is that at any given time the polymerase can dissociate from the template and have to reattach. Even if you could engineer the polymerase to bind more tightly, you'd have to deal with the tradeoff between binding strength, replication rate, and error rate (i.e., a more tightly binding polymerase would likely copy more slowly).
The article doesn’t mention but now I’m curious what kind of read length and error rate they are achieving. This could have huge impacts across all sequencing.
In the movie he mentions Oxford Nanopore tech and using reads of 100.000 to 1.000.000 base pairs
I thought the human genome was mapped in 2003, when the Human Genome Project wrapped up: https://en.wikipedia.org/wiki/Human_Genome_Project What's different about this?
https://news.ycombinator.com/item?id=23852177 explains it, with a quote from the article. They weren't able to map the whole thing, because of repeating patterns. That's now starting to change.
So how do you actually isolate one chromosome to sequence it?
Step 1: the researchers use a diploid cell line where the entire diploid X chromosome is homozygous: both copies of the X chromosome in this cell line are identical. This is part of why the researchers chose to look at the X chromosome. > To circumvent the complexity of assembling both haplotypes of a diploid genome, we selected the effectively haploid CHM13hTERT cell line for sequencing (abbr. CHM13) Incidentally, t…
In the old good (?) days some chromosomal libraries were constructed by using flow sorting.
Not sure how often this is being used nowadays for genome/chromosome sequencing projects.
So 20 years ago when we "sequenced the human genome", we actually didn't? If you'd asked me whether or not we had a complete sequence of an X chromosome before I saw this I would have said, "Of course we have one, for over 20 years".
That's right -- sequenced genomes are typically assemblies of short fragments. The assembly algorithms fail in areas of low complexity or when large sequences are repeated an unknown number of times.
So what DID we achieve 20 years ago? Like, what happened then that led to the claim of "human genome has been sequenced" and what is the additional progress that was made now?