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Ghent University to Use Roche LightCycler 1536 for HT PCR-based Cancer Studies

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Roche said this week that researchers at Ghent University are using Roche's LightCycler 1536 real-time PCR instrument in various cancer research projects at the university.

Although Roche said that it signed an agreement with Ghent University in general, the instrument will primarily be used in the laboratory of Jo Vandesompele, professor of functional cancer genomics and applied bioinformatics at the university, and one of the pre-eminent researchers in the qPCR field.

Vandesompele and others at the university will use the LightCycler 1536 in cancer research studies such as multigene expression signature profiling on tumor samples and digital PCR for detecting mutant cancer cells in normal cell backgrounds.

Other examples will include DNA methylation analysis, copy number variant screening, and amplicon generation for next-generation sequencing.

In addition, Roche said that researchers at the university plan to conduct a qPCR-based, transcriptome-wide profiling study, in order to measure all human genes in the four reference RNA samples created by the Microarray Quality Control Consortium.

The company also noted that it expects the LightCycler instrument to be used as part of an integrated workflow at Ghent along with the Roche 454 Genome Sequencer FLX system.

It is unclear whether the university has purchased the LightCycler 1536 as part of the agreement. Matthias Hinzpeter, head of program management for qPCR and NAP Systems at Roche Diagnostics, told PCR Insider this week that financial details of the agreement were confidential.

Vandesompele was unable to be reached for comment. Iin a statement, he said that researchers at Ghent "are quite enthusiastic and foresee many exciting studies and possible applications of the LightCycler 1536 instrument in our work."

Roche launched the LightCycler 1536 in May 2009. The platform is based on the company's flagship LightCycler 480 platform, but its ability to run 1,536 simultaneous PCR reactions gives it the highest-density PCR plate format on the market.

The LightCycler 1,536-well plate uses a technology called Thermaxis, which enables thermal cycling in reaction volumes ranging from 0.5 µL to 2 µL. The plate comprises a thermally conductive unit containing well-like structures for the reaction liquid and an insulating top layer that prevents the heated lid of the instrument from affecting analysis, Roche said.

The platform also combines two excitation filters with two detection filters optimized for detecting green intercalating dyes, monocolor probes, and dual-color hydrolysis probes. These features make optical readout on the platform as specific as possible for chemical detection formats, Roche said, while reducing the overall complexity of high-throughput experimental layouts.

Since its launch, Roche has placed "more than 20" of the LightCycler 1536 instruments, Hinzpeter said, though he declined to disclose whether the placements were purchase agreements.

Vandesompele's lab is fast becoming a sought-after collaborator for companies developing new PCR technologies.

"Professor Vandesompele is known to have lots of innovative approaches to qPCR research, and is well known in this field," Hinzpeter told PCR Insider. "So we're very happy that he has selected the LightCycler 1536 to do part of his research. For us this [provides] a very good reputation."

In March, Wafergen announced that Vandesompele's lab had signed an agreement with the company to become an early-access customer for its SmartChip real-time PCR system, currently in development and set to be launched later this year (PCR Insider, 3/18/2010).

Vandesompele also is the co-founder and CEO of Biogazelle, a company that provides real-time PCR data analysis software and service.

Hinzpeter said that Biogazelle's flagship software platform for qPCR data analysis, qBase PLUS, is one of several data-analysis packages that Roche recommends to its customers for use with the LightCycler 1536. "We are very open to any software out there that will do the job," Hinzpeter said. "But we leave that more or less to the customer."

However, he added there is no overlap between the agreement signed with Ghent University and the work Vandesompele is doing for Biogazelle.

"Anybody who is doing qPCR can purchase this software," Hinzpeter said. "It's not related to any particular instrument … and has nothing to do with this research agreement. But in his experiments with [the LightCycler 1536] he is using part of that software."