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Broad's New CLIA Lab to Provide Exome Sequencing to Partners; Cancer Panel Next

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The Broad Institute said this week that it has established a CLIA-certified Clinical Research Sequencing Platform, or CRSP, that will provide clinical sequencing services to partners in academia and industry.

The institute recently passed its inspection by the state of Massachusetts and is now approved to process clinical samples under CLIA (GWDN 10/21/2013).

Stacey Gabriel, director of the Broad's genomics platform, told Clinical Sequencing News that the new CLIA lab is co-located with the institute's main sequencing facility. The process to become CLIA-certified took about eight months, she said.

Part of the laboratory is now dedicated to handling clinical samples and preparing sequencing libraries for them, and three or four of the Broad's fleet of HiSeq 2500 sequencers have been set aside for sequencing clinical samples, which requires an extra level of quality control and validation compared to research sequencing. In addition, several staff members have received additional training for CLIA sequencing.

The institute does not currently plan to bring other sequencing platforms into the CLIA lab, though it is always evaluating new platforms, Gabriel said.

The first and so far only assay the Broad has certified under CLIA is an exome sequencing assay, for which the institute expects demand to be the greatest initially.

Broad is currently in the process of validating a cancer panel of about 400 genes and some other genomic regions, and plans to have it CLIA certified and available to researchers early next year.

The institute also plans to add a CLIA whole-genome sequencing assay sometime in the future.

Right now, the CLIA lab has capacity for about 100 exomes per week, which can be expanded with increased demand. "Our plan right now is to start out small, because we think right now the demand is not nearly at the level of our research lab," Gabriel said, adding that the lab wants to "[do] this very well and provide very high-quality service."

The institute plans to offer its CLIA sequencing services to a variety of partners and is currently talking to academic medical centers, large hospitals, biotechnology firms, and pharmaceutical companies. "We don't have any partnerships at present that we're announcing," Gabriel said.

While some of these partnerships could be fee-for-service contracts, the institute is also looking for research collaborations as part of its academic mission, she said.

However, the Broad does not see its role as a provider of routine clinical sequencing services. "We are a research institute, primarily," Gabriel said. "We're really here to apply what we've learned about sequencing, and about analysis of sequence data, at this early stage of sequencing in the clinic. Once it becomes a completely routine activity … that's the time when it would not really be something that we're doing."

Besides new partnerships, the Broad plans to bring CLIA sequencing to an existing tumor exome sequencing project, a collaboration with the Dana-Farber Cancer Institute that is funded under the NIH's Clinical Sequencing Exploratory Research program (CSN 3/14/2012). At the moment, the institute sequences tumor exomes for that project in a research setting, and relevant results are confirmed in a CLIA lab prior to being returned to patients. "The idea is, we just skip that step and have the exome from the beginning sequenced in a CLIA lab," Gabriel said. But before switching to CLIA exomes, the Broad is validating its analysis pipeline for calling somatic variants and copy number changes in cancer samples, so those software tools can be used in a CLIA setting.

In addition to becoming CLIA-certified, the Broad has also applied for accreditation of its lab by the College of American Pathologists, which it hopes to obtain in early 2014, Gabriel said.

Finally, it is looking into the requirements for becoming compliant with the US Food and Drug Administration's Quality Systems Regulations, which she said will be most relevant for sequencing for clinical trials.

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