ctDNA Kinetics Research Articles

1472P Circulating tumor DNA in unresectable pancreatic cancer is a strong predictor of response to first-line therapy: The KRASCIPANC study

Prognosis of unresectable pancreatic cancer (uPC) remains poor with short overall survival (OS) and no robust predictive marker of response. KRAS mutation is observed in 90% of PCs and GNAS mutation in about 60% still poorly studied. KRAS-mutated circulating tumor DNA (KRAS-mut ctDNA) emerges as prognostic marker but whether ctDNA kinetics is a reliable predictor of response to chemotherapy (CT) remains uncertain. KRASCIPANC study evaluated KRAS-mut ctDNA kinetic as early predictor of response to 1st line CT in uPCs.

886P Circulating tumor DNA kinetics in recurrent/metastatic head & neck squamous cell cancer (R/M HNSCC) patients

Immuno-oncology agents (IO) have become a standard-of-care in the treatment of R/M HNSCC, however only a subset of patients (pts) benefit. Liquid biopsy offers access to circulating tumor DNA (ctDNA); currently data on ctDNA kinetics under treatment selection pressure is limited.

Next-Generation Sequencing Based Monitoring of Circulating-Tumor DNA in Untreated Peripheral T-Cell Lymphoma

Background: Peripheral T-cell lymphomas (PTCLs) are aggressive lymphomas with a wide range of clinical outcomes. Overall prognosis is worse for PTCL than B-cell lymphomas, but pts who achieve remission can be cured. After initial therapy, controversy exists regarding consolidation with autologous stem cell transplant, and clinical decisions are largely empirical. Circulating-tumor DNA (ctDNA) is emerging as a promising non-invasive biomarker that may aid clinical decision-making. Quantitative baseline levels of ctDNA and kinetics of ctDNA clearance during therapy may provide prognostic information. Further, novel methods that detect disease relapse prior to imaging may improve outcomes. We studied a high-throughput DNA sequencing method of detecting T-cell receptor (TCR) β and γ gene sequences in serum with a sensitivity of 1 lymphoma molecule per million leukocytes. Using this platform, we determined the predictive ability of monitoring ctDNA in pts undergoing frontline therapy for PTCL.Methods: All pts had PTCL undergoing frontline EPOCH-based chemotherapy between May 1993 through December 2015. Pre-treatment FFPE biopsy samples and/or baseline serum samples were sent for VDJ amplification and TCR sequencing calibration. High-throughput TCR sequencing of the CDR3s of TCRβ/TCRγ genes was employed to provide a comprehensive and quantitative analysis of distinct T-cell clones within each sample, the relative frequency of each clone, and the exact unique nucleotide sequences of each clone's CDR3 regions. Pts with a calibrating TCRβ/TCRγ sequence had all available serum samples sent for identification and quantification. Prospectively collected serum sample time points included baseline, start of each cycle, and each follow-up visit until disease progression. Clinic visits after therapy included paired contrast CT scans performed at 3, 4, 6, 12 and 12 mos. intervals for the first 5 years, respectively. All analyses for ctDNA were performed blinded to clinical outcomes.Results: Fifty PTCL pts had a pre-treatment FFPE or serum sample available for calibration. Nineteen of 23 (83%) pts with pre-treatment FFPE had a calibrating rearrangement; Fourteen of 27 (52%) pts with only pre-treatment serum available had a calibrating rearrangement; 1 pt who did not calibrate on FFPE had a dominant sequence identified in serum. Overall, tumor-specific clonotypes were identified in 34 (68%) of 50 pts tested. Ten of 18 (56%) pts with both FFPE and serum available had dominant clones in both compartments. Of the 44 calibrating pre-treatment samples, 1 calibrated for TCRβ only, 15 for TCRγ only, and 28 for both loci. Pt characteristics shown in Table 1. Of 34 study pts, 20 (59%) progressed and 14 (41%) were non-progressors. Quantitative baseline ctDNA levels were significantly higher in pts with stage IV disease compared to stages I-III (p=0.014) but did not correlate with LDH levels (p=0.53).We analyzed the predictive ability of ctDNA as a measure of minimal residual disease (MRD) within 1 month of completing therapy in 28 pts. We compared pts who became MRD- to those who remained MRD+ and identified a trend towards improved PFS in those who became MRD- (median, NR vs. 208 days, p=0.07) (Figure 1). In 20 pts who achieved remission, we studied the use of ctDNA monitoring as a surveillance tool. Of the 10 pts who progressed after remission, ctDNA was detected prior to clinical relapse in 6 cases with a median lead-time of 13.2 mos. (range, 2.7 to 88.5) and 4 with detectable ctDNA > 12 mos. prior to clinical relapse. Four pts progressed without detectable ctDNA prior to clinical relapse. Interestingly, of the 10 non-progressors followed in surveillance, 5 pts developed low-level ctDNA positivity without clinical progression. Results of interim ctDNA kinetics and TCRβ testing is ongoing and will be presented at the meeting.Conclusions: Next-generation based sequencing of the TCR can identify tumor-specific clonotypic sequences in the majority of pts from both FFPE and serum. As a marker of MRD, monitoring TCR sequences in serum may identify pts who do not benefit from treatment intensification, but further studies are needed. Surveillance monitoring of ctDNA in serum identifies TCR sequences months before clinical progression but not all pts with clonotypic sequences progressed clinically in our series. Further studies are needed to investigate surveillance monitoring methods and optimize clinical utility. [Display omitted] DisclosuresJacob:Adaptive Biotechnologies: Employment, Equity Ownership. Chan:Adaptive Biotechnologies: Employment. Vignali:Adaptive Biotechnologies: Employment.

