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Mass General Taps PerkinElmer to Develop Bioinformatics Platform for Cancer Sequencing Assay

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PerkinElmer is developing a custom bioinformatics platform for Massachusetts General Hospital as part of an effort at MGH to move a PCR-based cancer genotyping assay to a next-generation sequencing platform.

MGH researchers will use the software to analyze data for an NGS-based cancer genotyping assay it is developing for use in the research setting, though the hospital intends to move it into clinical use within the next year and a half.

For several years, MGH’s clinical pathology lab has been using a PCR-based test called SNaPshot to identify more than 100 mutations across several cancer genes, John Iafrate, MGH’s director of molecular pathology and an associate professor of pathology at Harvard Medical School, explained to BioInform.

Although that system has worked well, it can't provide information beyond point mutations that are known to be recurrent in cancer, Long Le, an assistant pathologist at MGH, told BioInform. “We actually are looking to do probably on the order of 800 to 1,000 genes sequenced in their entire coding regions … That technology would not be compatible with it.”

Furthermore, “as all of the genome projects get completed, the demands [for genomic data associated with cancer] are going to continue to increase across all tumor types,” Iafrate noted.

The expanded informatics infrastructure will “allow us to ramp up the amount of genetic information we can provide to our oncologists and clinicians,” he said.

Under the terms of the agreement, PerkinElmer will work with MGH to develop an automated sample preparation and data analysis system that will be used for cancer genotyping in clinical research efforts at the hospital, the company said.

On the informatics side, PerkinElmer will customize its GeneSifter Laboratory and Analysis software systems — products it acquired along with privately held bioinformatics firm Geospiza in 2011 (BI 5/6/2011) — for use in cancer research projects at the hospital.

Todd Smith, Geospiza’s founder and chief scientific officer, told BioInform that the partners plan to incorporate existing open source algorithms, such as the Broad Institute’s Genome Analysis ToolKit and SAMtools, into GeneSifter for use in detecting variants in exome and RNA sequence data as well as for finding translocations. They also plan to develop capabilities to pull in information from public resources such as the Catalog of Somatic Mutations in Cancer, he said.

The financial details of the arrangement with PerkinElmer aren’t being disclosed.

MGH’s Le told BioInform that the hospital had tried to develop informatics tools to meet its NGS data analysis needs internally but soon realized “that if this assay were to become a clinical assay down the road, we are going to need to look for more enterprise solutions that are more turnkey — something that’s well supported with the caveat that we would still need to understand on our end how to operate it with our own informatics team.”

He said that the hospital had looked at solutions from a number of companies including CLC Bio, SoftGenetics, Partek, and DNAStar, but ultimately chose Geospiza’s platform because it offered “more of an enterprise solution” with a single analysis pipeline capable of handling multiple samples.

At MGH, clinical researchers will use the software to analyze genetic variants in tumors as well as to identify biomarkers from genotype information that could be used to develop new cancer treatments. The partners will also integrate the software with existing laboratory processes and equipment at the hospital.

“For cancer, we will be dealing with somatic mutations that may be down to very low frequency so we would hope that our assay will be sensitive enough to capture that but that also the analysis tools … would be good enough or sensitive enough to pick up those mutations in a clear-cut manner” as well as “allow us to do tumor versus normal comparisons,” Le said.

MGH hopes to have its assay ready for use within three to six months; and then have it validated and ready for clinical use in a year and a half, Le said.

PerkinElmer is doing the sequencing for MGH while the assay is in development, but the hospital is considering purchasing its own equipment down the road so that it can handle some of the sequencing internally.

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