Launch of RT Analyzer offers bespoke biochips, expanding applications.
By Kevin Davies
Oct. 8, 2008 | Michelle Lyles has a flying pig in her office. It’s a long story—something to do with her former employer and the challenges of raising fat sums of venture capital. She hopes it’s a good omen for her latest challenge at febit, which has reached a critical crossroads in its efforts to wrest business away from the titans of the microarray field—Illumina, Affymetrix, Agilent, and Nimblegen. Febit hopes that the commercial release last month of the Geniom RT (RealTime) Analyzer, a $100,000 benchtop instrument, will provide the flexibility and affordability researchers are seeking.
Febit was launched in Heidelberg, Germany, in the late 1990s. Of the name, “Fe” is derived from the last name of the co-founders, Cord and Peer Staehler (meaning ‘steel’ in German), while the bit is for bits and bytes. The majority shareholder is Dietmar Hopp, who co-founded SAP and is a major stakeholder in German biotechnology.
Last month’s launch of the RT Analyzer is a strategic shift away from the company’s flagship instrument, the Geniom One, which both synthesizes the biochips and serves as the experimental platform. “The mission is the same but the commercialization path has changed, because the market changed,” says Lyles, VP sales and marketing. “By the time we got out there with the Geniom product, you had the Affys and Illuminas and Agilents that provided the commercial high-density chips.”
14 Geniom One instruments have been sold since 2006. It is expensive (around $275,000) and has a lower probe density than competitors that provide high density chips. The RT Analyzer provides the same core array technology, but now febit is handling the rapid custom synthesis.
Lyles says febit has “three pillars of technology”—engineering, bioinformatics, and applications. The engineering strength is in the microfluidics, integrated with temperature control and digital micromirror device (DMD) technology from Texas Instruments. “It’s the same DLP chip you find in a projector,” says Anthony Caruso, VP global informatics and former president of LION Bioscience. “When febit first started, they’d buy projectors and take the DLP chips out of the machine, because we were too small to get them from directly Texas Instruments.”
The integration of microfluidics and DMD technology provides rapid, highly customizable synthesis of biochips. The mirrors shine certain wavelengths onto the light-sensitive protector groups at the tip of each oligo probe, enabling elongation to occur. The array is not a single glass slide but a sandwich, providing a 3-D tunnel with eight microchannels and temperature control.
The other two pillars are bioinformatics and applications, which include HybSelect (see, “Hope for HybSelect”) for resequencing on next-gen sequencing platforms, synthetic biology, and microRNA.
Febit is probably not the platform for those contemplating large-scale, genome-wide association studies. “We thought about competing with Affy [initially], but given that they have ten times as many features, we made the strategic decision to turn our focus to targeted analysis and enhanced applications” says Caurso. “We can’t do as many features, but you don’t need to do as many features if you’re doing targeted analysis and new applications.”
Theoretically, febit could design up to 500,000 SNPs on a biochip by utilizing every mirror. But Caruso points out the Geniom CCD camera does not offer the same resolution as a scanner, so he prefers to leave a space between the features. The highest practical density for expression profiling is about 250,000 features in a checkerboard pattern, all of it completely programmable on the instrument. Using every feature might be feasible in HybSelect and other applications that do not require imaging.
Adds Lyles: “Because we’re using CCD imaging for detection rather than fluorescence scanning (which employs a laser), you can read the chip over and over again, so you get data in real time. This enables dynamic detection and opens the door to new applications for microarrays including melting curves, and thermocycling, which you can’t do with other technologies.” Researchers can do PCR amplification and primer extension on the chip, which enables applications such as FFPE (formalin-fixed paraffin embedded) analysis. “You can’t do that on an Affy or an Illumina,” she says.
Febit has also found that many researchers preferred not to synthesize the oligo probes themselves when they had the convenience of ordering bespoke biochips. “We’ll synthesize the chip for you and send it to you,” says Caruso. “Then you use the RT Analyzer for the experiment.” Alternatively, researchers can use febit’s experimental service.
“It’s like the Apple store,” he says. “If you have the RT Analyzer and you can’t synthesize the chip, you still have all the tools available. You can go to the febit store—you can pick the genes you’re interested in, and then electronically—once you’ve designed what you want—you send it to the febit store. We get the order, synthesize the chip, and send it back to you.”
For targeted resequencing or HybSelect, febit provides users with software that takes genomic and SNP data and calls the probes in any given chromosomal region. Synthesizing a biochip of “shortmers” (about 25mers) would take a mere six hours—whether in Germany or febit’s U.S. facility in Lexington, Mass. Febit promises a two-week turnaround time, though Lyles expects it will be quicker than that. And once the chip has been designed, febit will keep it in stock if requested. “We’re encouraging people to run a trial first, including the design of a chip. For a customer that wanted to start an experiment, you could do a trial run using our services,” says Lyles.