Dynamics of circulating tumor DNA during postoperative radiotherapy in patients with residual triple-negative breast cancer following neoadjuvant chemotherapy: a prospective observational study.

This study was performed to evaluate circulating tumor DNA (ctDNA) kinetics during postoperative radiotherapy (PORT) in patients with residual triple-negative breast cancer (TNBC) at surgery following neoadjuvant chemotherapy (NAC). Stage II/III patients with post-NAC residual TNBC who required PORT were prospectively included in this study between March 2019 and July 2020. For 11 TNBC patients, next-generation sequencing targeting 38 genes was conducted in 55 samples, including tumor tissue, three plasma samples, and leukocytes from each patient. The plasma samples were collected at three-time points; pre-PORT (T0), after 3weeks of PORT (T1), and 1month after PORT (T2). Serial changes in ctDNA variant allele frequency (VAF) were analyzed. Somatic variants were found in the tumor specimens in 9 out of 11 (81.8%) patients. Mutated genes included TP53 (n = 7); PIK3CA (n = 2); and AKT1, APC, CSMD3, MYC, PTEN, and RB1 (n = 1). These tumor mutations were not found in plasma samples. Plasma ctDNA variants were detected in three (27.3%) patients at T0. Mutations in EGFR (n = 1), CTNNB1 (n = 1), and MAP2K (n = 1) was identified with ctDNA analysis. In two (18.2%) patients, the ctDNA VAF decreased through T1 and T2 while increasing at T2 in one (9.1%) patient. After a median follow-up of 22months, no patient showed cancer recurrence. Among patients with post-NAC residual TNBC, more than a quarter exhibited a detectable amount of ctDNA after curative surgery. The ctDNA VAF changed variably during the course of PORT. Therefore, ctDNA kinetics can serve as a biomarker for optimizing adjuvant treatment.

Abstract PO-069: Circulating tumor DNA kinetics to identify genomic predictors of rapid response to chemoradiation in non-small cell lung cancer

