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WaferGen-NuGen Pact Aims to Prep Scant, Degraded Samples for Gene-Expression Studies


By Ben Butkus

NuGen and WaferGen Biosystems have struck a pact to develop and market workflows that combine NuGen's sample prep and preamplification technology with WaferGen's SmartChip high-density and –throughput real-time PCR system.

The partnership is expected to enable WaferGen's customers to conduct SmartChip-based gene expression experiments starting with exceedingly little or degraded genetic material, the company said.

Meantime, the agreement adds to a roster of companies in the real-time PCR, microarray, and sequencing sectors that offer NuGen's sample prep products on the front end of their genetic analysis platforms.

Under the terms of the agreement, WaferGen and NuGen will conduct joint product-development projects to construct "validated workflows" using NuGen's proprietary sample prep and single-primer isothermal linear amplification, or SPIA, technology along with WaferGen's SmartChip real-time PCR system.

These projects will focus on sample preparation, preamplification, and nucleic acid detection for gene expression and target enrichment from various sample types, the companies said.

Financial terms of the agreement were not disclosed.

According to Alnoor Shivji, CEO of Fremont, Calif.-based WaferGen, customers of the company's SmartChip platform have increasingly been requesting protocols for preamplification of genetic material prior to analyzing it with SmartChip.

"Previously they could do preamplification, but it wasn't optimized for our [SmartChip] panels," while the NuGen technologies will be, Shivji told PCR Insider.

"Since we believe we have the best platform in the industry in terms of scalability, and also throughput, it allows someone to really take advantage of this capability of using almost any kind of sample on our platform," Shivji said. "That's pretty significant, because you can actually use a very small sample over a very large throughput."

In addition, WaferGen's customers have been interested in using genetic material from scant or degraded samples, particularly FFPE tissue, Shivji said.

WaferGen launched the SmartChip system in August (PCR Insider, 8/5/2010). The system, which WaferGen markets to customers for high-throughput gene-expression studies and biomarker discovery and validation, comprises consumable chips with 5,184 nanowells preloaded with target-specific primers; a single-sample or multi-sample nanodispenser; and the SmartChip cycler, which performs PCR thermal cycling, data collection, and amplicon melting.

NuGen, based in San Carlos, Calif., has in the past mostly offered sample prep products for the microarray and next-generation sequencing markets, Yan Zhang, vice president of marketing for NuGen, told PCR Insider.

However, it has also previously forged partnerships in the real-time PCR space, including with Roche, which integrated NuGen's technology in its LightCycler RNA pre-amplification kit; and Fluidigm, with whom NuGen collaborates to offer sample prep for mutual customers, Zhang said.

The WaferGen system represents a unique downstream analysis format for NuGen's sample-prep technologies, and "adds another level of flexibility to our products, which are completely platform-agnostic," Zhang said.

A key aspect of the WaferGen deal is NuGen's SPIA technology, which enables rapid, continuous, linear DNA amplification at a constant temperature, eliminating the need for thermocycling, reducing assay complexity, and enhancing speed and throughput of preamplification, according to the company.

SPIA "can amplify whole genomes or whole transcriptomes and maintain fidelity for all downstream analyses that may be required, including microarrays and sequencing," Zhang said. As such, she added, it is "critical for very small amounts of genetic material, for example from fine-needle aspirates, biopsies, circulating tumor cells — any case where there is a very small amount of patient material."

Zhang also said that SPIA is useful for highly degraded samples, such as FFPE tissues, as well as for low-abundance targets, such as fetal DNA in maternal blood.

NuGen also has technology for direct cell lysis prior to preamplification, which may be useful to WaferGen customers using SmartChip to conduct single-cell, high-throughput, gene-expression studies. And the company offers post-amplification labeling technologies, "though these are not really applicable" to the WaferGen agreement, Zhang said.

The alliance between WaferGen and NuGen obviously increases WaferGen's marketing footprint in that NuGen has "15 or 20 people on their operational team, so we can leverage that," Shivji said. It also may help increase NuGen's global footprint, Shivji said, as WaferGen has personnel and distributors in Asia, particularly China, Japan, and Korea.

Have topics you'd like to see covered in PCR Insider? Contact the editor at bbutkus [at] genomeweb [.] com.

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