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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

#11

Post by bioinformatics »

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?

There's a lot of differences, especially because 23andme just checks the "different" nucleotides for some specific genes. Having your full genome sequenced would mean that we would know every single nucleotide from you, so things we still don't know are important might become vital in the future.

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

#12

Post by gourneau »

tocomment wrote: post #8
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…

So how does Django relate to gene sequencing?

It helps to think of our machines as fancy scanners. We have to build software to help our users manage their petabytes 'scanned' of data.

We also build developer tools to help the researchers and scientist extend our system with plugins.

One cool thing is that all of our software is open source. Check out the Django project I work on here.

https://github.com/iontorrent/TS/tree/master/dbReports

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

#13

Post by bioinformatics »

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…

If I can telcommute I have some free time.

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

#14

Post by 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.

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

#16

Post by waiquoo »

hxrts wrote: post #5

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 o…

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.

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

#17

Post by gngeal »

bioinformatics wrote: post #11
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?

There's a lot of differences, especially because 23andme just checks the "different" nucleotides for some specific genes. Having your full genome sequenced would mean that we would know every single nucleotide from you, so things we still don't know are important might become vital in the future.

"Having your full genome sequenced would mean that we would know every single nucleotide from you"

Unless he's a genetic mosaic, also known as the "reality is hard to squeeze into our all too simplistic data model" problem.

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

#18

Post by waiquoo »

corwinbad wrote: post #15

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.

"Forget reading, we have the ability to write"

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

#19

Post by datz »

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 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.

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

#20

Post by datz »

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…

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