Another key advantage of the febit chip is flexibility says Caruso: “One of the beauties of the instrument is we can do any organism at this point.” A good example is the first draft of the sea urchin genome. “We cherry picked probes for those genes including replicates,” says Caruso. “You couldn’t go with Affy because they don’t make sea urchin chips.”
The ease of biochip synthesis affords a convenient shuttling between theoretical bioinformatics calculations and empirical wet lab experiments. These allow several iterations of a particular chip design to allow researchers to run a few cycles during a week or two to develop the optimal assay. “The flexibility doesn’t cost us anything extra,” adds Lyles. “We don’t hold customers hostage to the idea that they want to customize. We treat a ‘custom design’ the same as something off the shelf design.”
Febit is one of several vendors that will be featured in an imminent publication from Harvard Medical School scientist Winston Kuo, comparing a handful of array platforms. The study evaluated emerging array and nanoscale volume technologies including ABI Taqman, BioTrove, Fluidigm, Roche 480, NanoString, and Phalanx Biotech. “We are witnessing a trend in the microarray community towards developing and utilizing focused arrays,” says Kuo. Full details must await publication, but Caruso says, “Our performance is very respectable.”
Among the near-term applications for the RT Analyzer will be targeted enrichment for next-gen resequencing. “You can use HybSelect to reduce the complexity of your genomic DNA sample by targeted hybridization and elution of regions of interest,” says Lyles, who anticipates a huge market in the coming years. Unlike other services, “we’re the only ones who offer the hardware to do that,” says Lyles. Caruso is working on a suite of bioinformatics modules to design chips for the RT Analyzer for targeted sample enrichment. Customers would purchase the module, put in the instrument to enable the Analyzer to do the hybridization and elution.
Another growing area is microRNA profiling. “We have the chip. We’re always the first,” says Lyles. Four months after releasing miRBase 11.0 biochip, febit is out with version 12.0—one day following release of miRBase 12.0 from the Wellcome Trust Sanger Institute. And there’s additional room on the biochip for groups to add their own microRNA targets. Disease chips, pathway chips, and protein-DNA binding round out the offerings.
Lyles admits the market demand to synthesize custom chips is currently lacking, but expects febit’s new commercialization path to be ready when it rebounds. “The RT Analyzer will be the workhorse, and once it has a foothold in the market, then let’s put the Geniom One in core facilities to feed chips to the satellites.”
Febit’s U.S. facility is awaiting its first RT Analyzer. The second is promised to Prognosys in San Diego, a company founded by Mark Chee, who previously founded Illumina. The company hopes it will be the first of many.
Hope for HybSelect
The first pilot user of febit’s HybSelect technology is associate investigator Matthew Huentelman at the Translational Genomics Research Institute (TGen) in Phoenix. Febit plans to officially introduce the technology in early 2009.
Huentelman is an enthusiastic user of the Geniom One, which TGen has used since 2006. “It’s exciting because it’s fully user programmable,” he says. “You can print whatever you want—whatever you dream up today, you can print it and come in the next day and use it in your experiments.” He studies the genetics of autism and Alzheimer’s disease. “We can tile across an interesting region of the genome with full customizability. You’re able to make the chip in the same machine that you use it.” The chip design comes into its own “when you’re ready to validate some regions. The power is the customizability.”
The TGen group might start by identifying copy number variations (CNVs) using a typical SNP array. From there, it uses the Geniom One to fine map the CNV region and identify the relevant genes. The HybSelect protocol selects specific regions for targeted resequencing using next-gen platforms. “The goal is to use this approach to sequence focused regions of the genome across large numbers of individuals,” says Huentelman.
One typical experiment might be to take 100 key genes, make a custom array of exons of those genes to enrich those sequences from the rest of the genome. Those genes are captured on the chip, eluted, and then run on a next-gen sequencing platform.
The probe design process is “user friendly as long as you have a good bioinformatics team on board,” Huentelman says. “You want to provide intelligently designed probes to ensure the highest quality data. You need to have a standalone oligo picker that picks the probes for you. We prefer to pick the probes ourselves. The output from that gets uploaded.”
Huentelman admits, “we’re still trying to fully characterize the degree of enrichment we are seeing when using HybSelect.” If he has one major criticism, it is the number of features on the chip. “It’s great to be customizable but we need a jump in density for them to be competitive.” He adds: “The field would really benefit from a robust cost-effective approach for enriching regions of the genome for sequencing—that’s the ultimate goal in our pilot use of febit’s HybSelect.”
This article appeared in Bio-IT World Magazine.
Subscriptions are free for qualifying individuals. Apply Today.