No gene left behind
October 2012
by Amy Swinderman  |  Email the author


BOSTONó"We would like to cure all cancer; we don't turn any cancer away," says Dr. Long Le of Massachusetts General Hospital (MGH), which is engaged in a quest to identify genetic changes in tumors for use in advanced cancer research. But as any genetic researcher will tell you, the road to that quest is usually paved with bottlenecks and pitfalls.
Clinical researchers who are engaged in next-generation sequencing applications are often challenged by the informatics arising from instrumentation use. While working to maintain efficiency and throughput, researchers often struggle with ensuring that the informatics driving their instrumentation provides transparency and traceability for the entire process. For MGH, a recently announced collaboration with PerkinElmer Inc. aims to streamline that process.

"At the end of the day, we care about good data in, good results out and having plenty of time to spend on interpreting it rather than worrying about the nuts and bolts of the system itself," says Le, a pathologist in MGH's Diagnostic Molecular Pathology lab.
Le's colleague, Dr. Darrell R. Borger, co-director of MGH's Translational Research Laboratory, stresses, "We need efficient ways to interpret and manage that data. The recent challenge for us has been developing the infrastructure to allow us to do that."

Enter PerkinElmer, which, thanks to its recent acquisitions of Caliper Life Sciences Inc. and Geospiza, is able to offer MGH a "one-stop shop" for advanced cancer research with its end-to-end offerings of lab automation and informatics software, and everything in between.

"As PerkinElmer brought all of these organizations together, the opportunity to help them was really fantastic, because we now have a sequencing lab, lab automation equipment and now software to bring to the table," says Kevin Hrusovsky, president of Life Sciences & Technology at PerkinElmer and formerly the president and CEO of Caliper.

Under an agreement announced Aug. 28, MGH and PerkinElmer will work together to develop a sequencing informatics system that enables researchers to define key genetic targets from which clinically relevant information can be leveraged. The collaboration, notes Todd Smith, senior leader of research and application at PerkinElmer, is "multifaceted."

"There are two parts to this. One is reporting on what we know today, and the other is identifying and doing discovery work on different kinds of biomarkers," says Smith.
In one aspect of the collaboration, MGH's Pathology Department and Cancer Center are using PerkinElmer's DNA Sequencing Services group and Sciclone automated liquid handling platform and the NGS Express Workstation for benchtop sequencers. In another aspect, the parties will work together to create a sequencing informatics system that will actually be a tweak to Geospiza's informatics platforms, which have been deployed in a similar fashion within research groups such as the Mayo Clinic that are studying cancer and gene expression and variance.

"What is different here," Smith explains, "and is still changing in the field, is that we have enough understanding of genetics today to begin to use sequencing to figure out what measures of therapy to use. We were one of the first to advance the clinical reporting side of these technologies, but this represents an evolution in that process."

The Geospiza GeneSifter Laboratory and Analysis edition software platforms will be enhanced with sophisticated variant detection algorithms. The new system will also integrate existing laboratory processes and equipment with enhanced LIMS and data analysis capabilities.

The result, says Le, will be a "one-stop-shop solution that will allow us to push forward genotyping to the next-generation level."

Although Le and his colleagues have for some time been focused on lung cancer, this collaboration will allow them to apply their work to other types of cancer.

"Our thinking is, you shouldn't pigeonhole yourself into one specific cancer," he says. "We'd like to come up with a good cancer assay and apply it across all cancers."

"There are a number of cancers where this type of genotype-directed therapy has solid roots and directions, but finding a number of cancer types that are not yet identified as main drivers could serve as robust therapeutic targets," adds Borger. "If you have a certain cancer type, and you can find a specific genetic alteration in another cancer type, you can start to identify these genetic signatures. This information could really identify therapies in certain cancers that could potentially work for other cancer patients."

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