Abstract Introduction: Despite evidence that a subset of patients with locoregionally advanced non-small cell lung cancer (NSCLC) can be cured with radiation doses less than 60 Gy, there are currently no validated approaches to identify patients that could benefit from radiation dose de-escalation. Normal tissue changes including inflammation and fibrosis can be difficult to distinguish from residual disease on standard imaging during and following chemoradiation therapy (CRT), making assessment of treatment response and identification of favorable responders challenging. We hypothesized that circulating tumor DNA (ctDNA) kinetics during CRT could be used as a surrogate of response to identify genomic predictors of rapid response to treatment. Methods: We applied cancer personalized profiling by deep sequencing (CAPP-Seq) ctDNA analysis to 61 patients treated with CRT for Stage II-III NSCLC. We quantified ctDNA concentrations pre-CRT and a median of 21 days into CRT (mid-CRT) to determine the log-fold change in ctDNA concentration and identify “rapid responders.” The association between ctDNA log-fold change as a continuous variable with progression-free survival (PFS) was analyzed using univariable and multivariable regression, including gender, age, and stage as co-variables. The prevalence of driver gene single nucleotide variants in rapid responders versus slow responders was compared for each gene using Fisher’s exact tests with P-values adjusted using the Benjamini-Hochberg procedure. Results: Mid-CRT ctDNA log-fold change was significantly associated with progression-free survival as a continuous variable on both univariable (P=0.02) and multivariable analysis (P=0.03). Among patients whose ctDNA log-fold change was more negative than -2.15, 10/11 (91%) did not recur within the radiation field. We defined ctDNA rapid responders as the 10 patients with the largest decrease in ctDNA concentration mid-CRT without local progression. Compared with slow responders, ctDNA rapid responders had a trend towards more TP53 mutations (P=0.12), but no driver mutations were significantly enriched in rapid responders. Notably, mutations in common driver genes KEAP1, NFE2L2, KRAS, and EGFR were observed in 36% of slow responders and 0% of rapid responders (P=0.03). Conclusions: Our results suggest that ctDNA kinetics during CRT can identify patients responding favorably to treatment. Additional molecular characterization of ctDNA rapid responders may enable identification of patients who could benefit from treatment de-escalation. Citation Format: Everett J. Moding, Yufei Liu, Angela B. Hui, Jianzhong He, Yawei Qiao, Ting Xu, Luyang Yao, Saumil Gandhi, Zhongxing Liao, Millie Das, Kavitha J. Ramchandran, Sukhmani K. Padda, Joel W. Neal, Heather A. Wakelee, Billy W. Loo, Steven H. Lin, Ash A. Alizadeh, Maximilian Diehn. Circulating tumor DNA kinetics to identify genomic predictors of rapid response to chemoradiation in non-small cell lung cancer [abstract]. In: Proceedings of the AACR Virtual Special Conference on Radiation Science and Medicine; 2021 Mar 2-3. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(8_Suppl):Abstract nr PO-069.

Circulating Tumor DNA Early Kinetics Predict Response of Metastatic Melanoma to Anti-PD1 Immunotherapy: Validation Study.

Simple SummaryThe early detection of primary resistance to anti-PD1 immunotherapies remains a major challenge in the management of metastatic melanoma. In a previous study, we suggested that early monitoring of circulating tumor DNA (ctDNA) using well-defined evaluation criteria allows the identification of primary resistance to anti-PD1 immunotherapies as early as the second week of treatment. We used the same criteria to analyze first-month ctDNA kinetics in a validation cohort. We confirmed that an initial “biological progression” (i.e., a significant increase in ctDNA levels) was an early predictor of a complete lack of clinical benefit under anti-PD1, both in the validation cohort and by pooling the validation and derivation cohorts. Moreover, ctDNA detection at first-line treatment initiation was an independent prognostic factor for overall survival and progression-free survival. The results confirm that early quantitative ctDNA monitoring can detect primary resistance of metastatic melanoma to anti-PD1 immunotherapies.The ability of early (first weeks of treatment) ctDNA kinetics to identify primary resistance to anti-PD1 immunotherapies was evaluated with a validation cohort of 49 patients treated with anti-PD1 for metastatic BRAF or NRAS-mutated melanoma, alone and pooled with the 53 patients from a previously described derivation cohort. BRAF or NRAS mutations were quantified on plasma DNA by digital PCR at baseline and after two or four weeks of treatment. ctDNA kinetics were interpreted according to pre-established biological response criteria. A biological progression (bP, i.e., a significant increase in ctDNA levels) at week two or week four was associated with a lack of benefit from anti-PD1 (4-month PFS = 0%; 1-year OS = 13%; n = 12/102). Patients without initial bP had significantly better PFS and OS (4-month PFS = 78%; 1-year OS = 73%; n = 26/102), as did patients whose ctDNA kinetics were not evaluable, due to low/undetectable baseline ctDNA (4-month PFS = 80%; 1-year OS = 81%; n = 64/102). ctDNA detection at first-line anti-PD1 initiation was an independent prognostic factor for OS and PFS in multivariate analysis. Overall, early ctDNA quantitative monitoring may allow the detection of primary resistances of metastatic melanoma to anti-PD1 immunotherapies.

