By Justin Petrone

Ocimum Biosolutions will use the proceeds of a recent fundraising round to expand its microarray services and add next-generation sequencing capabilities, according to its CEO.

Anuradha Acharya told BioArray News this week that the Hyderabad, India-based company will use the proceeds from the $8 million round to build out its “Research as a Service” platform. Investors in the new round came from multiple sources, including its founders and existing shareholders, she said.

The RaaS platform was designed to provide outsourcing of the entire genomics research workflow, from storage of biological samples to DNA- and RNA-based services, to biomarker validation. As part of the expansion, Acharya said that the company will add offerings to support clinical trial support services, biomarker discovery, and biobanking.

“Our clinical trial support services will be expanded to accommodate large-scale trials,” Acharya said. In addition to Ocimum’s sample management and storage, automated extraction process, and informatics support, Acharya said that “high-throughput genotyping technologies” will “feature highly” in the expanded service offerings.

She noted that the expansion will include microarray services, but said the firm is unlikely to invest in new array platforms. “In terms of technology, we already offer all the major platforms” including Affymetrix, Agilent Technologies, and Illumina, she noted. Ocimum also maintains its own gene expression microarray platform, called OciChip, that it mainly employs in projects that require custom designs (BAN 9/7/2010).

Because Ocimum already has built out its array offering, Acharya said the firm’s next investment will be in the next-generation sequencing space. “Looking to the future, high-throughput third-generation DNA or RNA sequencing will become an important player in clinical genotyping,” Acharya said. “We intend to access and develop our service offerings in that space.” She did not elaborate.

Part of the recent financing will also go toward completion of a 360,000-square-foot facility, which will house Ocimum’s GLP-compliant, genomic, and diagnostics laboratories, Acharya said. She said that the firm will “significantly expand our offering of validated genotyping assays” and will secure Clinical Laboratory Improvement Amendments certification to complement its current GLP qualified services.

Located in Hyderabad, the new Ocimum campus is spread across four acres and is scheduled to become operational in March 2011.

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

Agilent Technologies will soon enable customers to perform SNP genotyping on its arrays in addition to comparative genomic hybridization, BioArray News has learned.

The addition of SNP probes will further enable cytogeneticists using Agilent arrays to detect constitutional abnormalities, and could make the company more competitive against firms like Affymetrix and Illumina that currently sell SNP platforms for cytogenetic research.

Until now, researchers who used Agilent’s CGH arrays to detect uniparental disomy or copy-neutral loss of heterozygosity had to rely on SNP chips sold by other vendors to do so.

UPD occurs when a person receives two copies of a chromosome, or part of a chromosome, from one parent and no copies from the other parent. It is known to cause several genetic disorders, including Prader-Willi, Angelman, and Beckwith Wiedemann syndromes. Copy-neutral LOH is associated in some individuals with a lack of functional tumor-suppressant gene alleles.

Anniek De Witte, CGH product manager in Agilent’s Life Sciences Group, told BioArray News last week that the firm’s SurePrint G3 CGH microarrays will soon be extended to include a set of SNP probes on the same microarray.

The addition of the new SNP probes “allows for the detection of blocks of copy-neutral LOH or UPD down to 5 megabases without compromising the performance of the CGH probes,” she said. De Witte did not provide a hard date for the new product launch, but said that they will appear “in the next couple of weeks.”

According to De Witte, Agilent will launch more than one catalog SurePrint CGH+SNP array that will contain probes for approximately 60,000 SNPs. These SNPs will result in between 5 and 10 megabase resolution for LOH/UPD detection across the genome, she said. De Witte did not elaborate on how the catalog arrays will differ from each other.

In addition, Agilent will print customer-designed arrays ordered through its online eArray tool. De Witte said that Agilent will make available the 60,000-SNP probe set in addition to the 28 million CGH probes for the generation of custom SurePrint CGH+SNP arrays.

Agilent believes the availability to perform SNP genotyping to detect LOH and UPD, as well as CGH on one array will give it an advantage in the market.

