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Startup Envisagenics Nabs NIH Grant to Develop Alternative Splicing Analysis Tech

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NEW YORK (GenomeWeb) – Just weeks after securing $100,000 in seed financing, bioinformatics startup Envisagenics has been awarded $225,000 grant from the National Institutes of Health to create a prototype of its core technology — a cloud-based platform for the detection, quantification, and interpretation of alternative splicing (AS) variation from next-generation sequencing data.

With the funding, the Cold Spring Harbor Laboratory spinout hopes to lay the groundwork for a commercial launch of the platform as early as 2017, Envisagenics Co-founder and CEO Maria Luisa Pineda told GenomeWeb.

Amid growing interest in RNA therapeutics and a number of alternative splicing-targeting drugs moving through clinical trials, "a lot of pharmaceutical [companies] have recently focused their efforts in RNA sequencing," Pineda said.

Adrian Krainer, a CSHL researcher and Envisagenics advisor, noted in a statement that "alternative splicing is a crucial aspect of gene expression, and keeping track of the various isoforms expressed from each gene is really essential to understand everything that a gene does, as well as what happens when the gene is mutated or expressed inappropriately. This knowledge, in turn, can greatly facilitate drug development."

But while RNA-seq is a powerful tool for identifying disease-causing splicing defects, the sheer amount of data generated by such experiments making doing so a challenge. "We want to … have a robust cloud platform where [researchers] can upload their data … and, without knowing any bioinformatics, get a report back with specific [drug] targets they can then validate on the bench," Pineda said.

That platform, dubbed SpliceCore, essentially comprises three proprietary algorithms: SpliceTrap, which detects AS profiles; SpliceDuo, which identifies significant AS variation; and SpliceImpact, which prioritizes biologically relevant AS events with therapeutic potential.

The algorithms were developed by Envisagenics Co-founder and CTO Martin Akerman with CSHL collaborators including Krainer.

While the specific details of the algorithms remain confidential, the investigators recently published a paper in which they were used to examine how splicing activators and repressors interact with the core spliceosome. Envisagenics also continues to work with its CSHL partners to investigate AS events in breast cancer and spinal muscular atrophy.

Commercializing the algorithms, however, will require the creation of a computational platform that is accessible to researchers globally and can handle the demands of multiple users working simultaneously, Pineda said. To meet that goal, Envisagenics recently obtained seed funding from Accelerate Long Island and the Long Island Emerging Technologies Fund, and now the NIH award, a six-month Phase I Small Business Innovation Research grant.

The grant will specifically be used to streamline SpliceCore's data-processing and predictive methods in order to reduce cloud expenditures, boost the platform's detection sensitivity by enabling the discovery of novel AS, and generate a database of cancer-specific AS events, according to the grant's abstract. It will also be used to improve SpliceImpact's ability to identify relevant AS events by "developing human-computer interaction through object recognition and new quantitative metrics."

The company noted that this work is being done in collaboration with Memorial Sloan Kettering Cancer Center's Gunnar Ratsch, who specializes in computational methods for big data analysis.

Pineda said that Envisagenics intends to then pursue a Phase II SBIR grant to support a soft launch of SpliceCore to a limited number of beta testers and to hire another employee to assist with backend development of the platform.

Assuming success on that front, she said that a full commercial rollout could happen sometime in 2017.

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