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SynapDx Raises $15M to Develop NGS-Based Autism Test That Could Challenge Lineagen, Others

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Companies that sell or are developing microarray-based tests for early stage autism diagnosis will soon face off against a competitor with a next-generation sequencing-based offering.

SynapDx this week said that it has raised $15.4 million to support the completion of its clinical study of its sequencing-based test for genetic predisposition to autism.

CEO Stanley Lapidus told BioArray News that the Lexington, Mass.-based company will use the proceeds to finish the study, as well as subsequent data analysis and R&D for the launch of its first test, though he declined to provide a launch date.

The test, which is based on gene expression profiling, is targeted to children aged 18 months and older.

He said that the study, which the firm believes to be the "largest multicenter diagnostic study in autism ever done," involves the RNA and DNA sequencing of 660 patient samples collected from 20 different sites.

While the firm in the past had used gene expression microarrays to develop its test, Lapidus said that it decided to move to next-generation sequencing two years ago and obtained its first Illumina HiSeq instrument in the first quarter of 2012. Earlier this year, SynapDx entered into an alliance with Illumina to develop early detection tools for autism spectrum disorders.

"We are now focused exclusively on getting answers through sequencing," Lapidus said. He said that before switching technology platforms, the company did carry out an internal comparison. "In the end, the cost trajectory of sequencing combined with the exceptional reproducibility of sequencing data tilted us in favor of sequencing," Lapidus said.

That preference for next-generation sequencing will differentiate SynapDx from other players in the nascent market for early-stage autism tests.

Salt Lake City-based Lineagen offers a test called FirstStepDx that is based on a custom chromosomal microarray manufactured by Affymetrix (BAN 1/15/2013). Other firms developing chip-based tests include Melville, NY-based Population Diagnostics, which is developing tests based on Agilent Technologies' array platform; and Evry, France-based Integragen, which is developing an autism test on Fluidigm's integrated fluidic circuit platform.

All of these firms wish to deliver to market diagnostics that can detect variants associated with progression to autism in children with suspected developmental delay. According to SynapDx, while the average age of autism diagnosis based on patient observation and medical history is 4.5 years, the average age of first concern is often just 19 months. However, with early treatment, about a fifth of suspected autism cases improve to the point that they are no longer classified as being autistic, and others, while retaining the diagnosis, show improvement in cognitive skills and behavior.

According to Lapidus, the market for SynapDx's test is for children who are displaying signs of what could turn out to be developmental delay. "Often pediatricians and parents wish to do watchful waiting in such circumstances," said Lapidus. "This is when tragic cases occur for children who could have had intervention that could have made things better," he said. "Too often, that's not happening."

Though Lapidus declined to discuss the company's competitors, he said that the market for such tests will not be determined by platform alone.

"History shows us that across the laboratory testing business, it is a combination of [diagnostic] markers, technology, distribution, and quality publications that determine a company's outcome," Lapidus said. "I think that ultimately this will be a very large market, and there will be different [technological] approaches," he added.

According to Lapidus, the proceeds of SynapDx's latest financing will go almost exclusively to R&D. He said that of the firm's 18 employees, 12 are focused on test development. In addition to its early-stage autism susceptibility test, the company is looking into developing tests for children younger than 18 months, as well as tests to determine which patients will benefit best from therapy.

SynapDx's recent financing was led by new investors Google Ventures and Foundation Medical Partners, with contributions from existing investors North Bridge Venture Partners and General Catalyst Partners.

The firm raised an undisclosed sum from the Kraft Group in March, and Laboratory Corporation of America invested $2 million in SynapDx in February.

Of the SynapDx's relations with Google and LabCorp, Lapidus said that the firm looked forward to collaborating with both, and that it will make announcements as those partnerships develop.

"Google is a formidable IT company," Lapidus noted. "They understand big data better than anyone, and what this [project] needs is an understanding of big data."

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