Circulating tumor DNA analysis of genomic alterations in metastatic urothelial carcinoma from NCT03113266 study.

486 Background: Recent studies have suggested the predictive value of liquid biopsies for immune checkpoint inhibitors. NCT03113266 is a multicenter phase II trial to evaluate the safety and efficacy of toripalimab (anti-PD-1) in metastatic urothelial carcinoma (mUC). Here we report the initial circulating tumor DNA (ctDNA) analysis of genomic alterations from a single-institution biomarker cohort. Methods: Twenty-seven mUC patients receiving toripalimab (3 mg/kg Q2W) at Ren Ji Hospital were enrolled and consented to Institutional Review Board-approved protocols permitting biomaterial collection and genetic sequencing. Serial plasma specimens were obtained at baseline and every two cycles. The 600-gene panel (PredicineATLAS) liquid biopsy assay was applied to assess somatic variants and blood tumor mutational burden (bTMB). Results: The ctDNA assays were performed successfully for 100% of baseline samples (n = 27) with average read depth of 24,389 (range 14,000-31,700). A total of 571 non-synonymous mutations were identified, demonstrating prevalent aberrations in TP53 (63%), TERT promoter (30%), KDM2D (26%), PPM1D (26%), and KDM6A (26%). In 5 patients, FGFR3 variants were detected, including 6 missense sites and 4 FGFR3- TACC3 fusion events. Copy number gain ( FGFR1, ERBB2) and loss ( PTEN, BRCA2, CDKN2A) were pinpointed. TMB estimation revealed one case with an exceptionally high bTMB (62.6 mutations/Mb) and genomic features of microsatellite instability (MSI). Concordance with tumor-based genotyping and ctDNA kinetics during toripalimab treatment are being determined. Conclusions: Prospective ctDNA analysis using the PredicineATLAS liquid biopsy assay is feasible and represents a minimally invasive approach to detecting cancer-specific genetic landscape and potentially guiding personalized therapeutic decisions in mUC patients. Clinical trial information: NCT03113266 . Research Sponsor: Shanghai Junshi BioSciences; Huidu Shanghai Medical Sciences Ltd

