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Illumina, Leaning on Amazon, Looks to Be Hub of Genomic Computing

Xconomy San Diego — 

[Updated: 11:35 am PT] Illumina wants to be not just a hardware company, but really an integrated hardware/software company that’s the Apple of the genomics business. Now the San Diego-based company is moving that direction, in a bid that could help the genomics community grow, by offering lots of free storage and processing of DNA data from its machines to go with a store full of apps people can buy to help interpret genomics information.

Illumina (NASDAQ: ILMN) is announcing today that its Basespace computing program is graduating from free beta-test mode into a new line of business. The company is using a “freemium” model in which its customers will get 1 terabyte of free storage of DNA data (about 10 genomes at today’s data compression rates). An extra terabyte will cost $250 per month or $2,000 a year, says Alex Dickinson, Illumina’s senior vice president of cloud genomics.

The Basespace program will also throw in free data processing to align the 3 billion base units of DNA and detect variants in a genome, which typically costs about $1,000 per genome and takes about 48 hours, Dickinson says. Illumina is offering that for free, and says it can do it in about a day, partly through some of its own algorithm improvements for DNA processing, and by leaning heavily on cloud computing infrastructure provided by its partner, Amazon Web Services.

By offering so much storage and processing power for free, Illumina is hoping to broaden the appeal of genomics to more biomedical scientists and physicians who aren’t already fully equipped like the elite sequencing centers, such as the Broad Institute or University of Washington.

As sequencing itself has gotten much faster and cheaper—estimates are that sequences can be generated for $1,000 and a day’s work by year’s end—scientists have been struggling to turn that data into useful knowledge. To help customers sift through it all, Illumina’s vision is to enable customers to sequence a genome, have the data available on cloud servers at the end of a day’s run, and then offer a snazzy app store full of programs third-party vendors offer to help analyze and interpret the results at the click of a mouse.

Alex Dickinson, senior vice president of cloud genomics at Illumina

“We think this will create a rich ecosystem for our customers,” Dickinson says.

The Basespace program is a significant strategic move for Illumina. It’s the market-leading maker of gene sequencers, and has traditionally made its money by selling hardware and consumable chemicals to run its instruments, not on computing. The company isn’t saying how much it has invested in this effort to provide computational support, or how long it expects it will be before it turns from a loss leader into a profit center. But Illumina clearly does see computing becoming an increasingly important part of business, particularly through creating an app store on Basespace.

Just like Apple does on the iPhone and iPad, Illumina plans to take a 30 percent cut of the sales from each of the software apps that customers buy when they use its sequencing hardware.

“Illumina is very serious about this,” says Doug Bassett, the chief scientific officer of Redwood City, CA-based Ingenuity Systems, a genetic analysis software company and Basespace partner. “They are very engaged as a partner, and committed to seeing this through and making it a success for their customers. It feels like they are making all the right moves.”

While much has been made about the rapid innovation in DNA sequencing itself, less attention is paid to all the extra time and money scientists spend storing, processing, and attempting to analyze and interpret all those terabytes of DNA data to gain some biological insight. Goldman Sachs analyst Isaac Ro said in a report last fall that sequencing labs are looking to boost their spending on bioinformatics from 2 percent of their budget to 10 percent in the short term, and potentially 50 percent over a period of years.

Illumina started offering Basespace storage for free last October to customers who were using its $125,000 MiSeq instrument, a bench-top sequencer designed to appeal to scientists outside of the hard-core sequencing labs and to compete with a low-cost bench-top sequencer from Ion Torrent Systems, a unit of Carlsbad, CA-based Life Technologies. The Basespace program will be integrated into the workhorse HiSeq product line in the early fall, Illumina spokeswoman Jennifer Temple says. The HiSeq 2000 model of today retails for $640,000 and the HiSeq 2500 coming in the fall will retail for $740,000, Temple says.

If the Basespace program is successful, it will end up simplifying some almost comical inefficiencies in the way DNA data is managed today. Genomic researchers, some of whom are leery of sending so much of their precious data to a cloud server that could be somewhere in rural Oregon, are known to keep files on their own storage disks and share them with colleagues via FedEx. Many researchers depend on open-source software applications that are designed to do narrow tasks, and it’s common for researchers to store DNA data in old school Excel spreadsheets that were never intended to hold such information.

By simplifying so much of the way the data is generated, stored, processed, transferred, secured, downloaded, and analyzed, Illumina is hoping its Basespace program will appeal to customers who don’t have the time or inclination for such hairy IT issues. By managing the data side of the problem, Dickinson says Illumina is hoping to provide a more attractive suite of offerings to the next big wave of customers—physicians and hospitals who are becoming interested in using genomics to help improve patient care.

Over time, Dickinson says, the Basespace ecosystem should become more and more valuable to Illumina and its customers. As data compression technology improves in a couple of years, 1 terabyte of free storage could hold 10 times more genomes, he says.

Even without third-party apps available for beta customers to play with, the majority of MiSeq customers who have Basespace are using it to store and process their data, and they are “regularly connecting,” he says. Illumina is hoping that as more apps get developed, it will make the whole experience more valuable to the customer.

While some entrepreneurs might chafe at letting Illumina maintain the billing relationship with customers, and letting it take a 30 percent cut of app sales, it will be fascinating to see what the Basespace program does for bioinformatics companies. Bassett, for one, says he’s excited that Ingenuity’s analysis software will be essentially right in front of the customer’s nose at the exact moment he or she finishes a sequencing run and is looking for new ways to slice, dice and analyze the data. The simplicity of getting analysis done will be especially critical if demand is really going to take off for clinical genomics, Bassett says.

“As you move into the clinic, not every clinical lab has a SWAT team of computational biologists and bioinformaticians with next-gen sequencing data pipelines,” Bassett says. “They want it done, the data canned and available and delivered in a robust way.”

There are issues with the coming demand for clinical genomics, which I cautioned about a few weeks ago, but there’s no denying the surge of interest in this new real-world use of genomic medicine, which was described in a recent New York Times series. Illumina clearly has its eye on these kinds of customers as it seeks to fend off competitors, and continue to hold a dominant position in the gene sequencing business.

“From a competitive point of view, we want to take our strong market share in the instrument area and flip that into a strong opportunity to build an ecosystem,” Dickinson says. “We’re seeing that with MiSeq, what the industry really needs is a place where you have a vibrant ecosystem, full of competing and complementary choices on how bioinformatics gets done.”

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  • dkural

    Seven Bridges Genomics launched an app store for genomics, processed hundreds of genomes and terabytes of data in our online genomics platform at http://www.sbgenomics.com – and represent a hardware-neutral solution to create an ecosystem. There is an SDK for app developers, collaboration features for permission-based data sharing, and many open source apps.