Speeding single-cell genomics

FREMONT, Calif.—WaferGen Biosystems Inc., a life-sciences company that offers genomic solutions for clinical testing and research, has signed a research collaboration with Genentech, a member of the Roche Group, to evaluate and apply WaferGen’s SmartChip  platform in single-cell sequencing. The work is designed to validate the usefulness of the SmartChip technology for isolating single cells from various tissues and preparing libraries for next-generation sequencing (NGS) in drug discovery. Genentech is WaferGen’s initial partner in its single-cell genomics technology-focused Early Access Program.

 

“The collaboration is related to single-cell research as applied to Genentech’s internal goals,” explains Dr. Rolland D. Carlson, WaferGen president and CEO. “The company’s chief technical officer, Maithreyan Srinivasan, gave a presentation to Genentech scientists about the technology using early-stage proof-of-concept data generated in-house. Genentech scientists saw potential to use the technology for single-cell processing, and it made sense to enter into a collaboration to pursue common interests.”

 

Genentech, which was founded in 1976 by a venture capitalist and a biochemist, is a pioneer in the field of recombinant DNA technology. Its researchers were the first to successfully express a human gene in bacteria when they produced the hormone somatostatin in 1977, and then the company produced synthetic human insulin in 1978. Roche purchased Genentech in 2009.

 

WaferGen, which successfully completed separate proof-of-concept studies related to isolating single cells with the SmartChip earlier this year with both the Broad Institute and BGI, brings in the technological know-how to perform hundreds to thousands of single-cell isolations, and Genentech brings its deep scientific knowledge as a pioneering biotechnology company with an outstanding scientific track record of innovation, Carlson says. In addition, WaferGen’s scientists have successfully isolated single cells and produced excellent results in downstream processing of these individual cells, including RNA sequencing, according to Carlson.

 

At a throughput level scalable to several thousand cells per sample, the cells' genetic composition was successfully analyzed via the NGS method, thus demonstrating increased discovery potential in a single workflow. WaferGen projects that the SmartChip technology will be able to yield a 50-fold increase in the production of single cells per chip versus current technologies at a fraction of the per cell cost. Single-cell measurements have already resulted in critical discoveries of novel cell types that play an important role in disease mechanisms. This type of analysis has the potential to establish a significant role in the development of an approach to disease treatment and prevention that takes into account individual variability in genes, environment and lifestyle for each person, which is an emerging healthcare trend, Carlson noted.

 

The program is ongoing, with no specific time frame announced. WaferGen continues to expect that the company will launch its first commercial single-cell analysis product by the end of 2015.

 

The SmartChip MyDesign Real-Time PCR System is a high-throughput genetic analysis platform for profiling and validating molecular biomarkers via microRNA and mRNA gene expression profiling, as well as single nucleotide polymorphism genotyping. The SmartChip TE System is designed for target enrichment geared toward clinical next-gen sequencing. The Seq-Ready TE System, powered by SmartChip massively-parallel singleplex PCR technology, is a one-step target enrichment and library preparation solution. WaferGen also offers the Apollo 324 product line used in library preparation for NGS. These three complementary technologies are said to offer a powerful set of tools enabling more accurate, faster and cheaper genetic analysis based on NGS and real-time PCR.