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Ion Torrent’s chip-based genome sequencer is poised to revolutionize medicine

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Re: Ion Torrent’s chip-based genome sequencer is poised to revolutionize medicine

#31

Post by lifeisstillgood »

monochromatic wrote: post #28

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?

I struggle to believe this is true - as a simple one the different cancers that can be identified by gene sequencing tell doctors which treatments will be more or at all effective even when physical symptoms look similar.

There are i am sure many more examples - what do you expect - a couple of flashing LEDs and hey presto cured?

Re: Ion Torrent’s chip-based genome sequencer is poised to revolutionize medicine

#32

Post by youngerdryas »

datz wrote: post #19
patdennis wrote: post #7

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?

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…

I can't find the reference but micro-RNA as short as two base pairs has been shown to affect gene expression. Nonlinearity may seriously inhibit meaningful analysis.

Re: Ion Torrent’s chip-based genome sequencer is poised to revolutionize medicine

#33

Post by owlmonkey »

hxrts wrote: post #24
waiquoo wrote: post #16

Earlier quoted context omitted.

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…

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 tim…

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

Re: Ion Torrent’s chip-based genome sequencer is poised to revolutionize medicine

#34

Post by owlmonkey »

datz wrote: post #14

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…

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.)

Re: Ion Torrent’s chip-based genome sequencer is poised to revolutionize medicine

#35

Post by owlmonkey »

patdennis wrote: post #7

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?

Some interesting structural differences are not captured by 23andMe nor even with technology like Ion Torrent, for example repeat sequences related to ALS, Huntington's, etc. To get the full picture ultimately you'll need a full sequence with longer read lengths to span the structural variants, and you'll also want the methylation/epigenetic markers which convey which genes are turned on or turned off. Just knowing you have the gene doesn't mean nearly as much without knowing if it is turned on!

Re: Ion Torrent’s chip-based genome sequencer is poised to revolutionize medicine

#36

Post by Kliment »

gourneau wrote: post #2

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 engin…

How do you deal with patents? In my view, an open source shop is not compatible with holding patents, but the space is very heavily patent-encumbered. How do you resolve the conflict?

Re: Ion Torrent’s chip-based genome sequencer is poised to revolutionize medicine

#37

Post by jostmey »

monochromatic wrote: post #28

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?

Really? By what standard are you holding this revolution? From my perspective, the field is growing rapidly and I believe it will eventually take off.

Re: Ion Torrent’s chip-based genome sequencer is poised to revolutionize medicine

#38

Post by Retric »

hyperbovine wrote: post #30
xaa wrote: post #27

Earlier quoted context omitted.

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/ ~800MB for human genome

That is roughly the size needed to represent 3.3 billion ACTGs , however sequencer output is much larger since each base is sequenced many times, and accompanying metadata (quality information) is also included. File sizes for current sequencer output is on the order of 100-300gb compressed. It's big enough to create real roadblocks when you are trying to do analysis.

It can also end up well below 800MB per person if you encode it as known sequences of DNA + tiny new random variations.

Re: Ion Torrent’s chip-based genome sequencer is poised to revolutionize medicine

#39

Post by hyperbovine »

Retric wrote: post #38
hyperbovine wrote: post #30

Earlier quoted context omitted.

That is roughly the size needed to represent 3.3 billion ACTGs , however sequencer output is much larger since each base is sequenced many times, and accompanying metadata (quality information) is also included. File sizes for current sequencer output is on the order of 100-300gb compressed. It's big enough to create real roadblocks when you are trying to do analysis.

It can also end up well below 800MB per person if you encode it as known sequences of DNA + tiny new random variations.

True, but in order to do that you have to know what the new random variations are. Output from existing sequencers, as well as the current crop of algorithms, are not good enough to do that with high confidence. Thus, people tend to keep everything. You can get some gain by doing reference-based compression, but you're still looking at on the order of 100s of gb per sample.

Re: Ion Torrent’s chip-based genome sequencer is poised to revolutionize medicine

#40

Post by monochromatic »

jostmey wrote: post #37
monochromatic wrote: post #28

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?

Really? By what standard are you holding this revolution? From my perspective, the field is growing rapidly and I believe it will eventually take off.

See, e.g., http://pipeline.corante.com/archives/2010/06/18/the_economic...
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