Illumina has received US Patent No. 7,803,537, “Parallel genotyping of multiple patient samples.” The patent claims a method for the parallel genotyping, or other sample analysis, of multiple patients by direct sample immobilization onto microspheres of an array. The patient beads can then be used in a variety of target analyte analyses, according to the patent.

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Illumina has also received US Patent No. 7,803,751, “Compositions and methods for detecting phosphomonoester.” The patent provides a method of modifying a phosphomonoester moiety of a target compound by: a) providing a target compound having an electrophilic moiety and a phosphomonoester moiety; b) contacting the target compound with a first carbodiimide compound under conditions for preferential addition of the first carbodiimide compound to the electrophilic moiety over the phosphomonoester moiety, forming an electrophile-protected target compound; and c) contacting the electrophile-protected target compound with a second carbodiimide compound and a nucleophilic compound under conditions for addition of the nucleophilic compound to the phosphomonoester.

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Panomics, now Affymetrix, has received US Patent No. 7,803,541, “Multiplex branched-chain DNA assays.” The patent claims methods for detecting two or more nucleic acids in a multiplex branched-chain DNA assay. Different nucleic acids are captured through cooperative hybridization events on different, identifiable subsets of particles or at different selected positions on a spatially addressable solid support. Kits are also provided.

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Affymetrix has also received US Patent No. 7,803,609, “System, method, and product for generating patterned illumination.” A method for generating an interference pattern at a probe array is described. The method includes directing light at a first waveguide and second waveguide, where the first and second waveguides are positioned adjacent to each other and the output from the first and second waveguides produce an interference pattern; and directing the interference pattern at the probe array. According to the patent, the probe array has a biopolymer affixed to the surface of a support selected from the group consisting of nucleic acids, oligonucleotides, amino acids, proteins, peptides, hormones, oligosaccharides, lipids, glycolipids, lipopolysaccharides, phospholipids, inverted nucleotides, peptide nucleic acids, and meta-DNA. The detector can be a charge-coupled device; an electron-multiplying, charge-coupled device, a complementary metal-oxide semiconductor, active pixel sensor, or photomultiplier tube.

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The University of California of Oakland has received US Patent No. 7,803,542, “Signal-on architecture for electronic, oligonucleotide-based detectors.” The patent provides architecture for oligonucleotide-based detectors that lead to order-of-magnitude increases in signal gain and sensitivity compared to other detectors. The detectors rely on base pairing between two oligonucleotide strands, the sensor strand and the blocker strand. The formation of comparatively rigid, duplex DNA prevents the redox moiety from approaching the electrode surface, suppressing Faradaic currents, according to the patent. When a target is added to the system, the target displaces the blocker strand and binds to the sensor strand, liberating the end of the redox-labeled oligonucleotide to produce a flexible element. This, in turn, allows the redox moiety to collide with the electrode surface, producing a readily detectable Faradaic current.

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Chung Hua University of Hsinchu, Taiwan, has received US Patent No. 7,805,175, “Microarray bioprobe device integrated with a semiconductor amplifier module on a flexible substrate.” The patent provides a microarray integrated with a semiconductor amplifier module, which integrates microarray probes and thin film transistors on a substrate by micro-electro-mechanical system processes and semiconductor processes. According to the patent, a signal from the microarray is amplified through a near amplifier to increase signal-to-noise ratio and impendence matching.

By Justin Petrone

The microarray market is poised to grow to $900 million by 2013, according to an Illumina official, who noted that the company hopes to capture its share with next-generation genotyping arrays for future genome-wide association studies.

At the same time, high demand for its chips and instruments has led to manufacturing constraints that the firm is now working to overcome, according to CEO Jay Flatley.

Flatley said this week that the San Diego company estimates the global market for microarrays today is approximately $800 million, and expects it to grow 13 percent to around $900 million within two years.

This market is characterized by growth in demand for genotyping arrays accompanied by “shrinkage” in the gene-expression market, he said.

Flatley made his comments this week at the UBS Global Life Sciences Conference in New York, which was webcast.

The bulk of Illumina’s current array sales are to researchers conducting genome-wide association studies, and Flatley said that after a slowdown in demand for whole-genome genotyping chips last year, the company experienced consecutive sales growth for its arrays. He noted that Illumina has seen a “very rapid transition” of customers to its HumanOmni2.5-Quad DNA Analysis BeadChip.

