NEW YORK (GenomeWeb) – Investigators have published some of the first results from the UK's TARGET (Tumor chARacterisation to Guide Experimental Targeted therapy) study, which add new evidence for the feasibility and potential utility of liquid biopsy to identify clinically actionable mutations and guide clinical trial enrollment for patients with advanced cancer.
The authors of a letter appearing in Nature Medicine today wrote that they designed TARGET in two parts. Part A, which involved 100 initial patients in the Manchester area, makes up the data currently described.
The group concluded that their Part A effort "to develop a robust workflow … with a data turnaround time compatible with clinical practice and at an affordable cost," was a success. Blood-based sequencing results were sufficiently concordant with tissue, actionable mutations were frequently detected, and a small but significant number of patients were directed to molecularly targeted trials based on the results.
At the very least the data support continued application of liquid biopsy as an adjunct, the authors wrote. However, further refinement may also support the type of "'blood-first paradigm' — now becoming a focus for commercial liquid biopsy firms — in which certain cancer patients might be assigned to liquid biopsy up front with tissue analysis only applied in cases with known confounding factors like low tumor burden or poor circulating tumor DNA (ctDNA) yield.
TARGET was funded by Cancer Research UK, The Christie Charity, AstraZeneca and the NIHR Manchester Biomedical Research Centre (BRC). For the analysis of the first 100 patients, investigators first designed and optimized a 641-gene liquid biopsy panel using Agilent SureSelect technology. Sequenced subjects were spread over 22 tumor types, with a median age of 56 years and a median of two prior lines of therapy.
Authors reported that they generated ctDNA NGS data successfully in 99 percent of patients, compared with tumor tissue sequencing, which only worked in 95 percent.
Looking at the data, the authors wrote that ctDNA showed "good concordance" with matched tumor results, and testing was successfully turned around within a "clinically acceptable" timeframe for review by the program's molecular tumor board — a crucial milestone toward implementation in patient care.
The group's tissue-blood concordance calculations were somewhat limited because tumor tissue analysis was variable across the cohort, with some patients tested using much smaller gene panels than the group's new ctDNA assay and only a subset having more comprehensive data from Foundation Medicine's FoundationOne test, which shared about 230 genes in common with the study's liquid biopsy panel.
Given that caveat, the group wrote that 69 non-synonymous mutations were identified in tumor tissue from 54 patients overall. Analysis of corresponding ctDNA NGS data revealed good concordance, with 54 of 69 alterations (78 percent) also detected in plasma.
Investigators applied a 2.5 percent variant allele frequency (VAF) threshold for liquid biopsy variant calling. And even with this relatively high cutoff, the assay was able to identify actionable mutations in the blood of 41 of 100 patients, 11 of whom received a matched therapy.
"While our 2.5 [percent] VAF threshold might result in 'false negatives' and inherently bias toward patients with higher disease burden, it will reduce 'false positives' … [while facilitating] broad panel testing for a diverse range of alterations required in the phase I trial setting," the authors explained.
Using the 2.5 percent cutoff, the team saw a 75 percent concordance (70 of 94 cases) between ctDNA and tissue results in patients with both tumor and ctDNA data.
Among the 24 discordance cases, 20 had tumor tissue mutations that were not recapitulated in the liquid biopsy sequencing. Of these, nine were actually present in sequence reads, but fell below the VAF cutoff. Four additional individuals had ctDNA mutations that were not represented in corresponding tissue sequencing.
Some of these mismatches could be ascribed to either a biological or clinical consequence, authors added. For example, one patient with colorectal cancer exhibited a KRAS c.34G>T mutation in their ctDNA, which was not detected in the archival tumor specimen collected 26 months previously. Most likely the presence of the mutation in blood is "linked to the administration of anti-EGFR therapy … in the intervening period, to which KRAS mutation is a well-described mechanism of resistance," the team wrote.
Recognizing that there have been disappointing results from precision medicine trials in the past, the TARGET team also implemented several reporting and review strategies to try to make sure that as many genomic alterations as possible would actually lead to patients being funneled to a trial for a targeted agent.
Still, of 41 patients with a variant deemed actionable, only 11 received a matched therapy. Another 17 received a "non-matched therapy, the group wrote, "largely due to trial availability." And 13 either had no trials available, deteriorated too quickly, or went on to a chemotherapy drug.
Hearteningly, for the 11 patients that did receive matched therapy, four had a partial response and seven had at least three months of stable disease. In contrast none of the non-matched therapy patients showed response, and only four had stable disease.
Authors highlighted one case example; a 57-year-old female with lung adenocarcinoma who had progressed through first-line chemotherapy. Her ctDNA profiling revealed an NRAS mutation, also confirmed in her archival tumor. The patient was matched to a phase I trial of a first-in-human MEK inhibitor and demonstrated partial response with a 60 percent reduction in marker lesions. Her disease remained controlled for 12 months, the team reported.
According to the TARGET investigators, the overall results in this first arm of the effort were promising enough to support further pursuit of the trial's goals. The results also add to growing evidence for clinical utility of ctDNA sequencing to funnel patients to molecularly stargeted drug trials.
"Now that we have demonstrated the feasibility of matching clinical trials for patients who have not responded to previous treatments by analyzing the tumor DNA in their blood, we are working to improve our blood testing approach," Caroline Dive, the laboratory lead author of the study from Cancer Research UK, said in a statement.
"We are making the test more sensitive and adding new elements to it in order to understand more about a patient's disease. We are also taking several blood samples over time to see if a faulty gene is disappearing with treatment, or if there is emergence of a new genetic fault that could lead to treatment resistance. This would allow us to stop a failing treatment and consider new options to stay a step ahead of the disease," she added.
Based on the results from the trial's first phase, TARGET's 'Part B' began recruiting a planned 450 patients in 2017 and is ongoing. With this expansion, investigators are more tightly focused on recording and analyzing the frequency at which patients can be referred to ctDNA-driven targeted treatment and the impact that this has on their outcomes.