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PierianDx Buys Tute Genomics to Improve Clinical Informatics Workflow for Constitutional Disorders

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NEW YORK (GenomeWeb) –  PierianDx has acquired Provo, Utah-based bioinformatics company Tute Genomics in an asset purchase that closed on Sept. 30.

Tute officially became part of PierianDx on Oct. 1. As part of the transaction, Tute CEO and Co-Founder Reid Robison will join PierianDx's board of directors. Tute Chief Operating Officer Andy Olson and Vice President of Product Development Bryce Daines will also join PierianDx in the company's St Louis office. Meanwhile, Tute Co-Founder and President Kai Wang will join the advisory board at PierianDx. Tute's new owners will also maintain a small development team in Provo, Utah. In total, seven employees from Tute are crossing over to PierianDx, bringing that company's total headcount to 63 employees.

According to PierianDx CEO Ted Briscoe, the acquisition furthers his company's goal to provide a single, comprehensive platform for personalized medicine to clinical laboratories. "Our core business is focused on enabling our lab partners to have a platform from analysis to interpretation to reporting to support their personalized medicine testing," he told GenomeWeb. "We don't believe that platforms should have multiple partners for different tests, and so we are taking steps to continue to extend the flexibility and comprehensiveness of our platform to make sure we can cover as much of their molecular testing needs as possible."

More specifically, the acquisition will enable PierianDx to extend its proprietary Clinical Genomicist Workspace (CGW) solution to include stronger informatics support for constitutional disorders testing, he told GenomeWeb. The CGW, which was developed in the Genomics and Pathology Services laboratory of Washington University, St. Louis, provides tools primarily for processing, storing, and reporting the results of next-generation sequencing-based cancer assays. PierianDx licensed the solution from WUSTL in 2014 and has since built a business around the tool offering software-as-a-service for analyzing mutations in somatic cancer samples as well as for constitutional disorders such as cardiomyopathy. The commercial version of the software includes a database of curated literature, biological information, population frequency data, clinical trials, treatment guidelines, and more as well as a scoring tool that is intended to help clinicians prioritize actionable variants. 

Recently, PierianDx raised $9.25 million in a Series A financing round led by Health Catalyst Capital Management. The company said that among other things it planned to use the funds to develop new capabilities for the CGW as well as to hire curators to help expand the content contained in its underlying knowledgebase to support both cancer and constitutional disorder testing. Although it has made some investments in workflows and content for the constitutional disorders testing market, because the CGW was initially developed with oncology testing in mind, PierianDx's current offering is strongest in the somatic cancer space, Briscoe said.

The list of customers that have tapped its offerings for oncology testing include Phoenix Children's Hospital, which collaborated with the company on the development of sequencing-based test for use in a pediatric cancer study. That test, according to the partners, would cover non-malignant exome, cancer exome, and RNA sequencing. Also included in the company's roster is the University of Arizona. Researchers in the genomics core at the institution tapped the CGW to develop and validate a cancer panel of more than 500 genes. 

Meanwhile, last year, the company signed an agreement with Syapse to integrate the CGW with the Syapse precision medicine platform in order to provide pathology labs with an end-to-end genomic testing workflow for oncology testing. PierianDx also signed a co-marketing and licensing agreement with ArcherDx that allowed the company to integrate Archer's FusionPlex and VariantPlex oncology target enrichment assays and software with the CGW. 

In addition, PierianDx launched a new program late last year called NGS Gateway, a program that is designed to connect new testing laboratories to temporary resources that they need to begin offering tests while they work on setting up their internal infrastructure and obtaining appropriate certifications. For example, the company offered to connect labs to sequencing service providers to handle sample prep and sequencing as well as medical professionals to review and sign out testing results. As of January this year, testing services available to labs through the program focused on solid tumor, hematopoietic disorders, CNS tumors, and melanomas, although the company planned to add services focused on constitutional disorder testing as well. 

Tute does offer some analysis capabilities for somatic cancer testing, but the company was primarily focused on the constitutional testing market, Briscoe told GenomeWeb. This focus was further "solidified" after Tute acquired assets from the now defunct genomics company Knome, according to Briscoe. In fact, "one of our initial attractions to Tute was the increase in market traction they experienced since [the] acquisition," he told GenomeWeb. "We have a lot of our own constitutional capability ... [but] there are things that are more at a technology level that we felt were really important additional to our core offering."