Interim Cell-Free Circulating Lymphoma DNA Analysis of the Phase 2 Accept Trial

Introduction Plasma cell-free DNA (cfDNA) and circulating tumor DNA (ctDNA) genotyping in Diffuse Large B-cell Lymphoma (DLBCL) holds great promise for early detection and response prediction. DLBCL is a highly heterogenous disease with diverse tumor behaviour and outcomes, yet the delineation of poor- risk groups remains challenging. Genomically driven molecular risk stratification, using ultradeep next generation sequencing (NGS) provides a comprehensive view of the mutational landscape of lymphoma and enables ultrasensitive disease detection. Here, we present an interim analysis of ctDNA kinetics from ACCEPT, a phase Ib/II study of acalabrutinib with rituximab, cyclophosphamide, doxorubicin, vincristine and prednisolone (R-CHOP) for patients with previously untreated DLBCL. Methods Plasma samples were collected at four time points, at baseline and before the second, third and final cycles of chemotherapy. Extracted cell-free DNA (cfDNA) was quantified by fluorometry, prior to undergoing library preparation and next-generation sequencing using the CAncer Personalized Profiling by deep Sequencing (CAPP-Seq) methodology. The targeted sequencing panel covered 799 regions over 50 genes (>200Kb) known to be involved in lymphomagenesis. Analysis was carried out with a custom bioinformatics pipeline using error-corrected deduplication and a database of known artefacts to reduce background noise and improve sensitivity for low-level somatic variant detection. Patients were closely monitored through the study period by clinical examination and PET-CT scanning to provide objective endpoints against which the ctDNA response could be correlated. Results Fifteen patients had samples analysed for all four time points at the time of the interim analysis and were included in the study. Ten (66%) had late stage disease, nine (60%) poor risk disease (IPI > 2). Early vs late stage of disease at presentation showed a strong correlation with baseline levels of both total cfDNA (3,946 HGE/ml vs 21,613 HGE/ml) and ctDNA (842HGE/ml vs 6,380 HGE/ml). Twelve patients (80%) had trackable variants detected at baseline. The majority of these cleared after the first cycle of chemotherapy (Figure A; representative patient). Two cases (Figures B and C) had variants persistently detectable at high variant allele frequency (VAF) (0.059 and 0.068). These patients both had primary refractory disease. One patient from the first acalabrutinib dose escalation cohort and the second patient was found to be ineligible and withdrawn from the primary analysis because of continuous co-administration of omeprazole during therapy which inhibits acalabrutinib absorption. All others achieved a metabolic complete metabolic remission (mCR) after the final cycle of therapy. A third pattern of response noted was (Figure D) showing disappearance of detectable variants at baseline but progressive emergence of an acquired TP53 variant throughout follow-up that was not detected in the patient's germline sample. This high-risk patient with IPI of 5 and triple-hit DLBCL achieved a mCR and remains in remission in follow-up. Conclusion The clearance of ctDNA from the plasma of the responding patients in our study is consistent with the prior literature, as is the poor prognostic significance of persisting variants after the first cycle of chemotherapy. The rapid kinetics of the changes in ctDNA is noted and is potentially of advantage over other modalities of monitoring, such as PET-CT scan. Data on the entire cohort (n=30) and longer follow-up will be available at the time of the meeting. Figure 1 Disclosures Davies: Roche: Other: TRAVEL, ACCOMMODATIONS, EXPENSES; Roche, Celgene, Kite Pharma, Acerta, Karyopharma, Regeneron, Incyte: Consultancy; Roche, Acerta Pharma, AstraZeneca, Celgene, Gilead, ADC Therapeutics, Gilead: Research Funding; Celegene, Roche, Kite Pharma, Celegene: Honoraria. Johnson:Oncimmune: Consultancy; Bristol-Myers: Honoraria; Celgene: Honoraria; Genmab: Honoraria; Incyte: Honoraria; Kite Pharma: Honoraria; Kymera: Honoraria; MorphoSys: Honoraria; Novartis: Honoraria; Takeda: Honoraria; Boehringer Ingelheim: Consultancy; Epizyme: Consultancy, Research Funding; Janssen: Consultancy; Oncimmune: Consultancy; Epizyme: Consultancy, Research Funding; Janssen: Consultancy. Schuh:Illumina: Other: Consulting fees; Roche: Other: Consulting fees; Gilead: Other: Consulting fees; Abbvie: Other: Consulting fees.

Transformation or Progression from Adenocarcinoma to Small Cell Lung Cancer Detected by Serially Tracking Mutations in the Blood

Background: Circulating tumour DNA (ctDNA) has emerged as a promising biomarker for monitoring non-small-cell lung cancer (NSCLC). This has enabled the monitoring of clinically actionable mutations over the course of therapy. Case presentation: We present the case of a 74-year-old female who was treated with EGFR inhibitors for NSCLC which later transformed to SCLC. The kinetics of ctDNA was monitored by measuring the EGFR Exon 19 mutant L747–A750 > P and PIK3CA E545K over the course of therapy. Stabilisation of the PIK3CA mutation was found in response to therapy, however there appeared to be increasing levels of the EGFR mutant, potentially reflective of untreated EGFR-driven disease. Conclusion: The key finding described here, revealed by mutational tracking of mutations from the blood, is that clinically actionable mutations are assessable and may demonstrate clinical utility in measuring disease burden, multiple clones and progression non-invasively for lung cancer.

