Lineagen to Launch Autism, Developmental Disorder Sequencing Test to Complement Existing Array Test

posted - AUG 20, 2014

By Julia Karow

NEW YORK (GenomeWeb)  Genetic testing firm Lineagen this year plans to launch asequencing-based diagnostic test for autism spectrum disorder (ASD), developmental delay,and other childhood developmental disorders that will complement its existing microarray-basedtest.

Developmental disorders affect about 15 percent of children, and Lineagen already offers acustomized chromosomal microarray test, called FirstStepDx Plus, as a first-line diagnostic testfor their clinical evaluation. According to the firm, the test has a clinical detection rate of about30 percent. Microarray-based testing is recommended by the American College of MedicalGenetics and Genomics.

The new test, called NextStepDx Plus, promises to increase the detection rate to up to 50percent by scanning for disease-relevant single-nucleotide variants that the array test does notcover. Lineagen plans to offer it as a reflex test for patients where FirstStepDx Plus provided nogenetic diagnosis. "[The two tests] identify different types of genetic variants, and we believeboth are very critical to get the best genetic diagnosis possible," said CEO Michael Paul.

NextStepDx Plus will sequence the exome, and possibly the mitochondrial genome, andanalyze the data for SNVs that have been linked to ASD and childhood development disorders.Like FirstStep Dx Plus, it will mostly use DNA from cheek swabs rather than blood.

Variants will include those that Lineagen researchers and their collaborators at the Children'sHospital of Philadelphia, the University of Utah, and Golden Helix published in Molecular Autism earlier this year. They identified 39 variants in 36 genes that may increase the risk of ASD bystudying multi-generational families from the Utah Population Database. Eleven of thesevariants were also present in unrelated ASD cases.

Lineagen is currently deciding which exome capture technology and sequencing platform toemploy for the test. It is also finalizing which variants to include – variants need to be validatedin the clinical literature as pathogenic or likely pathogenic for disorders of childhooddevelopment. New variants can easily be added in the future, Paul said.

Genome annotation and interpretation firm Tute Genomics will analyze the sequencing datafrom NextStepDx Plus under a partnership the firms announced last month. Results will bereviewed by a certified molecular cytogeneticist prior to reporting.

Prior to launch, Lineagen will validate the test analytically in its CLIA laboratory using previouslyanalyzed samples. However, at least initially NextStepDx Plus will be run by an undisclosedpartner CLIA laboratory that also performs the company's FirstStepDx Plus test.

Lineagen plans to start offering NextStepDx Plus this quarter to individuals who have alreadyreceived FirstStepDx Plus but not received a firm diagnosis and will roll the test out morebroadly in the fourth quarter. The company markets its existing test to pediatric specialists, and,to a smaller degree, primary care physicians and will maintain that strategy.

Pricing for NextStepDx Plus has not been determined yet. Prices may differ between individualsbased on a patient's insurance carrier and coverage, Paul said. While FirstStepDx Plus andother chromosomal microarray-based tests are covered by most private payors, reimbursementfor sequencing-based tests is less clear cut. "We do know that there are certain payors that arepaying for the technology, although we don't know how much and we don't know what thecoverage policies might be," he said. "That's something that we're going to be testing as part ofour initial launch phase."

A number of other molecular diagnostic laboratories, such as Ambry Genetics, GeneDx,SynapDx, and Signature Genomics also offer microarray- or sequencing-based diagnostic testsfor ASD. But Paul said that Lineagen's two consecutive tests, as well as its service, whichincludes genetic counseling, differentiate it. "Our mission is to provide the best test for themajority of individuals with developmental delays, with an emphasis on autism but not limited toautism," he said, adding that the clinical detection rate of FirstStepDx Plus is higher than that ofcompeting array tests.

Asked whether sequencing-based tests will likely replace array-based ASD tests in the future,Paul said that Lineagen generally follows the recommendations of clinical societies, "and rightnow, chromosomal arrays are recommended as a first-line test."

"We will always be looking at when the technology is advanced enough to be competitive withan array, and also when medical organizations and payors believe that a test should beperformed as a first-line test," he said. "Right now, [next-gen sequencing] is recommended as asecond step."

Besides launching NextStepDx Plus, Lineagen is looking to expand reporting for FirstStepDxPlus by including variants for epileptic seizure. In addition, the company is working on a newtest to predict the risk of multiple sclerosis.

Lineagen is in the process of raising up to $7 million in a second round of Series C financing,which it hopes to close in the third quarter. At that time, Lineagen will also report on debtfinancing it closed after the first round of the Series C financing, which closed late last year andraised $3.5 million.

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