Overview

The Knight Diagnostic Laboratories (KDL) were among the first to adopt next-generation sequencing (NGS) for clinical use. The KDL took delivery of an Ion Torrent PGM in March 2011, and subsequently published their initial experience with this system in the Journal of Molecular Diagnostics.¹

The GeneTrails^® Solid Tumor Panel is a fully customized product of the KDL. It combines an amplicon-based library preparation with sequencing on either the Ion Torrent PGM or Ion Torrent Proton system. The panel was first made available as a laboratory developed test in April of 2013. To date, more than 1060 clinical cancer samples have been screened for mutations using this panel, which is run at an average read depth of 1,000 reads and has a lower limit of detection of 5% mutant allele. During 2013, the KDL developed a custom algorithm to assess gene copy number alterations from the sequencing data (J Molec Diag, in review). This algorithm is now routinely applied in the analysis of clinical samples with the Solid Tumor Panel, broadening the utility of the panel.

Actionable Results

Predicting Drug Sensitivity

Compared with other products on the market, the GeneTrails^® Solid Tumor Panel is modest in size, but that is because it is focused on cancer gene alterations that are truly actionable. We define actionable as falling into these two categories: 1) there is an FDA-approved drug available for the target, either on- or off-label, and published clinical data supporting its use (e.g. case report, small series); 2) there is a clinical trial investigating a new compound relevant to the target. Note that we purposefully excluded genes that are only ‘theoretically’ targetable based solely on pre-clinical cell line or xenograft data.

The table at the end of this report lists all 37 genes included on the panel. For 20 of the genes (more than half the panel), the presence of a mutation would justify the use of an FDA-approved therapeutic, either on- or off-label. Alterations in 14 of the remaining 17 genes would support enrollment in a trial of one or more compounds currently in clinical development. Only 3 genes on the panel are not actionable with available therapeutics, although this might change in the future.

The addition of copy number assessment provides important information in the setting of breast and gastric carcinoma, where HER2 amplification is an established target. It can also bring to light other gene amplifications of interest in current clinical trials, including MET and PIK3CA. Gene losses, such as in CDKN2A or RB1, may also have an impact on trial eligibility.

Predicting Drug Resistance

In addition to providing information on which targeted therapeutics might be appropriate for a specific tumor, the panel is also useful in predicting resistance to certain drugs. For example, in the case of a colorectal carcinoma, the presence of a mutation in KRAS, NRAS, BRAF or PIK3CA would indicate resistance to the EGFR-targeted therapies cetuximab and panitumumab. Recent editorials from ASCO have endorsed broadening the screening of these cancers beyond KRAS, and running a small/medium-sized panel is a cost-effective way of doing so. The panel can also detect the EGFR T790M mutation that causes erlotinib resistance in lung cancer, as well as PTEN mutations that may indicate a shorter response to vemurafenib in the setting of BRAF-mutant melanoma.

Proven Clinical Utility

In 2013, the KDL partnered with Cancer Clinics of Excellence, a network of community-based oncology practices, and began screening advanced solid tumor cases with the GeneTrails panel to look for actionable mutations. A retrospective analysis was performed on 632 cases that were sequenced, and this work was presented at the 2014 ASCO meeting.^2,3

Among 632 solid tumors, representing the full spectrum of cancer types treated in the community, 57% (n=360) were found to have at least 1 actionable mutation. Within this subset, the results for 178 cases were available at the time important treatment decisions were being made. In 35% of these cases (n=63), the sequencing results had an impact, with 40 patients being considered for a clinical trial (21 enrolled), 15 patients receiving FDA-approved therapies off-label, and 8 patients continuing on standard of care. These results show that the GeneTrails^® Solid Tumor Panel is useful in the management of patients with advanced stage cancers.

Links and References:

1. Beadling C, Neff TL, Heinrich MC, Rhodes K, Thornton M, Leamon J, Andersen M, Corless CL. Combining highly multiplexed PCR with semiconductor-based sequencing for rapid cancer genotyping. J Mol Diagn. 2013 Mar;15(2):171-6.  PMID: 23274167
2. ASCO Abstract: http://abstracts.asco.org/144/AbstView_144_128879.html
3. ASCO Poster: http://origin.library.constantcontact.com/download/get/file/1116839265733-14/ASCO+2014+Poster+5-24-14+LO+PDF.pdf

GeneTrails® Solid Tumor Panel

*Drug resistance mutations