Timothy Blewett

Purpose: Circulating tumor DNA (ctDNA) could be a powerful prognostic biomarker for patients with locally advanced esophageal cancer but higher sensitivity is needed. An ultrasensitive test could enable improved treatment decision-making by accurately identifying patients with residual disease. Experimental Design: 331 plasma samples from 36 patients were collected both preoperatively and postoperatively. We applied MAESTRO-Pool (Minor Allele Enriched Sequencing Through Recognition Oligonucleotides) of the Broad Institute and the Oncodetect® V2 test of Exact Sciences, two MAESTRO-based, ultrasensitive, tumor-informed, mutation enrichment sequencing tests, to all samples. Results: With the Oncodetect V2 test, we found 9 of 14 patients (64%) with recurrence and postoperative plasma available tested ctDNA-positive at their first postoperative sample and all 14 patients tested ctDNA-positive for at least one postoperative sample prior to recurrence. ctDNA was detected below the limit of detection for first-generation assays in 59% of all samples in which we detected ctDNA. By tracking a median of 2.1-fold more mutations per patient (up to 5,000 total mutations per patient), the Oncodetect V2 test showed highly concordant results (98.9% positive percent agreement), improved ctDNA detection, and longer lead times to recurrence as compared to MAESTRO-Pool. Conclusion: ctDNA detection after curative-intent therapy for locally advanced esophageal cancer had strong positive and negative predictive values for recurrence. Given the low ctDNA levels observed, and that all patients with recurrence were eventually ctDNA-positive, ctDNA testing in esophageal cancer may benefit from ultrasensitive tests that detect part-per-million levels of ctDNA.

Despite responses of chimeric antigen receptor (CAR)-T cells in patients with relapsed/refractory large B-cell lymphoma (LBCL), over half of patients eventually relapse. Methods to detect early disease persistence are needed to identify patients at high risk of treatment failure. We recently developed MAESTRO, an ultrasensitive, tumor-informed measurable residual disease (MRD) assay, which can detect parts-per-million (ppm) levels of circulating tumor DNA (ctDNA) using minimal sequencing. We applied MAESTRO to 140 samples from 28 patients (15 durable responders at 12 months and 13 nonresponders) to identify treatment failure after axicabtagene ciloleucel (axi-cel), administered at our institution between 2018 and 2022. Responder and nonresponder patients had similar baseline tumor burden. By 1 week after infusion, responders had marked ctDNA reduction compared to nonresponders (P < .001). At weeks 2 and 4, responders had ctDNA levels approaching 0 ppm, whereas nonresponders had persistence of ctDNA (each P < .001). At day 0, up to 21% of patients had ctDNA fractions <0.01%; hence, these individuals would not have qualified for ctDNA monitoring with a less sensitive test. Our results confirm the feasibility of highly sensitive MRD detection by ctDNA for early identification of patients at high risk of disease progression from axi-cel.

Purpose:Although ctDNA is a promising biomarker for minimal residual disease (MRD) detection in head and neck squamous cell carcinoma (HNSCC), more sensitive assays are needed for accurate MRD detection at clinically relevant time points. Ultrasensitive MRD detection early after surgery could guide adjuvant therapy decisions, but early ctDNA dynamics are poorly understood.Experimental Design:We applied minor allele–enriched sequencing through recognition oligonucleotides (MAESTRO), a whole-genome, tumor-informed, mutation enrichment sequencing assay, in a pooled testing format called MAESTRO-Pool, to plasma samples from patients with HNSCC collected shortly after surgery and during surveillance. We evaluated whether early MRD detection could predict outcomes.Results:Among 24 patients with predominantly human papillomavirus–independent (95.8%) HNSCC, rapid ctDNA clearance occurred by the first postoperative sample (1–3 days postoperatively) in nine patients without an event (recurrence or death). Thirteen of fifteen patients with an event were MRD-positive (positive predictive value = 92.9%; negative predictive value = 80%) with a median tumor fraction (TFx) of 54 parts per million (ppm; range 6–1,177 ppm). In the first and last samples of the early postoperative window, 8/13 and 10/13 patients, respectively, had TFx below 100 ppm, the detection limit of leading commercial assays. Early MRD detection correlated with worse overall survival (HR, 8.3; 95% confidence interval, 1.1–66.1; P = 0.02) and event-free survival (HR, 27.4; 95% confidence interval, 3.5–214.5; P < 0.0001) independent of high-risk pathology.Conclusions:Early postoperative MRD detection by MAESTRO was associated with recurrence and worse survival. Given the ultralow TFxs observed, ultrasensitive assays will be essential for reliable MRD detection during early postoperative time points to enable personalized adjuvant therapy decision-making in HNSCC.See related article by Bryan et al., p. 3483

Purpose: Although ctDNA is a promising biomarker for minimal residual disease (MRD) detection in head and neck squamous cell carcinoma (HNSCC), more sensitive assays are needed for accurate MRD detection at clinically relevant time points. Ultrasensitive MRD detection early after surgery could guide adjuvant therapy decisions, but early ctDNA dynamics are poorly understood. Experimental Design: We applied minor allele–enriched sequencing through recognition oligonucleotides (MAESTRO), a whole-genome, tumor-informed, mutation enrichment sequencing assay, in a pooled testing format called MAESTRO-Pool, to plasma samples from patients with HNSCC collected shortly after surgery and during surveillance. We evaluated whether early MRD detection could predict outcomes. Results: Among 24 patients with predominantly human papillomavirus–independent (95.8%) HNSCC, rapid ctDNA clearance occurred by the first postoperative sample (1–3 days postoperatively) in nine patients without an event (recurrence or death). Thirteen of fifteen patients with an event were MRD-positive (positive predictive value = 92.9%; negative predictive value = 80%) with a median tumor fraction (TFx) of 54 parts per million (ppm; range 6–1,177 ppm). In the first and last samples of the early postoperative window, 8/13 and 10/13 patients, respectively, had TFx below 100 ppm, the detection limit of leading commercial assays. Early MRD detection correlated with worse overall survival (HR, 8.3; 95% confidence interval, 1.1–66.1; P = 0.02) and event-free survival (HR, 27.4; 95% confidence interval, 3.5–214.5; P < 0.0001) independent of high-risk pathology. Conclusions: Early postoperative MRD detection by MAESTRO was associated with recurrence and worse survival. Given the ultralow TFxs observed, ultrasensitive assays will be essential for reliable MRD detection during early postoperative time points to enable personalized adjuvant therapy decision-making in HNSCC. See related article by Bryan et al., p. XX .