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Startup Variantyx Sees Itself As 'Virtual Lab' for Diagnostic Decision Support


CHICAGO (GenomeWeb) – Diagnostic decision support company Variantyx is betting on two notions: that clinicians need help sorting through genomic data from next-generation sequencing and that the trend is toward whole-genome sequencing.

"We feel like the future is going to be about whole genomes," said Muthu Meyyappan, chief commercial officer of the Framingham, Massachusetts-based vendor.

Variantyx, which started in 2014 as a spin-out from Tel Aviv University in Israel, introduced its cloud-based Genomic Intelligence platform at the American Society of Human Genetics annual conference in October. The formal US launch of the product was at the American College of Medical Genetics meeting in March.

The platform is built to handle whole-genome sequencing, though it also can analyze genome panels and whole-exome sequences. It generates reports in a matter of minutes for diagnosis decision support, according to Meyyappan.

Specifically, Genomic Intelligence automates the complete NGS testing process, from sample collection to sequencing, data analysis, interpretation, and report generation, offering clinically actionable suggestions from algorithms and support from board-certified geneticists. Meyyappan described Variatryx as a "virtual lab" for health systems without large genomics operations and for laboratories looking to expand their test menus.

Unlike many other genomics decision support systems, however, Genomic Intelligence is squarely aimed at clinicians. "Commercial labs can benefit from the platform we have built for whole genomes," Meyyappan said, but practitioners are "our main bread and butter."

The sequencing itself is outsourced to third parties, including Macrogen and Otogenics, through nonexclusive arrangements with those firms. There is no markup for Variantyx customers, just a pass-through cost from the sequencers.

Variantyx offers the analysis for cancer predisposition testing, carrier screening, rare disease testing, and prenatal screening. Reports can be white-labeled for health systems or labs to add their own branding, Meyyappan said.

Currently, reports integrate with laboratory information management systems, but not with any electronic health records. Meyyappan said that EHR links are planned for the future, but he didn't offer specifics.

To date, Variantyx has been self-funded by its founders, including Noam Shomron, head of the genomics intelligence team at Tel Aviv University and director of the Rare Genomics Institute's Israel chapter. Shomrom serves as chief scientific officer of the company.

Variantyx sells an end-to-end service by subscription, with no licensing fees or up-front payments, Meyyappan said. There is a pay-per-test option as well, with pricing per full exome or genome. "We hardly ever handle panels," Meyyappan said, noting that plenty of other companies offer that service.

Customers also can opt for just decision-support services as well.

As an introductory offer, Variantyx is offering no-cost second opinions to practicing clinicians for previously undiagnosed cases — where panels might be an option. Clinicians simply have the testing lab send FASTQ or BAM files of panel, whole-exome, or whole-genome sequences to Variantyx to produce a clinical report.

Virginia Kimonis, principal investigator in the Division of Genetics and Genomics Medicine at the University of California, Irvine, School of Medicine, has taken advantage of this free service.

"They actually did a really good job of doing a case involving an exome," said Kimonis, a clinical geneticist specializing in rare, hereditary diseases, particularly of the neuromuscular kind. "They found a mutation in no time at all."

The work involved a class of rare, hereditary neuromuscular diseases called inclusion body myopathies for a patient that had self-referred to UC-Irvine. Kimonis said she happened upon a case from several years ago in which she tested for a mutation in the valosin-containing protein, or VCP, gene — a marker of inclusion body myopathy — but the test came up negative. This time, she ordered an exome test and, using the Genomic Intelligence platform, was able to find evidence of the rare condition.

"[The original lab] found a mutation, but didn't perceive it as being important," Kimonis said. She had her suspicions, though, and ordered a sequence of the whole genome for the same patient.

"That lab didn't help with the analysis, but they did help with connecting me with Variantyx," Kimonis said.

Like Variantyx, Kimonis is a believer in the power of exome or whole-genome sequencing and believes that the future is now. "It's a waste of money to do one gene test at a time when you can just do it all at once," she said.