Hacker News Board Hacker News, browsed like a classic message board
Live data from Hacker News

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

beta.spectrum.ieee.org

Post reply on HN
Print view View original

21–30 of 46 posts

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

#21

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…

We hope as more data becomes available, the field will become more and more definite. We will use indefinite mathematics in genomic interpretation until we have near perfect information.

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

#22

Post by jonathansizz »

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?

It doesn't make a whole lot of difference at the moment; at present the main utility is related to genealogy rather than health, which the current genotyping chips are adequate for. Until our ability to interpret whole genomes progresses beyond its current rudimentary level, there isn't much more for you to get excited about.

In any case, you just have to wait a few more years and you'll be able to get (the non-junk bits of) your genome sequenced for close to $50 anyway.

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

#23

Post by Natsu »

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…

Incidentally, anyone who wants to play with some genome processing is encouraged to download pygr[1]. You can connect to worldbase[2] and explore all the different genomes they have on their server using Python.

[1] http://code.google.com/p/pygr/ [2] http://code.google.com/p/pygr/wiki/ServingDataUsingWorldbase

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

#24

Post by hxrts »

waiquoo wrote: post #16
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…

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.

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

#25

Post by JulianMorrison »

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 big is a fully sequenced genome, as a file?

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

#26

Post by barryrandall »

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.

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

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

#27

Post by xaa »

JulianMorrison wrote: post #25
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 big is a fully sequenced genome, as a file?

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/

~800MB for human genome

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

#29

Post by lifeisstillgood »

gourneau wrote: post #12
tocomment wrote: post #8

Earlier quoted context omitted.

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

Are you now open to receiving pull requests - there seemed to be a legal problem accepting a patch on the above, and if so what issues do you need fixed :-)

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

#30

Post by hyperbovine »

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

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.
Post reply on HN