

1 machine, 4 weeks now enough to sequence human genome - MikeCapone
http://arstechnica.com/science/news/2009/08/human-genome-completed-using-one-machine-for-four-weeks.ars

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timr
Well, no. Not really:

 _"Fragments this small probably can't be assembled into a complete genome,
but the authors were able to compare them to the reference human genome
maintained by the National Institutes of Health. They were able to align
sequences totaling 2.5 billion bases to the published version of the human
genome."_

So, it's apparently now possible to generate redundant, small-fragment
coverage of the human genome in four weeks, but that's a _long_ way from a
full, assembled genome. The researchers had to cheat by performing alignments
of the tiny fragments with the known, assembled human genome sequence. This
was the same game that Celera Genomics had to play to claim a "fully
assembled" genome from shotgun sequencing -- but they were using larger reads,
and still failed to be scientifically convincing.

This is interesting technology, but the title is a massive exaggeration.

~~~
Devilboy
It's still a very important step for third generation sequencing machines.

 _...the HeliScope generates DNA sequence data as a massive collection of very
short reads - but while the Illumina platform is now routinely generating
reads over 100 bases long, the HeliScope generates reads on average just 32
bases long, with only a tiny fraction exceeding 50 bases in length. In fact,
the reads are deliberately filtered to exclude any extending for over 70
bases, as these are highly enriched for technical artefacts.

Stitching together a genome sequence with such short reads is a substantial
challenge, especially in regions where the sequence is repetitive - and indeed
the technology can only cover 90% of the reference genome compared to 99.9%
for a genome recently sequenced to similar depth with Illumina._

[http://scienceblogs.com/geneticfuture/2009/08/first_human_ge...](http://scienceblogs.com/geneticfuture/2009/08/first_human_genome_sequenced_u.php)

So they can still stitch together 90% of your genome within a month, and
there's no reason to think this will not improve in the future.

~~~
dflock
I would imagine that they could get the cost down and the speed up but I
wouldn't imagine that the coverage would improve much if they continue to use
short reads - i.e. small ~32 base bits of DNA.

As I understand it, there's enough repetition and duplication in the genome
that many of these little lengths are going to be identical: AAAA...AAAA or
GGGAGGGA...GGGA etc. and that these little strips will match in many different
places when placed alongside a fully assembled reference genome. They will
also match and overlap a lot with each other. This means that you can't tell
where they're supposed to go when you try to re-assemble your collection of
little bits into a complete sequence. This means that you're always going to
be left with a collection of bits left over that you have no way of placing
into the sequence, hence less than 100% coverage.

I guess you would need to be using reads long enough to ensure that each of
your fragments was unique to get 100% coverage.

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dskhatri
There's a $10 million prize for sequencing 100 genomes in 10 days:
[http://genomics.xprize.org/archon-x-prize-for-
genomics/prize...](http://genomics.xprize.org/archon-x-prize-for-
genomics/prize-overview)

------
physcab
Can someone with knowledge in this field give some perspective about how great
this achievement is? I read parts of the article but I just don't know enough
about the challenge to think that 4 weeks is all that impressive.

~~~
gnaritas
It took 13 years and a shitload of computers to sequence the first one.

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philwelch
That's in the price range of a medical procedure.

