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Transgenomic Launches NGS-Based Mitochondrial Disease Test, Developing Autism Risk Test


By Monica Heger

Transgenomic is taking a tentative step into the next-generation sequencing space with the launch of its Nuclear Mitome Test to diagnose mitochondrial disease. The test is initially being launched through the Seattle Children's Hospital on an Illumina HiSeq, but will later be offered through Transgenomic's Omaha, Neb.-based headquarters once the company acquires a next-gen sequencer, Transgenomic CEO Craig Tuttle told Clinical Sequencing News.

The Nuclear Mitome Test analyzes mutations in 400 genes. The company is using Agilent's Sure Select in-solution capture technology and will validate the mutations using Sanger sequencing. The test will be launched through Seattle Children's Hospital's CLIA-certified lab.

Tuttle expects to offer the test through Transgenomics' own lab within one year, and is considering both the HiSeq and MiSeq instruments. He said he is also looking to expand the test to analyze between 800 and 900 genes, depending on the "performance and clinical findings from the 400-gene assay."

Additionally, the company has hired clinical molecular geneticist Jeana DaRe, who will serve as the assistant lab director for the assay at the Seattle Children's Hospital, and then move to Transgenomic's facility when it adopts the test.

Currently, mitochondrial diseases are diagnosed primarily through biochemical analyses, and preliminary data comparing the mutational assessment from the sequencing-based assay to the biochemical analysis has found that the two do not correlate and that the sequencing-based assay is more accurate, said Tuttle.

The company will be offering the test for $17,000. Tuttle said the price was determined by a "straight stacking" of Current Procedural Terminology codes, in line with the Blue Cross Blue Shield fee schedule.

Tuttle said he expects to run several hundred tests a year, and that at the recent United Mitochondrial Disease Foundation meeting in Illinois, interest in the test was "quite high" among physicians.

Aside from the mitochondrial disease test, the company is also developing an autism test based on next-gen sequencing, which will analyze 95 genes and predict the risk of developing autism in a child who already has an older sibling diagnosed with autism spectrum disorder. The test is being developed by IntegraGen, who licensed autism-related intellectual property to Transgenomic last year.

Tuttle said that IntegraGen has already completed a trial of the test, and if the data proves to be good, it could be launched by the end of the year.

'Not Yet Ready for Prime Time'

Tuttle said, however, that these first forays into next-gen sequencing don't represent a shift in the company's strategy, which has so far been focused on Sanger sequencing and PCR technologies for molecular diagnostics.

Earlier this year, for instance, the company developed a method called BLOCker sequencing, which increases the sensitivity of Sanger sequencing for specific mutations (CSN 4/26/2011).

"Next-gen sequencing is not yet ready for prime time," said Tuttle, adding that the company will only begin to implement it where it makes economic sense. For most applications, Sanger sequencing, particularly with the company's BLOCker technology, is still more cost-effective, he said. "As that cost structure shifts, so will we."

Tuttle added that the company would look at switching over its current molecular diagnostic tests to a next-gen sequencing platform, as well as develop new tests or license such tests from other groups.

While many companies and academic researchers think that cancer is a ripe area for the use of next-gen sequencing, Tuttle said that he planned to continue to use the company's Cold-PCR and BLOCker sequencing technology to develop tests for the cancer setting. The company's technology enriches for mutants, he said, making them easier to detect, unlike next-gen sequencing, which amplifies both mutations and wild-type DNA alike. "I don't see any need to shift [our oncology assays] to next-gen," he said.

The company is planning to launch research assay kits that combine Ice COLD-PCR and BLOCker sequencing to detect mutations in cancer genes such as KRAS, NRAS, BRAF, TP53, EGFR, and PIC3CA later this year.

Additionally, it already offers its pharmaceutical partners, through its pharmacogenomic services laboratory, assays that combine the two techniques for detecting mutations in cancer genes.

Have topics you'd like to see covered by Clinical Sequencing News? Contact the editor at mheger [at] genomeweb [.] com.