Appistry’s Vision for Clinical Lab Analysis

By Allison Proffitt

July 15, 2016 | “About twelve months ago, Appistry started building a product called GenomePilot. The intent of that product is really to support the clinical sequencing lab in collecting, managing, analyzing next generation sequencing data as it comes off of the sequencer,” Trevor Heritage, Appistry’s Chief Strategy Officer tells Bio-IT World.

Lab technicians processing clinical samples usually aren’t bioinformaticians, Heritage explains. The goal for GenomePilot is to, “take the raw data from the sequencer, and perform a robust, compliant process through which the clinical dataset is created, and to do that in a very intuitive environment so that a lab director or lab technician could feel comfortable using that tool, and feel comfortable that they are doing something that is scientifically correct and clinically viable.”

Appistry is working on collecting the very best scientific tools for the GenomePilot pipeline—both publicly-available and commercial—and integrating them into a seamless pipeline. In late May, Appistry integrated VarScan, a software for variant detection in massively parallel sequencing data developed at the Genome Institute at Washington University into GenomePilot.

“VarScan is one of the most widely-published variant callers, with a particularly impressive performance in the oncology space for somatic variations,” Heritage says. “We wanted to make that tool available through the GenomePilot user interface and environment.”

Late last month, Appistry announced the next of its offerings meant to smooth clinical laboratories’ testing and analysis processed.

“If you think about a molecular testing lab, maybe they go out and purchase a myeloid testing kit from Illumina and maybe they purchase a MiSeq or something like that to do the sequencing,” Heritage posits. “Ideally what they would like is a package that handles the data management, the data flow, the data analysis that sits behind that technology that they just purchased and enables them to execute their full test from A to Z.”

Appistry’s Managed Services are meant to fill that role.

“Customers were saying to us, ‘It’s great that GenomePilot can do all these things, but we need help with the set-up, with the installation, with the deployment. We need help with what’s the right pathway through the bioinformatics tools. What are the right parameters?” Heritage recounts. “And then on a day-to-day basis, [we need help] executing that workflow and making sure the system is running exactly as it should be.”

The Managed Services offering complements GenomePilot, delivering additional value for laboratories that don’t have the in-house expertise or infrastructure. This comprehensive service can handle the bioinformatics development and set-up of a lab’s NGS testing, the implementation of a robust IT infrastructure, the build out of compliance tracking, and the deployment and integration with a lab’s internal systems.

Labs will subscribe to the managed services on an annual basis. The fee depends on the number of clinical genomics tests they want to run. Labs buy their test kits and sequencers, and Appistry sets up the bioinformatics testing, data analysis, and workflow from the moment data come off the machine. Appistry will chose the right pipeline for whichever tests and platforms the lab is using.

Setup can take half a day for a simple panel-based test, or up to a week for a more extensive test menu. Appistry team members are on site for initial setup and watch the initial samples proceed through the pipeline. After that, Appistry monitors the pipeline remotely and is on call for questions or to add additional tests.

It’s meant to be a seamless process, but it does beg the question: why wouldn’t labs just outsource the whole process?

“In many cases, what we’ve found is that the hospital labs are under constant pressure to reduce the, ‘send out bill’. They’re basically looking to run any tests in house that they possibly can,” Heritage says. Sequencing companies have made the process of buying test kits and sequencers extremely straight forward. “We’re bringing the back level of that to a similar level of simplicity and ease of use.”