Pacific Biosciences Team Identifies Asian Origin for Haitian Cholera Bug

Rising importance of NGS for emerging infectious diseases!
excerpted from Bio-ITworld URL above

December 9, 2010 | In a dramatic piece of ultra-quick genetic detective work, next-generation sequencing company Pacific Biosciences has decoded the sequence of the strain of bacteria responsible for the deadly cholera outbreak in Haiti. The findings, which confirm the putative Asian origin for the devastating disease, are published online in the New England Journal of Medicine today. 
....

Each of the five strains took about one day to sequence to about 60X coverage. “They did an outstanding job in the analysis,” says Waldor. “Most of the credit for this project goes to Eric and his team.”  
“The rapidity and depth of the sequence using this 3^rd-generation sequencing technology has enormous potential to transform how we can analyze outbreaks of infectious disease and even the prediction of future outbreaks because of the power of their technology.” 
According to PacBio, the five cholera genomes were sequenced on November 12 to 12-15X coverage in less than two hours. Further runs bumped up the coverage to 60X over the course of the day. Over the next three days, the sequence data were subjected to in-depth analysis, including genome assembly, annotation, and sequence comparisons, including comparisons to nearly two dozen published cholera genomes.  
...
From PacBio’s perspective, Schadt says that “real-time monitoring” of pathogens opens the door to using his firm’s technology as “a routine surveillance method, for public health protection in addition to pandemic prevention and response.” 

At ASHG, Ion Torrent Drums Up Interest; Provides Preliminary Specs for PGM

WASHINGTON, DC – Ion Torrent revealed some preliminary specs for its Personal Genome Sequencer, due to be launched later this year, as the Life Technologies business unit presented the instrument to potential customers at its booth at the American Society for Human Genetics meeting this week. The speed of the instrument — a run takes approximately two hours, and several runs can be performed in a day — is what appears to be most attractive to potential customers, Maneesh Jain, Ion Torrent's vice president of marketing and business development, told In Sequence.
The first version of the PGM will sell for $49,500, plus a $16,500 server to analyze the data.
Initially, the machine will produce about 10 megabases of data per run, or about 100,000 reads of 100 base pairs each, using the so-called 314 chip, which has about 1.5 million wells and will cost $250. Reagent kits for template preparation, library preparation, and sequencing will cost another $250, bringing the total consumables cost per run to approximately $500.
In the first half of 2011, Ion Torrent plans to launch the 316 chip, with about 6 million wells, which will increase the output per run to 100 megabases and which will cost about twice as much as the 314. Additional chip upgrades will follow, with details to be revealed next year.
Sample prep, which Jain said takes about a day and can be done in batches of six to eight samples, requires an emulsion PCR protocol, which will be simplified over time. "We focused on the sequencing initially," he said, adding that the next step will be to optimize the sample prep. Life Technologies said previously that sample prep for the PGM would eventually be able to use the EZ Bead system, which was originally developed for the SOLiD system.
Read full article here

Re-Defining Storage for the Next Generation

Do have a go at this article citing David Dooling, assistant director of informatics at The Genome Center at Washington University and a few others 
Looking ahead, as genome sequencing costs lower there's going to be more data than ever generated. And the article rightly states that every postdoc with a different analysis method will have a copy of a canonical dataset. Personally, I think this is a calling for tools and data to be moved to the cloud.
Getting the data up there in the first is a choke point.
but using the cloud will most definitely force everyone to only use a single copy of shared data.
Google solved the problem of tackling large datasets with slow interconnects with map reduce paradigms.
There are tools available that make use of this already but they are not popular yet. I still get weird stares when I tell them about hadoop filesystems. Sigh. More education is needed!

In summary, my take on the matter would be to have a local hadoop FS for storing data with redundancy for analysis. and move a copy of the data to your favourite cloud as archival and sharing and possibly data analysis as well (mapreduce avail on Amazon as well)
Another issue is whether researchers are keeping data based on sentimentality or if there's a real scientific need.
I have kept copies of my PAGE gel scans from my Bsc days archived in some place where the sun doesn't shine. but honestly, I can't forsee myself going back to the data. Part of the reason I kept it was that I spent a lot of time and effort to get those.

Storage, large datasets, and computational needs are not new problems for the world. They are new to biologists however. I am afraid that because of miscommunication, alot of researchers out there are going to rush to overspec their cluster and storage when the money can be better spent on sequencing. I am sure that would make some IT vendors very happy though especially in this financial downturn for IT companies.

I don't know if I am missing anything though.. comments welcome!

Next-Next Gen Seq

Rofl I like the title!

Read all about 3rd gen sequencing or single molecule sequencing at the methagora blog

"While the technology feature, “DNA sequencing: generation next-next”, was at press, Pacific Biosciences of Menlo Park, California stunned the community with their announcement of a single molecule sequencing technology they claim will provide a complete human genome in 15 minutes by the year 2013. Although Pacific Biosciences was founded in 2004, the company had been very ‘hush hush’ about their technology development. But that veil of secrecy was lifted during the Advances in Genome Biology and Technology meeting held February 6th to 9th at Marco Island, Florida where Stephen Turner, chief technology officer, presented the first preliminary data on the system."