The Impact of Foundation Medicine Testing on Cancer Patients: A Single Academic Centre Experience

Abstract

BackgroundThe use of Next-Generation Sequencing (NGS) has recently allowed significant improvements in cancer treatment. Foundation Medicine® (FM) provides a genomic profiling test based on NGS for a variety of cancers. However, it is unclear if the Foundation Medicine test would result in a better outcome than the standard on-site molecular testing. In this retrospective chart review, we identified the FM cases from an academic Canadian hospital and determined whether these test results improved treatment options for those patients.Materials and MethodsA retrospective analysis was performed on patients with solid tumors who had FM testing between May 1, 2014 and May 1, 2018. Clinical factors and outcomes were measured using descriptive statistics using Microsoft Excel® Software.ResultsOut of 66 FM tests, eight patients (= 12%) had a direct change in therapy based on the FM tests. Identified were 285 oncogenic mutations (median 1, range 0–31); where TP53 (n = 31, 10.9%), CDKN2A (n = 19, 6.7%), KRAS (n = 16, 5.6%) and APC (n = 9, 3.2%) were the most common FM mutations identified.ConclusionA small proportion of FM reports identified actionable mutations and led to direct treatment change. FM testing is expensive and a few of the identified mutations are now part of routine on-site testing. NGS testing is likely to become more widespread, but this research suggests that its true clinical impact may be restricted to a minority of patients.

Clinical management of molecular alterations identified by high throughput sequencing in patients with advanced solid tumors in treatment failure: Real-world data from a French hospital

“…The most commonly altered genes by genetic variation of class 4-5 and VUS in this study were consistent with those published in the literature, with TP53 as the most common gene, followed by RAS, PIK3CA, and CDKN2A/B (15,16,19,20). In the present Cancers for which more than five patients had available sequencing results were analyzed.…”

“…The success rate was 78% for liquid biopsy samples and 88% for FFPE samples (40% of biopsies), indicating that the ability to detect alterations is lower for liquid biopsies. These data are consistent with the literature comparing liquid and tissue biopsy samples (14)(15)(16)(17)(18). Takeda et al showed that the success rate of the NGS assay performed with FFPE samples, including 34% of biopsy specimens, was 96.7% in different types of cancer (19).…”

Multi-omics alleviates the limitations of panel-sequencing for cancer drug response prediction

“…Although comprehensive genomic profiling using cancer gene panels has demonstrated value in broadening the treatment options for the patients based on matching a patient’s genomic lesions to cancer driver gene aberrations associated with FDA-approved treatment indications 8,9 , the presence/absence of mutations in such genes does not necessarily translate into improved predictive power for estimating the patient’s response to the potential treatments. While for some drugs, the variation in drug response can be explained by a very specific mutation, for instance, BRAF V600E mutation is a strong predictor for response to Vemurafenib in metastatic melanoma 4 , for many drugs, the knowledge of the mechanism of action is missing.…”

An Overview of Comprehensive Genomic Profiling Technologies to Inform Cancer Care

“…41 Another study using a different CGP test (FoundationOne), which has both liquid biopsy-and tissue biopsy-based assays, reported a cost of $4,700 per sample in 2021. 42 In the US, certain commercially available CGP tests require blood samples to be sent to central laboratories for analysis, and the results are reported to the donor's health care provider. One of these tests (Guardant360) costs US$5,000 for people paying out-of-pocket.…”