Re: Has the human genome been completely sequenced? (even the heterochromatin)

To put it another way, the incompletely sequenced areas can often be
represented algorithmically, so people aren't concerned if they don't
know the details. We know the telomere repeat, so we can say "usually
around this long", but no answer would be universal to everyone, so why
bother?

The repeats are useful, but their length may be irrelevant. For example,
the telomere repeat is part of its own lengthening mechanism, and the
centromere repeats are probably necessary for centromere-organising
protein-binding, but again; does it matter how many repeats there are?
We don't know, but it's not a critical question yet until we start
trying to engineer our own centromeres.

All that said, newer sequencing techniques will answer the question
soon, I expect. The nanopore-chip method being investigated by a few
groups would involve spooling intact DNA through a chip and reading each
base as it passes the sensor; this would give you a real-sequence read,
and would tell you exactly what the DNA contains. No longer a need to
assemble diced up sequences through algorithms, which fails on such
repetitive regions.

On 02/12/11 07:42, Patrik wrote:
> You're right, there are still areas around the centromeres and
> telomeres which are really hard to sequence and assemble correctly,
> because they consist mainly of highly repetitive sequence. However,
> because they are so repetitive, there's also very few active genes
> there, *and* the repeat copy numbers tend to vary some from person to
> person.
>
> So yes, there are still some gaps. But it would take a lot of effort
> to close them and in the end it might not tell you that much more
> anyway - do you really care if person A has 27 copies of a repeat in
> that region, whereas person B only has 26 copies?
>
> Heterochromatin - it's the new "junk DNA" :-D. Who knows; perhaps once
> we understand it better, it might turn out just as non-junk as the old
> "junk DNA". But for now, it's considered a fairly thankless area to
> put much effort into.

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