Illumina began shipping its Omni2.5 in June, along with its HumanOmni1S-8 BeadChip, which contains the majority of new content present on the Omni2.5 and provides a upgrade path for current or former users of Illumina’s Omni1-Quad or OmniExpress BeadChips (BAN 6/8/2010).

Illumina is also seeing demand for its HiScan SQ instrument, which allows customers to process arrays and sequence samples using a single system. Flatley noted, however, that the company is still experiencing manufacturing constraints that have forced it to delay delivering the HiScan to customers.

The reason for the constraints stems from the fact that Illumina has experienced even stronger demand for its high-throughput HiSeq 2000 sequencing instrument, which shares many components with the HiScan.

Illumina has made “substantial progress” on increasing the manufacturing output of HiSeq by 50 percent this quarter, Flatley said, but “constraints in the supply chain” mean that the company will carry over a “backlog of orders” into the fourth quarter.

That also means that production of the HiScan will “continued to be constrained” through the third quarter, Flatley said. “One of the design objectives was to make the imaging module of HiSeq almost identical to HiScan,” said Flatley. “While that in the long run is a great design goal, in the short run it’s stressing the supply chain.”

Flatley initially discussed Illumina’s effort to ramp up manufacturing during the firm’s second-quarter earnings call in July (BAN 8/3/2010).

Europe and Asia

Illumina is currently investing in manufacturing and logistics in general. During the UBS Global Life Sciences Conference this week, Flatley said that the company is currently expanding its regional distribution center in Europe, located in Eindhoven, the Netherlands, to meet local market demand.

“We have experienced a lot of ramp-up in our requirements for storing reagents and instrumentation locally in Europe,” Flatley said, noting that 30 percent of the firm’s revenues are generated there. Illumina is now quadrupling the capacity of its European regional distribution facility and expects the upgrade to be completed early next year.

“This is going to be huge in increasing our ability to deliver reagents, instruments, and spare parts to our customers in Europe,” Flatley said.

Meantime, Illumina is looking to move more of its product manufacturing from San Diego to Singapore. Looking to take advantage of Singapore’s geographic location, low-cost structure, and tax incentives, Illumina has leased a 36,000-square-foot facility in the Southeast Asian country since 2007 and began manufacturing its arrays there in 2008. It currently manufactures around half of its chips in Singapore (BAN 3/30/2010).

Citing the costs and proximity to larger Asian markets, such as India and China, Flatley this week said that Illumina hopes that by the second quarter of 2011 it will be able to manufacture 70 percent of its arrays in Singapore.

The company also said it aims to manufacture 50 percent of its sequencing consumables in Singapore by the end of next year, and will begin manufacturing some of its digital microbead-based BeadXpress and Eco RT-PCR systems in the country in Q2 2011.

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By Ben Butkus

DUBLIN – About a month and a half after Illumina announced its foray into the PCR space with the launch of its Eco real-time benchtop PCR system, marketing specialists from the company shared some additional information about the system and its potential applications at Select Biosciences’ qPCR Europe conference, held here this week.

In a technology showcase session at the conference, Judy Macemon, director of PCR marketing at Illumina, highlighted some of the rationale behind Eco’s development as well as technical specifications of the system that help it maintain industry-standard performance at a price point of about $13,900.

Meantime, in a separate conference presentation, Sandrine Miller, senior product manager at Illumina, discussed the Eco’s amenability to conducting affordable genotyping using high-resolution melt analysis.

Illumina unveiled the Eco system in late July along with the announcement that it had acquired privately held real-time PCR and nucleic acid-analysis firm Helixis in a deal worth as much as $105 million (PCR Insider, 7/29/10).

Helixis, founded in 2007 by the California Institute of Technology’s David Baltimore, Alex Dickinson, and Axel Scherer, had developed a qPCR system called Pixo that the company claimed would cost about a quarter the price of other qPCR systems while maintaining the same level of performance.

Illumina took over development of the platform leading up to its acquisition of Helixis, and at this week’s qPCR conference, Macemon said that the new platform began shipping in August, “rebranded and looking a little different.” She also identified the National Institutes of Health’s National Institute of Dental and Craniofacial Research as one of the first paying customers.

Macemon, who joined Illumina from Helixis, said that the company’s rationale for developing the platform was market research showing that the biggest barrier to wide adoption of real-time qPCR was pricing.

According to Macemon, Helixis’ research revealed that typically 10 or more people in a laboratory share an RT-qPCR instrument. In addition, she said that despite the recent industry trend to increase the throughput of RT-qPCR systems, about 80 percent of researchers use fewer than 50 sample wells per run; hence Helixis and Illumina’s decision to develop a 48-well platform.

