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New Tumor Profiling Unit at UK's Institute of Cancer Research to Offer Systematic Patient Analysis

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This article was originally posted Feb. 14.

The Institute of Cancer Research in London said last month that it is setting up a new center to profile patient tumors using next-generation sequencing that will enable doctors "to develop treatment programs that are tailored to the specific DNA mutations driving a cancer, at that particular point in time."

The new facility, called the Tumor Profiling Unit, will continue and expand existing efforts at the ICR to profile cancer patient samples using next-gen sequencing in order to help clinicians make treatment decisions, according to Amanda Swain, a research scientist at the institute who has been tasked with managing the new unit.

"At the moment, [sequencing patient samples] is a bit haphazard," she said. "Some patients do get sequenced, other patients don't," and only very few have their tumors analyzed several times over the course of treatment. "Now we want to do it in a much more systematic way and really integrate the clinic into the labs."

The new unit, which is being set up over the next three years and will integrate equipment already available at the institute, will enable patient tumor profiling to become more organized, she said, with the long-term goal of analyzing tumors of every patient treated at The Royal Marsden, a cancer hospital closely affiliated with the ICR.

The institute is currently raising £3.2 million ($5 million) for the new facility, which will pay for new staff, equipment, consumables, and lab refurbishments, and the lab recently hired a manager for its sequencing operations.

While the new unit will have close relationships with clinicians, it will not be operated as a diagnostic laboratory but as a research lab, Swain said, allowing it to remain flexible with regard to assays and equipment.

The existing sequencing laboratory, which has already analyzed several hundred patient samples as part of collaborations with individual physicians, is equipped with an Illumina HiSeq 2000 and a recently installed Life Technologies Ion Proton. Those platforms will move into the new unit's laboratory next month, at which point the HiSeq will be upgraded to a 2500.

So far, the lab has performed targeted sequencing on almost 200 genes implicated in cancer, of which fewer than 10 percent are considered "actionable."

"As more and more information becomes available about what drugs are available and what pathways are involved, we might extend that number," Swain said, noting that gene panels might differ for different types of cancer.

Initially, the new unit will focus on lung, pancreatic, prostate, ovarian, breast, and head and neck cancers, she said, especially on difficult-to-treat ones, although it will remain flexible about the types of tumors it will analyze.

Clinicians will send in samples, either from surgery or biopsies, that the lab will profile with a turnaround time fast enough – up to three weeks is generally accepted as sufficient, she said – to allow doctors to factor the results into their treatment decisions.

Rather than sending a report to physicians, the lab will discuss results with them for each individual case. "It's more to encourage clinicians to do more research and researchers to do more clinical work," Swain said.

The plan is to analyze tumors several times over the course of treatment to see how their mutation profile evolves, so doctors can react accordingly. "You can go back to the clinician and say, 'look, this treatment's not working, you're getting resistance here, it might be a good time to move on to something else or give the patient a break and see what happens," Swain explained.

Samples will come from The Royal Marsden, which runs many clinical trials, but might also involve other hospitals, for example as part of a London-wide lung cancer consortium that is currently being set up.

For cancer drug trials, the new center plans to analyze the genomes of particularly good responders in order to find genetic clues that might explain their response.

In addition to sequencing tumors, it will generate patient-derived xenografts in mice, which will be used as preclinical research models.

On the technology side, the new unit plans to develop methods to analyze tumor DNA in blood, which Swain said could avoid biopsies, and it is currently focusing on a blood test for prostate cancer. As sequencing technology improves, one priority of the lab will be to develop quicker and less expensive assays, Swain said.

A particular challenge is the bioinformatics analysis and being able to identify and classify cancer mutations quickly. "There is going to be a lot of work on the bioinformatics side of things, and that's going to need a big input," she said, adding that the ICR has already invested in high-performance computing and data storage.

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