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Claritas Expands NGS-based Diagnostic Tests for Pediatric Disorders, Broadens Customer Base

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NEW YORK (GenomeWeb) – Less than two years after spinning out of Boston Children's Hospital as an independent genetic diagnostic testing company, Claritas Genomics has added several next-gen sequencing tests for pediatric disorders to its menu and has broadened its customer base beyond its partner hospitals.

About a year ago, the firm, which has about 60 employees, among them eight clinical geneticists, moved into 16,000 square feet of space in Cambridge, Mass., which includes a CLIA-certified laboratory and a research laboratory.

Claritas' clinical lab is CLIA-certified and has state licenses from Massachusetts, Rhode Island, California, and Pennsylvania. The firm is working on becoming licensed in all states that require such and is already approved to perform certain unique tests in New York state.

At the end of 2013, the company closed a Series A funding round with cash and in-kind investments from Boston Children's Hospital, Cincinnati Children's Medical Center, Life Technologies, and Cerner, in which it raised on the order of $10 million to $20 million.

Claritas currently offers more than 100 tests, many of them single-gene Sanger sequencing assays. They include two next-generation sequencing panels, a muscular dystrophy panel that comprises 10 genes associated with childhood-onset forms of the disease, and the ClariFocus panel for nephrotic syndrome, launched last week, which covers 28 genes involved in pediatric nephrotic syndrome. Both tests, which have turnaround times of four to eight weeks, run on Life Tech's Ion Torrent sequencing platforms.

This summer, Claritas launched the ClariView Exome for Pediatric Neurology, the first of a family of exome-based assays that will each focus on a different disease area or clinical presentation.

The pediatric neurology exome test sequences the entire exome on both the Ion Proton and the Illumina MiSeq but analyzes a set of 614 genes that are related to pediatric neurological disorders, such as epilepsy and seizures, neuromuscular disorders, hereditary peripheral neuropathy, movement disorders, brain malformations, leukodystrophies, and mitochondrial encephalomyopathy.

The test uses two different enrichment methods: the Ion AmpliSeq technology, which is based on multiplex PCR, and a bait-based capture method to enrich areas that are not covered sufficiently by the AmpliSeq exome. According to Claritas' website, the test covers 90 percent of all exons more than 30-fold.

The exome test has a turnaround time of 12 to 16 weeks and a list price of $4,800 per sample, with discounts available for patient-parent trios.

Sequencing each sample on two different platforms provides a sort of self-confirmation of variants seen on both, which reduces the amount of confirmatory Sanger sequencing needed, according to Claritas CEO Patrice Milos.

And because the test focuses on a subset of the exome, it avoids incidental findings in genes unrelated to the patient's phenotype, including the 56 genes recommended for analysis by the American College of Medical Genetics and Genomics.

Over the next year or so, Claritas plans to offer additional condition-specific versions of the ClariView Exome. One will analyze genes associated with Mendelian childhood disorders and another will focus on autism, developmental delay, and intellectual disability. For the latter three conditions, Claritas already offers a chromosomal microarray-based test, ClariView Array, that detects copy number variants.

"Rather than casting a broad net, [we want to] really focus on disease conditions and build very deep knowledge around those with our pediatric partners," Milos said.

While tests for diseases that involve more than 50 genes will likely run as focused exome tests rather than targeted gene panels, "there will always be a need for small panels where the phenotypes are well defined," she said, noting that the turnaround time of its panels is currently lower than that of its exome-based test, which is partly due to the number of genes that need to be interpreted.

At the moment, Claritas bills hospitals for its tests, but the firm plans to bill insurance directly starting early next year. To obtain insurance coverage, it will be important to demonstrate the clinical utility of the tests, Milos said, and the company is working on strategies for that with its partners.

All of Claritas' tests are laboratory-developed, which means that they do not need to be cleared by the US Food and Drug Administration, but Milos said the company is watching the FDA's evolving guidance on LDTs closely. Regulating diagnostic tests for rare diseases will be challenging, she said, because of the small number of patients available.

While Boston Children's Hospital and Cincinnati Children's Medical Center remain Claritas' primary customers, the company has had orders from 80 to 90 other hospitals, Milos said, "and our focus now is on outreach to those hospitals so they can get to know us a little better." To that end, Claritas will showcase its offerings at the National Society of Genetic Counselors annual meeting in New Orleans this week and at the American Society of Human Genetics annual meeting in San Diego next month.

Besides its clinical laboratory, Claritas runs a research laboratory, which generates both revenue for the company and allows it to test new software, chemistries, and methods prior to implementing them in its CLIA lab.

The research laboratory can generate about 200 exome libraries per day at the moment and has a sequencing capacity of 100 to 200 exomes per day, which can be increased as needed, Milos said.

According to its website, Claritas offers exome sequencing on the Ion Proton at a base price of $800 per sample and with a turnaround time of four to six weeks for 96 samples.

Last year, Claritas won a one-year $9 million contract from the US Department of Veterans Affairs to sequence the exomes of veteran samples as part of the Million Veteran Program.

Milos said Claritas received the first veteran samples in April and has now obtained all 19,000 or so, which it is busy sequencing, generating 150 to 200 libraries per day and sequencing about 2,000 exomes per month. The company expects to complete work for the current contract in the first half of 2015.

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