In essence, she added, scientists were being forced to choose between high performance and low cost. Illumina is banking on the idea that the ubiquity of RT-qPCR has led at least the academic research market to the point where nearly every scientist would want their own affordable benchtop system to run everyday routine experiments.

The company is also claiming that, despite its low price, the Eco can deliver many of the same performance specifications as other, more expensive machines.

Macemon said that the Eco has demonstrated five-fold improved thermal uniformity and detection sensitivity as other platforms, though she didn’t identify specific competing machines.

The key to this performance is the core technology developed at CalTech: a hollow silver thermal plate system containing an electromagnetic-driven conductive fluid, which offers very precise and fast temperature control, low power requirements, and well-to-well uniformity.

Most other instruments use a solid block for thermal cycling, and the best of these offer somewhere in the neighborhood of 0.5°C well-to-well temperature variation. Meantime, in instrument specs Illumina claims Eco delivers well-to-well variation of 0.1°C, but Macemon said that researchers at the company have been able to achieve variations as little as 0.05°C.

The upshot of this temperature control is “higher quality and more uniform data,” Macemon said.

Other features of the instrument include LED array illumination, which provides four-color multiplexing; and proprietary “adaptive LED control,” which regulates the duration of LED exposure to reaction wells during cycles, thereby equalizing fluorescence across the plate and allowing for faster data collection.

Melting Away

Illumina is also marketing Eco’s ability to perform high-resolution melting, or HRM, a technique that has been gaining popularity as a way to extract information about DNA based on the dissociation or melting of double strands.

Illumina’s Miller, who also joined the company from Helixis, outlined how HRM, which is an enhancement of more traditional melt-curve analysis, can be used to conduct affordable SNP genotyping and other mutation analyses.

Miller said HRM is more cost-effective than sequencing- or probe-based genotyping, and that use of the technique in the scientific literature has spiked in the last few years, much in the way that publications involving RT-qPCR spiked rapidly when it was first introduced in the early 1990s.

According to Miller, HRM has three major requirements: chemistry, instrumentation, and software. By chemistry, Miller was referring to saturating dsDNA-binding dyes that are non-inhibitory to PCR, such as Life Technologies’ SYTO 9, Idaho Technologies’ LCGreen, or Biotium’s EvaGreen.

Meantime, HRM instrumentation requires precise temperature control and fast data acquisition; while software must feature specialized normalization algorithms and difference plots that show the difference in fluorescence from selected reference samples.

Miller noted that Life Tech’s ABI 7500 and Roche’s LightCycler are both capable of HRM, but that the Eco also offers all the necessary features at a lower price. Further, Miller said that the Eco may in fact offer superior HRM analysis, again due to its five-fold better well-to-well thermal uniformity.

Specifically, Miller highlighted data obtained from in-house research showing the ability of the Eco to distinguish DNA molecules down to a SNP using HRM. Further, she outlined how the Eco is capable of distinguishing Class 4 SNPs, which describe an A-to-T base change that has traditionally been very challenging to detect with HRM because it results in an extremely small melt curve shift – as little as 0.2°C.

Illumina will continue to develop HRM-based applications for the Eco as the instrument begins to gain traction in the market, Miller said.

The company has tested the Eco HRM application using four different HRM master mixes: Roche’s LightCycler HRM Master Mix; Life Technologies’ ABI MeltDoctor HRM Master Mix and Invitrogen Express SYBR GreenER SuperMix; and Bio-Rad’s SsoFast EvaGreen Supermix. Miller said that all mixes work well and none really performed better than others.

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Roche NimbleGen has selected Ambry Genetics as its first certified service provider for the NimbleGenSeqCap EZ Exome workflow. Ambry will provide target-enrichment services using NimbleGen SeqCap EZ Human Exome to capture all human coding sequence, coupled with next-generation sequencing services for genetic research.

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New England Biolabs has introduced a new line of reagents for sample prep — NEBNext mRNA Sample Prep Reagent Set 1 and Master Mix Set 1.

The new products include enzymes, buffers, and protocols to convert mRNA to DNA, and to then construct the library. The reagents are compatible with non-directional mRNA library prep on the Illumina platforms, and also for the preparation of expression libraries.

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Researchers at Johns Hopkins School of Public Health have released Myrna, a cloud computing tool for calculating gene expression in large RNA-seq data sets. Myrna uses Bowtie for short-read alignment, and is similar to another cloud-scale genotyping tool, Crossbow.