Digital polymerase chain (PCR) and targeted sequencing assays characterized the molecular profiles of circulating cell-free tumor DNA (ctDNA) with a high level of accuracy, according to results of a prospective study evaluating the efficacy and safety of targeted therapy in molecularly defined cohorts of patients with advanced breast cancer. These findings were published in Lancet Oncology.1

Although somatic mutations in ERBB2, ESR1, AKT1 represent potential molecular targets in advanced breast cancer, they are considered to be rare in this setting, present in only approximately 5% of patients with the disease. Moreover, while mutations in these genes may be acquired in the setting of relapsed disease while being absent from the archival tumor specimen, assessments of ctDNA offer the potential for noninvasively investigating the molecular status of the disease in real time.

The plasmaMATCH study (ClinicalTrials.gov Identifier: NCT03182634) is an ongoing parallel cohort, multicenter, nonrandomized, phase 2 clinical trial of patients with advanced breast cancer that was designed to evaluate the clinical validity of using ctDNA testing to investigate the somatic molecular profiles of adult patients with advanced breast cancer. In addition, a second study aim was to assess the clinical utility, including the safety and efficacy, of using such an approach to direct targeted therapy.

The primary endpoint of this study is the objective response rate in ctDNA-defined molecular cohorts of patients with advanced breast cancer receiving targeted therapy, with secondary endpoints including duration of response, clinical benefit rate, progression-free survival (PFS), safety, and the accuracy of ctDNA testing by agreement between ctDNA mutation status and tissue mutation status.


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Eligibility for enrollment on the plasmaMATCH trial included the presence of measurable, progressive advanced breast cancer that was not suitable for curative approaches. Furthermore, patients had to have received at least 1 prior treatment in the metastatic setting or to have experienced disease relapse within 12 months of receiving neoadjuvant/adjuvant therapy.

Of the 1051 patients enrolled in the study between December 21, 2016 and April 26, 2019, 1044 were screened by ctDNA-based testing using either digital polymerase chain reaction (PCR) testing for PIK3CA, ESR1, HER2, and AKT1 and/or a 73-gene ctDNA targeted sequencing assay, with results available for 1034 of these patients. Digital PCR testing, and targeted ctDNA sequencing was performed on 1025 and 800 (364 prospectively and 436 retrospectively) patients, respectively, with a positive result by either test considered sufficient for study entry.   

Of note, digital PCR is a method similar to quantitative PCR; however, it does not rely on a calibration curve for sample target quantification, nor are reference standards or endogenous controls used. Another difference with respect to digital PCR is that sample reaction mixture is partitioned into multiple wells prior to the amplification step, such that either 0 or 1 specific target is detected in each well, thereby allowing for improved detection and quantification of rare alleles, copy number variations, and other molecular endpoints.2

In addition, molecular characterizations of tumor tissue representative of advanced disease were performed retrospectively for 77 patients of the 136 patients who entered a therapy cohort.

Patients with a mutation in ESR1, ERBB2, AKT1 (in the setting of estrogen receptor-positive disease), or AKT1 (in the setting of estrogen receptor-negative disease, or an inactivating mutation/presence of homologous deletion in PTEN irrespective of tumor hormone receptor status) were included in 1 of 4 cohorts in which they were treated with fulvestrant (cohort A), neratinib with or without fulvestrant depending on tumor hormone receptor status (Cohort B), the AKT inhibitor, capivasertib, with fulvestrant (cohort C), and capivasertib monotherapy (cohort D), respectively.  

Some of the key findings from this study included the following:

  • A comparison of results of ctDNA testing by digital PCR and targeted sequencing showed 96% to 99% agreement in identifying mutations in specific genes.
  • Sensitivity (or percent-positive agreement reflecting the absence of gold standard) for digital PCR was 93% overall and 98% compared with tissue-based sequencing sin patients with contemporaneous biopsies.
  • Sensitivity for targeted ctDNA sequencing was 95% overall and 100% compared with tissue-based sequencing in patients with contemporaneous biopsies.
  • ORRs in cohorts B (21 individuals) and C (18 individuals) were 25% and 20%, respectively, and met or exceeded the target number of responses.
  • ORRs in cohorts A (84 individuals) and D (19 individuals) were 8% and 11%, respectively, and did not meet the target number of responses.
  • The most common grade 3 to 4 adverse events were elevated levels of gamma-glutamyltransferase 16%; cohort A); diarrhea (24%; cohort B); fatigue (22%; cohort C); and rash (26%; cohort D).
  • There was 1 treatment-related death in cohort C.

In their concluding remarks, the study authors noted that “ctDNA testing offers accurate, rapid genotyping that enables the selection of mutation-directed therapies for patients with breast cancer, with sufficient clinical validity for adoption into routine clinical practice.”

They further added that these results “demonstrate clinically relevant activity of targeted therapies against rare [ERBB2] and AKT1 mutations, confirming these mutations could be targetable for breast cancer treatment.”

References

  1. Turner NC, Kingston B, Kilburn LS, et al. Circulating tumour DNA analysis to direct therapy in advanced breast cancer (plasmaMATCH): a multicentre, multicohort, phase 2a, platform trial. Lancet Oncol. [published online September 10, 2020].  doi: 10.1016/S1470-2045(20)30444-7
  2. Hindson CR, Chevillet JR, Briggs HA, et al. Absolute quantification by droplet digital PCR versus analog real-time PCR. Nat Methods. 2013;10:1003-1005.