Personalized circulating tumor DNA analysis as a predictive biomarker in solid tumor patients treated with pembrolizumab.

Immune checkpoint blockade (ICB) provides clinical benefit to a subset of patients with cancer. However, existing biomarkers do not reliably predict treatment response across diverse cancer types. Limited data exist to show how serial circulating tumor DNA (ctDNA) testing may perform as a predictive biomarker in patients receiving ICB. We conducted a prospective phase II clinical trial to assess ctDNA in five distinct cohorts of patients with advanced solid tumors treated with pembrolizumab (NCT02644369). We applied bespoke ctDNA assays to 316 serial plasma samples obtained at baseline and every three cycles from 94 patients. Baseline ctDNA concentration correlated with progression-free survival, overall survival, clinical response and clinical benefit. This association became stronger when considering ctDNA kinetics during treatment. All 12 patients with ctDNA clearance during treatment were alive with median 25 months follow up. This study demonstrates the potential for broad clinical utility of ctDNA-based surveillance in patients treated with ICB.

Abstract IA23: ctDNA as predictive biomarkers for response and toxicity with immunotherapy

Abstract Immune checkpoint blockade (ICB) with anti-PD1/PD-L1 antibodies provides clinical benefit to a subset of cancer patients. However, existing biomarkers do not reliably predict treatment response across diverse cancer types. Limited data exist to show how serial circulating tumor (ct)DNA testing may perform as a predictive biomarker in patients receiving immune checkpoint blockade. In an investigator-initiated phase II study of the anti-PD1 antibody pembrolizumab in patients with advanced solid tumors (INSPIRE; NCT02644369), we collected plasma samples at baseline and prior to every third cycle. These samples were retrospectively analyzed using a validated patient-specific, amplicon-based sequencing assay to detect and quantify ctDNA levels at each plasma time point. In total, 94 patients with serial ctDNA collections in five cohorts of solid tumors received single-agent pembrolizumab 200 mg IV ever 3 weeks. Levels of ctDNA at serial time points and the change from baseline were correlated with overall survival (OS), progression-free survival (PFS), objective response rate (ORR by RECIST v1.1), and clinical benefit rate (CBR, CR + PR + SD > 6 cycles). Response was measured by RECIST v1.1. Across the five cancer cohorts, median number of pembrolizumab cycles received was 3 and median follow-up was 13.8 months. Baseline ctDNA concentration correlated with multiple efficacy measures. This association became stronger across the cohorts when considering ctDNA kinetics after treatment initiation. An early reduction in ctDNA levels (at about 6-7 weeks) was strongly correlated with OS, PFS, ORR, and CBR. Sustained ctDNA clearance during treatment preceded durable clinical response. Strikingly, all 14 patients with ctDNA clearance during treatment were alive with a median of 27.5 months follow-up. These results demonstrate the potential for broad clinical utility of ctDNA-based surveillance in patients treated with ICB for advanced solid tumors of diverse histologies. Limited by the number of patients with grade 2 or higher immune-related adverse events (irAEs, 23/94 patients, 24%), no correlation was seen between irAE and cell-free DNA levels in the INSPIRE cohort. Currently we are planning interventional ICB studies using early ctDNA dynamics as predictive biomarkers. Citation Format: Lillian L. Siu. ctDNA as predictive biomarkers for response and toxicity with immunotherapy [abstract]. In: Proceedings of the AACR Special Conference on Advancing Precision Medicine Drug Development: Incorporation of Real-World Data and Other Novel Strategies; Jan 9-12, 2020; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(12_Suppl_1):Abstract nr IA23.

