No gene left behind

PerkinElmer and Massachusetts General Hospital to develop a complete sequencing informatics system for cancer research

Amy Swinderman
BOSTON—"We would like to cure allcancer; we don't turn any cancer away," says Dr. Long Le ofMassachusetts General Hospital (MGH), which is engaged in a quest toidentify genetic changes in tumors for use in advanced cancerresearch. But as any genetic researcher will tell you, the road tothat quest is usually paved with bottlenecks and pitfalls.
 
Clinical researchers who are engaged innext-generation sequencing applications are often challenged by theinformatics arising from instrumentation use. While working tomaintain efficiency and throughput, researchers often struggle withensuring that the informatics driving their instrumentation providestransparency and traceability for the entire process. For MGH, arecently announced collaboration with PerkinElmer Inc. aims tostreamline that process.

"At the end of the day, we care aboutgood data in, good results out and having plenty of time to spend oninterpreting it rather than worrying about the nuts and bolts of thesystem itself," says Le, a pathologist in MGH's DiagnosticMolecular 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 thatdata. The recent challenge for us has been developing theinfrastructure to allow us to do that."

Enter PerkinElmer, which, thanks to itsrecent acquisitions of Caliper Life Sciences Inc. and Geospiza, isable to offer MGH a "one-stop shop" for advanced cancer researchwith its end-to-end offerings of lab automation and informaticssoftware, and everything in between.

"As PerkinElmer brought all of theseorganizations together, the opportunity to help them was reallyfantastic, because we now have a sequencing lab, lab automationequipment and now software to bring to the table," says KevinHrusovsky, president of Life Sciences & Technology at PerkinElmerand formerly the president and CEO of Caliper.

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

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

"What is different here," Smithexplains, "and is still changing in the field, is that we haveenough understanding of genetics today to begin to use sequencing tofigure out what measures of therapy to use. We were one of the firstto advance the clinical reporting side of these technologies, butthis represents an evolution in that process."

The Geospiza GeneSifter Laboratory andAnalysis edition software platforms will be enhanced withsophisticated variant detection algorithms. The new system will alsointegrate existing laboratory processes and equipment with enhancedLIMS and data analysis capabilities.

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

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

"Our thinking is, you shouldn'tpigeonhole yourself into one specific cancer," he says. "We'dlike to come up with a good cancer assay and apply it across allcancers."

"There are a number of cancers wherethis type of genotype-directed therapy has solid roots anddirections, but finding a number of cancer types that are not yetidentified as main drivers could serve as robust therapeutictargets," adds Borger. "If you have a certain cancer type, andyou can find a specific genetic alteration in another cancer type,you can start to identify these genetic signatures. This informationcould really identify therapies in certain cancers that couldpotentially work for other cancer patients."



Amy Swinderman

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