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Streamline Genomics Looks to Expand Variant Analysis Offering With Free Search, Paid Analytics


CHICAGO – Startup company Streamline Genomics moved into a new phase this fall when it introduced its SeeqBio genomic search engine in September, then this month released SeeqVCF, an application to filter VCF files to simplify genome analysis.

SeeqVCF resides locally in a browser so no sensitive data has to be sent over the internet to the cloud. Montreal-based Streamline claims that the app can produce results in less than a minute after the user loads a file and inputs target genes.

Both SeeqVCF and are free for individual users, though licenses are available for enterprises and power users.

These are the first two products Streamline has developed for individual, though the firm has had an enterprise genomic analysis platform for several years. This core enterprise product supports collaboration, including for such applications as virtual tumor boards. CEO Curtis Duggan called it a "classic SAS software offering," referring to the widely used statistical analytics package from data management giant SAS Institute.

The Seeq product platform represents a somewhat new, additional thrust for the firm. "As part of our strategy this year, we've identified that we want to make it available and deliver value to users in a way that's not necessarily behind an enterprise software contract," said Duggan, who joined Streamline a year ago.

"Our main goal right now is identifying that there's an aspect of looking up genomic information that hasn't had its 'Google moment' despite the existence of many genome browsers," Duggan said. In other words, genome browsers are not as intuitive as the ubiquitous Google search engine.

"What I mean by Google moment is making everything connect so it's as easy as looking up the weather in Tokyo to look for a variant and immediately get real-time dynamic information," such as clinical trial availability, Duggan explained.

For example, according to Duggan, many freely available browsers return thousands of links to literature related to a given gene or variant, but he said that structures the results in descending order of what the Streamline algorithm determines would be most useful to the user.

"[It's] an intentionally simple user interface where you can search a variant, a drug, a disease, or a condition," Duggan said. "You'll see all the results and you can double click and drill down very quickly to see the source of the information."

Duggan said that other free software from commercial entities sometimes limit the number of searches before users must purchase a paid version. "With us, they can keep searching," he said.

Users must pay for Streamline Genomics analytics services, however.

Duggan said that tiered payment models others offer create "siloed walled gardens." He compared it to a company like Yahoo making a directory of the internet and then charging for access, or, using an even older metaphor, a traveling encyclopedia salesperson coming back each year to sell an updated version.

Streamline wants to fill the niche between companies that offer free initial searches then charge for subsequent use, and free public software utilities that Duggan said lack modern user interfaces and sorting functionality.

"We're going to be constantly thinking through how we can surface to the top the most relevant, intuitive results," Duggan said. "For us, the goal is to connect and increase the volume of people searching and the volume of data that's coming in," Duggan said.

The search engine aggregates information from publicly available databases and directly from clients. The company builds its knowledge graph by aggregating search results. Duggan said that Streamline only uses anonymized data, not identifying what individuals search for.

In the future, Streamline is considering selling access to its aggregated data to researchers including pharmaceutical companies. "We really want to help get precision medicine adopted faster and remove friction for things like finding the right drugs and ultimately finding the right clinical trials," Duggan said.

"[Search data]is something that we can partner with companies like pharmaceutical companies on to help with our vision to accelerate the adoption of precision medicine," he added.

Duggan explained that Streamline's vision of personalized medicine, something that will take a lot more than just his company to realize, includes getting every patient who might benefit from genomics to have their genome sequenced.

He said that sequencing is close to becoming a commodity now, as is some genomic analysis. The real opportunity is in removing what Duggan called "the friction from leveraging the analysis to help physicians and their patients to find treatments" by automating workflow, building data connections, and producing clinical decision support that doctors will trust.

"There's just this fundamental underoptimization," Duggan said. "Physicians aren't practicing precision medicine."

Eventually, Duggan wants to get to a point where precision medicine is a standard of care whenever genetic factors are involved, particularly in oncology, and that physicians can derive value from the Streamline platform without having to go to a CIO or bioinformatician or sign an enterprise software contract. "There's always fundamentally a layer of what we do that's free to everyone," Duggan said.

Duggan said that the company's "ultimate vision," one he expects to be realized by early 2022, is for the search engine to return a list of active clinical trials that match the variants a user inputs, then allow the user to click through to a trial recruitment page.

Streamline is also developing an application programming interface so the firm can partner with organizations that want to incorporate its aggregated datasets into their own software utilities. Duggan said to expect the API in 2022.

The firm has largely been funded by revenues, though Streamline did go through the Techstars NYC incubator in 2018. Duggan said that the company is in the process of raising additional capital now, but did not elaborate.

He added that the firm is looking at how to make the two new, free utilities open-source.

"We will continue to look for ways to provide free utility to users and build out our ability to help everyone adopt precision medicine," Duggan said.