Abstract A65: Longitudinal detection of TERT-mutant plasma cell-free circulating tumor DNA in newly diagnosed glioblastoma patients

Abstract Introduction: Liquid biopsies, especially plasma cell-free circulating tumor DNA (ctDNA), provide a potential opportunity to be a noninvasive biomarker for the diagnosis and monitoring of glioblastoma (GBM) patients. Previously, we detected TERT promoter hotspot mutations (C228T and C250T) in ctDNA of IDH wild-type (IDHwt) TERT promoter mutant GBM patients with 100% specificity using mutation-specific droplet digital PCR (ddPCR) assays. Here, we examine the association between mutant TERT ctDNA levels and clinical outcomes in newly diagnosed GBM patients undergoing chemoradiation. Methods: We analyzed 76 serially collected plasma samples from 17 patients with suspected IDHwt GBM based on MRI before surgery. Twenty mL of whole blood was collected in EDTA tubes at predetermined times: pre- and postoperatively, at the end of chemoradiation, and 1, 3, and 6 months from the end of chemoradiation. TERT promoter mutations C228T or C250T were identified in FFPE tumor samples using ddPCR assays specific for these mutations. Plasma samples were analyzed for the patient’s tumor TERT mutation using the ddPCR assays. The analytically validated thresholds for positive ctDNA detection were 1.5 and 1.7 copies/mL for C228T and C250T, respectively. Results: Sixteen of 17 (94%) IDHwt tumors had TERT mutations (10 C228T, 6 C250T) with MGMT methylated, unmethylated, or unknown status in 10, 5, and 1, respectively. Fourteen of the 16 patients (87.5%) had detectable mutant ctDNA at one or more time points (range 1.66 to 22.13 copies/mL). Of the 2 patients with undetectable ctDNA, one had diffuse and non-avidly enhancing disease and the other only had pre/postop plasma samples collected. Six patients had detectable ctDNA preop, and most had a dominant rim-enhancing mass with additional nonenhancing or enhancing lesion(s). Ten patients had detectable ctDNA up to 4 days postop, half of whom had undergone gross total resection. For 3 of 5 patients for whom there was a question of pseudoprogression versus true progression, ctDNA kinetics matched the clinical outcome. One patient with MGMT unmethylated multifocal GBM achieved ctDNA zeroconversion at 6 months post radiation (RT), and did not progress for another five months. Another patient was negative at all time points until their 3-month post RT follow-up, at which time they developed a recurrence. Another patient achieved zeroconversion at the end of RT but developed a borderline positive ctDNA at 6 months after RT, 2 months before documented radiographic progression. Conclusions: In this pilot, prospective ctDNA monitoring study of IDHwt GBM, TERT mutant ctDNA was detected at one or more time points in the majority of patients. ctDNA kinetics were associated with clinical outcomes for some patients. These data suggest that additional, larger studies could refine how ctDNA monitoring may be used to enhance the clinical management of IDHwt GBM patients. Citation Format: Christine Cordova, Mahrukh M. Syeda, Broderick Corless, Jennifer M. Wiggins, Amie Patel, Sylvia C. Kurz, Malcolm Delara, Zacharia Sawaged, Minerva Utate, Dimitris Placantonakis, John Golfinos, Jessica Schafrick, Joshua S. Silverman, Rajan Jain, Matija Snuderl, David Zagzag, George Karlin-Neumann, David Polsky, Andrew S. Chi. Longitudinal detection of TERT-mutant plasma cell-free circulating tumor DNA in newly diagnosed glioblastoma patients [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr A65.

Early circulating tumour DNA kinetics measured by ultra-deep next-generation sequencing during radical radiotherapy for non-small cell lung cancer: a feasibility study

BackgroundThe evaluation of circulating tumour DNA (ctDNA) from clinical blood samples, liquid biopsy, offers several diagnostic advantages compared with traditional tissue biopsy, such as shorter processing time, reduced patient risk and the opportunity to assess tumour heterogeneity. The historically poor sensitivity of ctDNA testing, has restricted its integration into routine clinical practice for non-metastatic disease. The early kinetics of ctDNA during radical radiotherapy for localised NSCLC have not been described with ultra-deep next generation sequencing previously.Materials and methodsPatients with CT/PET-staged locally advanced, NSCLC prospectively consented to undergo serial venepuncture during the first week of radical radiotherapy alone. All patients received 55Gy in 20 fractions. Plasma samples were processed using the commercially available Roche AVENIO Expanded kit (Roche Sequencing Solutions, Pleasanton, CA, US) which targets 77 genes.ResultsTumour-specific mutations were found in all patients (1 in 3 patients; 2 in 1 patient, and 3 in 1 patient). The variant allele frequency of these mutations ranged from 0.05–3.35%. In 2 patients there was a transient increase in ctDNA levels at the 72 h timepoint compared to baseline. In all patients there was a non-significant decrease in ctDNA levels at the 7-day timepoint in comparison to baseline (p = 0.4627).ConclusionThis study demonstrates the feasibility of applying ctDNA-optimised NGS protocols through specified time-points in a small homogenous cohort of patients with localised lung cancer treated with radiotherapy. Studies are required to assess ctDNA kinetics as a predictive biomarker in radiotherapy. Priming tumours for liquid biopsy using radiation warrants further exploration.

