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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

#41

Post by tomkinstinch »

xaa wrote: post #27
JulianMorrison wrote: post #25

Earlier quoted context omitted.

How big is a fully sequenced genome, as a file?

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

When compressed relative to a reference genome, you can get a ~2.9Gbp human genome down to ~3.3MiB of data[1]. Sequences are actually pretty compressible in general, owing to conservation of functional domains and repeats.

Data from next-gen sequencers have many small overlapping segments though, so the raw output takes up MUCH more space.

By the way, for anyone looking for more information about some of the methods currently being used for sequencing (Illumina, 454), check out these videos from the WUSTL Genome Center:

http://gep.wustl.edu/curriculum/course_materials_WU/introduc...

They don't cover Ion Torrent, which is unfortunate because it is way cool. gourneau can probably point to a better video, but here are a couple for Ion Torrent:

http://www.youtube.com/watch?v=W3jPTBU9vF8

http://www.youtube.com/watch?v=yVf2295JqUg

...and the Nature paper:

http://www.nature.com/nature/journal/v475/n7356/full/nature1...

1. http://dhruvbird.com/genome_compression.pdf

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

#42

Post by Retric »

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?

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.

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

#43

Post by 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.

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

#44

Post by Retric »

monochromatic wrote: post #40
jostmey wrote: post #37

Earlier quoted context omitted.

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...

Don't confuse value with economic activity. Painkillers are a perfect example of something that's cheap because of manufacturing costs but whose impact on use is extreme.

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

#45

Post by monochromatic »

Retric wrote: post #42
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?

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 resea…

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

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

#46

Post by noreply11 »

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…

I emailed you about meeting up at Pycon but I never heard back.
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