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Lineagen Updates Autism Test to Include New Variants; Claims Two-Fold Increase in Detection Rate


Lineagen has updated its chromosomal microarray testing service to include new variants associated with autism spectrum disorders.

The company said that the latest iteration of its offering, called FirstStepDx Plus, enables a two-fold increase in the detection rate of markers thought to be associated with ASD. The new content was originally identified in a multigenerational population in Utah and then validated in a 9,000-person-genetic study detailed in a paper published online this week in PLOS One.

Lineagen CEO Michael Paul told BioArray News that the new content in FirstStepDx Plus gives the Salt Lake City-based firm an advantage over other CMA services being run with catalog arrays, as well as other players that are developing tests on technologies that are not yet recommended for clinical use by the American College of Medical Genetics and Genomics and other professional organizations, as CMAs are.

"Lineagen offers improvement in sensitivity over other cyto arrays, while still using a technology that is recommended by clinical practice guidelines and covered by a number of insurance companies," Paul said.

The company does face competition. In addition to CMA services offered by numerous labs within the US, a number of companies have developed or are developing array- and sequencing-based tests for the early diagnosis of ASD, including Population Diagnostics, Ambry Genetics, Athena Diagnostics, CombiMatrix, GeneDx, SynapDx, and Signature Genomics (BAN 12/11/2012).

Lineagen's new claim of offering a two-fold increase in actionable results is linked to the current PLOS One study and other past studies. After analyzing data from the 9,000-person validation study with researchers at the University of Utah, the Children's Hospital of Philadelphia, and bioinformatics firm Golden Helix, Lineagen and its collaborators were able to detect a validated genetic variant in 12 percent of individuals with ASD. Lineagen claims that current clinical tests are only able to detect validated genetic variants in between 5 percent and 7 percent of individuals with ASD.

Hakon Hakonarson, a lead researcher on the study and director of CHOP's Center for Applied Genomics, in a statement called the effort "one of the most comprehensive genetic studies of autism performed to date" and said that the "genetic variants confirmed by the study's large sample size give us confidence that they accurately represent the underlying biology of ASD."

According to Lineagen, CHOP and Golden Helix independently analyzed the study data using orthogonal techniques to identify statistically relevant results.

In addition to the increased detection rate, Paul said that the size of the study was significant. "There have been a number of studies published in recent years, but none have had the size to get statistical results relevant for clinical testing," he said. "This provides assurance that what we report to customers and individuals is the best information we can get."

In addition to providing a more comprehensive testing service, Lineagen sees the potential for partnerships with pharmaceutical and biotechnology companies developing ASD-related therapeutics. The company noted in a statement that the PLOS One study identified and confirmed the involvement of biological pathways and gene regions that have relevance to neural, cardiovascular, and immune functions, for which targeted treatments are being developed in clinical trials.

Of Lineagen's outreach to pharma, Paul commented that the firm is "looking to partner with pharma and biotech in drug development programs to provide access to our platform to advance those programs."

Ultimately, Lineagen believes that its test could be used both as a companion diagnostic for drug development programs, as well as a way to identify individuals suspected of having ASD for targeted interventions and personalized treatments.

The Center for Autism and Related Disorders, a provider of early intensive behavioral intervention for individuals with ASD, last month adopted Lineagen's FirstStepDx test as a service that it offers to its patients and their families (BAN 12/4/2012).

Based in Los Angeles, CARD maintains 23 centers globally. Patients receiving care in its Skills program — which, according to CARD's website, is focused on "minimizing challenging behaviors" and "maximizing skill acquisition" and is geared toward patients aged zero to eight — will have access to Lineagen's array-based test, the organization said at the time.

Paul said that Lineagen's planned incorporation of the new markers was "of interest" to CARD. He added that the partnership with CARD "reflects the benefits of using genetics to help determine treatment."

'Favorable' Response

Lineagen first launched FirstStepDx two years ago (BAN 1/11/2011). The test is run on a custom Affymetrix genotyping array that is based on the vendor's CytoScan offering. Since FirstStepDx's debut, Lineagen has modified its service to accept buccal cheek swabs in addition to blood samples.

According to Paul, the reliance on buccal swabs has been an advantage for individuals with ASD because it reduces their anxiety about being tested, and also because the firm has obtained better results compared to blood for the detection of mosaicism, as cheek cells have the same embryonic origin as brain cells.

Paul said that response has been "very favorable" to FirstStepDx, and that the firm has performed about 1,400 tests for more than 350 doctors. He said that about a quarter of orders come from doctors who have previously used the service, and that he expects satisfaction with Lineagen's offering would increase with the availability of FirstStepDx Plus.