Of particular interest to the company are Tute's phenotype-driven filtering and variant prioritization capabilities as well as querying mechanisms for complex inheritance models that will be "a nice extension to our workflow," he said. Since it now owns the Tute technology, the company will be able to integrate those features into the CGW in a much shorter time frame. In fact, PierianDx plans to have both platforms fully integrated by spring 2017, at which time it will launch version 6.0 of the CGW. That iteration of the solution will cover both the existing somatic cancer analysis capabilities as well as a new workflow for assessing constitutional disorders from the Tute platform.

"Our technology is assay agnostic, so we will support the full range of testing of our clinical lab customers, regardless of disease type," Briscoe said. Moreover, with analysts projecting revenues for the constitutional testing market to be between 50 percent to 100 percent of the somatic cancer testing market, "we expect our combined solution to further accelerate the growth of PierianDx's rapidly expanding customer base," he said.

Among Tute's customers are Newborn Screening Ontario, a molecular testing laboratory at the Children's Hospital of Eastern Ontario that tapped Tute to provide cloud-based pipelines for sequence alignment, variant calling, annotation, interpretation, and results reporting for two NGS-based panels for confirming the presence of rare but treatable conditions that have been diagnosed by biochemical testing. Other customers of the Tute solution include Brigham Young University who selected the platform to analyze NGS data for an Alzheimer's disease research project.

Among its industry deals, Tute had a software integration agreement with DNAnexus that allowed the companies to combine their respective platforms to provide an integrated solution for genomic data management, analysis, and interpretation. The company inked a similar integration deal with life sciences software and services firm Databiology to provide a one-stop shop for cancer information management, annotation, and reporting. Briscoe told GenomeWeb that these relationships will not change as a result of the acquisition and that the company will explore ways to extend the collaborations in the core CGW offering. 

PierianDx also intends to maintain the Tute platform as a standalone solution while the companies' platforms are integrated over the next several months. The company will also retain the Tute brand on the standalone product for current customers for the time being. "Both the Tute and Knome brands we think are potentially very valuable ... so we certainly will keep those and over time we'll figure out the appropriate way to use those brands," Briscoe told GenomeWeb. He also said that PierianDx is willing to support existing Tute customers who, for one reason or another, still need the standalone Tute offering even after the integrated product launches.

The acquisition also means that Tute will no longer pursue its direct-to-consumer genomics Kickstarter campaign. On Sept. 13, the company launched a program on the crowdfunding site through which it intended to offer whole-genome and whole-exome sequencing and analysis services directly to the general public. Backers would be provided with reports that included information on actionable variants in their DNA as well as their risks of developing a variety of diseases such as Alzheimer's disease and thrombosis conditions. Clients would be able to access both their raw sequence and variant reports via the so-called Knome portal, which serves as the front end to Tute's service.

However, just two days after the month-long campaign launched, the company received a letter from the US Food and Drug Administration regarding the project. It is not clear exactly what kind of letter Tute received as the company declined to share a copy of the letter with GenomeWeb and the FDA has not posted a copy on its web page — though GenomeWeb did file a request under the Freedom of Information Act to view the document. However, in a conversation with GenomeWeb, then Tute CEO Reid Robison said that the FDA had not issued a warning letter but simply asked for a dialogue with the company about the offering, as the company had not discussed the campaign with the agency before launching it. As a result of the letter, Tute decided to temporarily suspend the campaign while it hashed things out with the agency. At that point, the campaign had bagged 114 backers and raised nearly $75,000 of its $100,000 goal.

In a letter sent to backers explaining the decision, Reid Robison stated that the company was in touch with the FDA and was "proactively engaging" with the agency on "the right path forward to make this happen." However, Briscoe told GenomeWeb that as a condition of the acquisition, PierianDx asked Tute to terminate the campaign — it was launched before acquisition talks between the companies began.

"We did not want to bring that over," Briscoe told GenomeWeb. "It is a very interesting concept, but we asked [them] to pull that down because it wasn't a program that we were comfortable with launching the way that they had." According to the Tute Kickstarter page, the project was officially cancelled on Sept. 28.

Although it is shelving any DTC plans for now, Briscoe did not rule out the possibility of PierianDx making some kind of play in the space in future. In fact, the company is already exploring opportunities and ways to enter the market. "You certainly can expect to see us make moves in that general area but we are not ready to do that quite yet," he said. When the company does make its move "we will do it very carefully and very deliberately and in full cooperation and compliance with the FDA." 

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