
Ion Torrent’s chip-based genome sequencer is poised to revolutionize medicine - gourneau
http://beta.spectrum.ieee.org/biomedical/devices/the-gene-machine-and-me
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gourneau
I am developer at Ion Torrent. If you want to help hack the future of
medicine, I am looking for Python and Django hackers to join my team in San
Francisco. We are a totally open source shop.

We also need awesome electrical engineers, mechanical engineers, signal
processing engineers, CUDA hackers, FPGA developers, statisticians (we use R
too), bioinformatics folks, JavaScripters, UI people, distributed systems
engineers, documentation and developer evangelists, DevOps and SREs, and
testers. Not to mention all the wet lab bio stuff.

email me at josh@gourneau.com if you are interested

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steve19
Hi Ion Torrent dev. This is a really exciting project.

The article says "decipher a human genome in a few hours, and at the bargain-
basement price of $1000".

Does this mean the hardware will cost $1000, or does a complete sequence cost
$1000 of consumables/depreciation?

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gourneau
That means the cost of consumables is $1000.

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hxrts
One point worth mentioning. Ion Torrent is one of several companies that
develops high-throughput or 'nextgen' sequencing platforms 454 and Illumina
being the other big players right now. Each technology has a few important
nuances that make them better or worse for a particular project. Some of the
major things one looks at are cost of the device and library construction,
error rates due to PCR amplification steps or nucleotide calling, library
sizes, and maximum read length but there are many more. In addition, pore
technologies will definitely become important in the near future because they
enable single molecule experiments which are currently impossible without
amplification using the above platforms.

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waiquoo
Ion torrent appears to be the same platform as 454, but with detection via
chemical means (ISFETs) rather than optical transduction. One of the big
drawbacks of the 454 technology that doesn't get talked about a lot is that
the immulsion PCR/microbeads require a lot of preparation before the actual
sequencing run. On the 454, I believe the sequencing time was ~8hrs, but the
preparation time (at least at the facility where I was involved) typically
took more than 8 hrs. In terms of actual sequencing time, it's the best
system. But as you said, read length is a major issue with all of the current
"nextgen" systems that should be resolved with nanopore sequencing.

~~~
hxrts
From a clinical / experimental standpoint there's very little difference
between 4,8,16 hours. It's all essentially 'next day' right now because common
practice is to send the sample off to a genomics core and they drop the data
on a server for you after they've run it through their pipeline. Many
experiments require their own library construction but clinical pipelines
generally don't and again, the machine prep time is not the bottleneck it's
deciding what to include and how to lay things out. From what I understand 454
accommodates the longest read lengths right now but this seems to change month
to month, also from what I understand 454 has a lot of trouble with short
length libraries.

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owlmonkey
PacBio has average read length now of about 5000 bp whereas 454 is still only
about 1000 bp.

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patdennis
For $50, I had 23andme read my genotype for a pretty significant number of
already studied genes, but far from my complete genome.

How much of a difference does it make to the end user whether their complete
genome is sequenced, compared to 23andme's model?

~~~
datz
23andme is babyish relative to what's coming. Even exome sequencing does not
provide the whole story. There are so many conditionals, so many sequences
important in regulation, so much of the "dark" genome that actually codes for
RNA. Sure, some SNPs are highly predictive, but there are compensatory
mutations and regulatory gene circuits. Everything works together and must be
weighed together. Even with whole genome we still need epigenetics and we need
time-lapse data and sampled location specific (cell and organ system) genomic
data to really produce clinically relevant predictions.

~~~
datz
Interpretation is an indefinite field - statisticians and econometricians will
be highly valued.

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datz
The cost comes from the continuous washing and waves of nucleotide additions
(reagent costs). Illumina's technology suffers the same difficulty. The
promise of PacBio's technology is that it does not require this continuous
washing and staggering of nucleotide additions (unfortunately PacBio was not
able to translate its technology to high-throughput high-accuracy or
manufacture properly its version of "chips" [SMRT cells] for Single Molecule
Real-time Sequencing). I'm afraid the cost will not come down significantly
for iontorrent or illumina without a fundamental improvement in reagent
utilization techniques or reduction in reagent costs.

~~~
owlmonkey
I agree PacBio doesn't have the high-throughput of Illumina or similar
amplification approaches yet, but from last month's AGBT conference papers
it's clear that it's now more accurate than other systems with typical
coverage (no bias, covers repeats, Q50-60, etc.)

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kyriakos
I'm all in for technological progress and advanced medicine but how long
before Gattaca type scenarios become real? Will companies start screening
candidate employees? will this split the world in classes of good genes and
bad genes? how about dating? will you future wife to be check your genome
before saying YES?? its a future the scares me.

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thirdstation
The non-beta-site version of the article is here:
[http://spectrum.ieee.org/biomedical/devices/the-gene-
machine...](http://spectrum.ieee.org/biomedical/devices/the-gene-machine-and-
me)

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corwinbad
Forget sequencing - DNA synthesis and designing of new genetic programs/apps
(new creatures) using synthetic biology and software like Genome Compiler
(genomecompiler.com) is the interesting future.

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barryrandall
Sequencing is critical to quality control in synthetic biology.
Better/cheaper/faster sequencing = better/cheaper/faster synthesis. It's like
chocolate and peanut butter.

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caycep
Problem is there is still the "genome-clinic" gap.

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monochromatic
Genomics in general has failed to live up to its promises to revolutionize
medicine. Why will a cheaper version of the same thing fare significantly
better?

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Retric
It does not show up as just one thing.

There are several 'wonder' cancer drugs for example that came from analyzing
DNA and people know to use them by doing DNA sequencing. It's also helped
'cure' several rare but debilitating diseases. Honestly, it's rapidly
approaching the value of antibiotics which clearly was a major revolution.

Anyway, the reason why full DNA sequencing is so important has a lot to do
with research. When you know what some sequence does then you can look for
that. But, being able to build a database of say 100,000 peoples full DNA
sequence for say a billion or less let's you look for those sequences far more
easily.

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monochromatic
Approaching the value of antibiotics? That's a pretty bold claim, and it seems
entirely unsupported.