“The Agilent two-color CGH microarray platform provides superior copy number change detection thanks to Agilent’s high-fidelity 60-mer probes synthesized through inkjet printing technology in combination with a straightforward DNA sample processing workflow without amplification steps,” De Witte said. “The ability to detect LOH/UPD was the piece that was missing. Now one microarray can detect both.”

The SurePrint CGH+SNP arrays are based on Agilent’s own IP, according to De Witte. She said that scientists in Agilent Laboratories developed a way to “use the restriction digestion step in the CGH protocol to genotype SNPs located at the enzymes’ recognition sites.”

After the labeling, hybridization, and scanning, the data are analyzed “using novel algorithms contained within Agilent Genomic Workbench software,” she said.

Agilent expects that its new SurePrint G3 CGH+SNP microarrays will not just be used to study UPD related to constitutional abnormalities, but will have application in research areas like cancer. At the same time, De Witte warned that studying LOH in cancer samples will be more challenging, due to tumor heterogeneity, normal clone contamination, and the fact that many cancer samples are only available as formalin-fixed, paraffin-embedded tissue.

Over in Oxford

Agilent partner OGT has developed a proprietary methodology to combine CNV calling and SNP detection on the arrays produced for OGT by Agilent. The Oxford, UK-based company last week launched its CytoSure ISCA UPD 4 x 180K array. It enables researchers to simultaneously detect on one array DNA copy number variation on OGT’s International Standard Cytogenomic Array consortium-endorsed 4 x 180K aCGH Array, along with whole-chromosome UPD using SNP probes. OGT began selling its ISCA-designed CytoSure array earlier this year (BAN 2/9/2010).

By Justin Petrone

Illumina is preparing to launch more focused whole-genome genotyping arrays for use in genome-wide association studies, even as it gathers content for its next major BeadChip release, the Omni5, which is scheduled to launch next year.

Chief Financial Officer Christian Henry said this week that adoption of the firm’s HumanOmni2.5-Quad DNA Analysis BeadChip is “ahead of expectations,” and that its customers are “converting to the 2.5M from the 1M and other legacy products.”

Henry made his remarks during a presentation at Morgan Stanley’s Global Health Care Conference, held this week in New York.

Illumina launched the 2.5M in June. The chip contains common and rare variants from the 1000 Genomes Project, is available in a four-sample format composed of approximately 10 million markers per array, and is compatible with the company’s iScan or HiScan system (BAN 6/8/2010).

While Illumina moves customers to the 2.5M, the firm is planning more arrays to serve GWAS customers, starting with a 5-million SNP BeadChip that Illumina anticipates will launch next year. Beyond that, the company imagines making more focused genotyping arrays available to clients.

“We have launched the 2.5M, we will launch the 5M sometime later next year, and we will have the ability to launch a whole suite of products that will be dependent on various ethnicities,” Henry said. He added that the firm is ready to make and sell “different flavors of 2.5M or 5M or 1M, depending on what the customer base is telling us,” and hinted at even denser genotyping arrays. “Our new platform allows extension into 5M and even beyond that,” he said.

Illumina’s interest in making population-focused arrays available is not new. For instance, the firm has in the past sold a HumanHap650Y Genotyping BeadChip for studying African populations. At the same time, its main rival in the GWAS market, Affymetrix, has also pledged to introduce ethnicity-themed arrays to the marketplace, beginning with an Asian population-themed array later this year (BAN 8/3/2010).

While Illumina last year predicted that the GWAS market would return to high levels of growth in the second half of 2010, Henry this week said that this resurgence will occur next year instead.

“In 2009, we saw the business decline,” Henry said. “Our view was that people were waiting for content to come out of 1000 Genomes Project to reinitiate studies,” he said. “What we have seen in the first half of this year is that people are getting back into arrays, repowering studies with additional content, and are contemplating or starting to work on new studies.”

These early studies will “be foundational in driving what the next wave of GWAS will look like for the company,” Henry said. “Sometime in the first half of next year you will see that resurgence.”

Henry added that the fact that Illumina has seen its latest generation chips adopted in new projects is a sign of a market revival. “Just having new projects getting initiated gives you inertia,” he said. “Researchers talk to each other,” said Henry. “I think we have turned the corner overall.”