Illumina software supports cancer study

SAN DIEGO—In August, Illumina Inc. noted that the American Society of Clinical Oncology (ASCO) had launched its first ever clinical trial, the Targeted Agent and Profiling Utilization Registry (TAPUR) Study—and that Illumina software is along for the ride.

TAPUR is designed to evaluate molecularly targeted cancer drugs and collect data on clinical outcomes to learn about additional uses of these drugs outside of indications already approved by the U.S. Food and Drug Administration.

Qualifying cancer patients with advanced disease whose cancer has not responded to standard treatment are eligible to enter the study through one of the growing list of over 35 participating clinical sites, Illumina notes. If a patient has tumor genomic test results that reveal a potentially actionable genomic variation, a clinician will review drugs available through TAPUR that potentially target that variation.

Available in the study right now are 17 drugs providing 15 targeted therapies; however, if a relevant drug-target match is not described in the protocol, clinicians may consult the TAPUR study’s Molecular Tumor Board, which will review the clinical and genomic features of the case and identify potential treatment options on and off the study for consideration by the treating physician.

As Illumina notes, “Such a process can be cumbersome outside of the research setting because sequencing data are becoming more abundant and there are a number of drugs available—as such, it is increasingly difficult to search through and interpret the data.”

To support the process, the Molecular Tumor Board has access to information from Illumina’s BaseSpace Biomarker Repository software (formerly known as NextBio KnowledgeBase) to support and inform TAPUR participant case review.

Illumina says its KnowledgeBase product containing various drug-variant associations also informed development of the TAPUR automatic identification and selection rules. Subjects are annotated against the KnowledgeBase using BaseSpace Cohort Analyzer. For the study's Molecular Tumor Board, the focus is on reviewing a participant’s variants and possible associated drugs. TAPUR is designed to analyze efficacy and toxicity outcomes of patients who receive study therapy. To help automate the study workflow, ASCO also is using the Syapse Precision Medicine Platform.

In the short term, according to Illumina, the TAPUR study may benefit participating physicians by helping them learn to interpret genomic data, adding, “Likewise, participating pharmaceutical companies receive study data that may help identify potential new uses for existing cancer drugs. And most importantly, study participants gain access to experimental therapies that may not normally be available to them, as well as study researchers who have expertise in applying genomic information in a research setting.”

In the long run, the company notes, the potential benefit is even more profound, as “This study addresses the inherently iterative process required to improve cancer treatments by learning from every patient.”

In other Illumina software news from August, the company announced that it and FlowJo LLC had formed a partnership to develop and co-market analysis software for single-cell next-generation sequencing (NGS) data. Under the agreement FlowJo, the producer of FlowJo, a market-leading software solution for single cell analysis, will develop a new software application. It will provide additional secondary and tertiary analysis and visualization of datasets with an intuitive approach built on 19 years of experience working with cell biologists and immunologists in single cell phenotyping. The application is being designed to seamlessly integrate with Illumina’s Single Cell RNA BaseSpace app, and provide a solution accelerating discovery.

“We are excited to partner with Illumina on this project to bring new tools for analyzing and visualizing NGS data to cell biology,” said Dr. Michael Stadnisky, CEO of FlowJo. “The new offering will enhance the power of single cell biology research by empowering robust exploration of data from Illumina next-generation sequencing runs.”

The software will complement the end-to-end commercial solution for high-throughput sequencing of single cells that Illumina announced it is co-developing in partnership with Bio-Rad Laboratories. FlowJo and Illumina expect the software to be available in the first quarter of 2017.