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Cancer Research

On-target: Role of Illumina Software in Cancer Study

Illumina Software supports the TAPUR™ Molecular Tumor Board for precision medicine cancer study

On-target:  Role of Illumina Software in Cancer Study
02 August 2016

In August 2015, former U.S. President Jimmy Carter announced he would receive treatment for stage IV metastatic melanoma that had spread to his liver and brain. Despite optimism and reassurances he would receive the latest precision medicine, Carter had a prognosis ordinarily measured in months or even weeks.1 Yet, within a few short months, he had no detectable cancer cells. His announcement had many people wondering how he could so quickly go from having advanced stage cancer to being in remission – what was the miraculous treatment he received?

Carter received a newly approved, targeted immunotherapy drug. Unlike traditional chemotherapy, which affects both cancerous and healthy cells, targeted drugs are designed to specifically “target” a single gene, typically one that is deregulated in the tumor. In this case, the drug targets a gene called PDL1, allowing a patient’s own immune system to detect and destroy cancerous cells, leaving healthy tissue unharmed. Originally approved for use in melanoma, the drug Carter received is now being used in various clinical trials to determine whether it is effective in non-small-cell lung cancer, triple negative breast cancer, gastric cancer, and several other forms of cancer2.

If targeted drugs like the one Carter received can safely and efficaciously treat melanomas with a certain genomic profile, cancer researchers speculate that targeted drugs may also treat other cancer types with similar genomic profiles. It is for this reason that off-label use of certain cancer therapies is somewhat common3. Off-label describes those drugs that are prescribed for different indications, age groups, doses, or administration than what they were originally approved. However, there’s usually a catch: it can be difficult and costly for patients to get access to off-label drugs. Furthermore, oncologists and the cancer community don’t have a straightforward way to learn whether a particular drug was effective in a patient with particular characteristics. Historically, medical practice hasn’t routinely and systematically shared outcomes of patients who receive therapies off-label.

The American Society of Clinical Oncology, Inc. (ASCO®) has launched its first ever clinical trial, the Targeted Agent and Profiling Utilization Registry (TAPUR™) Study4 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 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. 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. At present, there are 17 drugs that provide 15 targeted therapies available in the study6. However, if a relevant drug-target match is not described in the protocol, the physician 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.

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, it is increasingly difficult to search through and interpret the data.

To support the process, the study Molecular Tumor Board is provided with information from Illumina’s BaseSpace Biomarker Repository* software (formerly known as NextBio KnowledgeBase) to support and inform TAPUR™ participant case review. Illumina’s KnowledgeBase of 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 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, the TAPUR™ study may benefit participating physicians by helping them learn to interpret genomic data. 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 potential benefit is even more profound. This study addresses the inherently iterative process required to improve cancer treatments by learning from every patient.

*For Research Use Only.  Not for use in diagnostic procedures.

American Society of Clinical Oncology, Inc. (ASCO®) is not a partner or affiliate of Illumina and does not recommend or endorse any vendor, product, or service. The ideas and opinions expressed herein are of the author and do not necessarily reflect those of ASCO®. ASCO® and TAPUR™ are trademarks of the American Society of Clinical Oncology, Inc. and are used with permission. All rights are reserved.



1.     Melanoma: Statistics | Cancer.Net. Cancer.Net 2012. Available at: Accessed May 20, 2016.

2.     Keytruda Impresses in Triple-Negative Breast Cancer. Medical News and Free CME from MedPage Today. Available at: Accessed May 20, 2016.

3.     3. Off-Label Drug Use in Cancer Treatment. National Cancer Institute. Available at: Accessed May 16, 2016.

4.     ASCO Kicks off Ground-Breaking Clinical Trial to Learn ... Available at: Accessed May 16, 2016.

5.     TAPUR: ASCO's First Clinical Trial Addresses Critical Gaps in Understanding of and Access to Targeted Therapies. TAPUR: 1st ASCO Clinical Trial on Access to Targeted Therapies. Available at:’s-first-clinical-trial-addresses-critical-gaps-understanding-and-access-targeted. Accessed May 20, 2016.


7.     Surveillance, Epidemiology, and End Results Program. Surveillance, Epidemiology, and End Results Program. Available at: Accessed May 16, 2016.

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