Residual circulating tumor DNA (ctDNA) after two months of therapy to predict progression-free and overall survival in patients treated on S1403 with afatinib +/- cetuximab.

9532 Background: ctDNA from patient plasma has demonstrated diagnostic utility in non-small cell lung cancer (NSCLC). Longitudinal changes in mutant allele frequency (MAF) have great potential to refine clinical management on targeted therapies. Methods: S1403 was a first-line phase II study of afatinib w or w/o cetuximab in pts with EGFR-mutant NSCLC. Between March, 2015 and April, 2018, 174 pts were randomized with 168 determined to be eligible. The study closed early due to futility. Plasma specimens were prospectively collected at baseline, Cycle 3 Day 1 (C3D1; 8 weeks) and at progression, and processed for batch analysis of ctDNA by next-generation sequencing (Guardant 360). A complete case analysis approach was used. The Kaplan-Meier method was used to estimate survival distributions, a Cox model to estimate hazard ratios and confidence bounds, and the log-rank test to compare distributions. A landmark analysis was used to assess predictive value of ctDNA clearance at C3D1. Results: 104 patients (62%) had analyzable baseline plasma specimens available, with EGFR mutations detected in 83 (80%). PFS was significantly shorter for pts with EGFR ctDNA positivity at baseline (p = 0.03) (Table) compared to those with no detectable ctDNA, likely a prognostic effect. Kinetic changes in ctDNA MAFs were analyzed in 79 pts with matching baseline and C3D1 specimens. Of 62 cases with detectable ctDNA at baseline, 68% (42/62) became undetectable at C3D1 (“ctDNA clearance”); ctDNA clearance relative to residual ctDNA was associated with significantly longer PFS (p = 0.00001) and OS (0.003) (Table). To date, 29 pts had matching at-progression samples. T790M mutations were observed at progression in 6/29 (24%) cases. Other putative emergent resistance factors include: a TACC3-FGFR3 and an EML4-ALK fusion, MET exon 14 skipping, multiple MET amplifications and NF1 frameshift mutations. Conclusions: Clearance of EGFR ctDNA after 60 days of therapy was associated with a substantial and statistically significant improvement in subsequent PFS and OS. Incorporation of ctDNA kinetics into routine clinical care represents a promising platform to identify patients with inferior outcomes on TKIs and detect targetable emergent resistance mechanisms. [Table: see text]

Circulating tumour DNA (ctDNA) as a biomarker in metachronous melanoma and colorectal cancer- a case report

BackgroundCirculating tumour DNA (ctDNA) has emerged as a promising blood-based biomarker for monitoring disease status of patients with advanced cancers. The presence of ctDNA in the blood is a result of biological processes, namely tumour cell apoptosis and/or necrosis, and can be used to monitor different cancers by targeting cancer-specific mutation.Case presentationWe present the case of a 67 year old Caucasian male that was initially treated with BRAF inhibitors followed by anti-CTLA4 and then anti-PD1 immunotherapy for metastatic melanoma but later developed colorectal cancer. The kinetics of ctDNA derived from each cancer type were monitored targeting BRAF V600R (melanoma) and KRAS G13D (colon cancer), specifically reflected the status of the patient’s tumours. In fact, the discordant pattern of BRAF and KRAS ctDNA was significantly correlated with the clinical response of melanoma to pembrolizumab treatment and progression of colorectal cancer noted by PET and/or CT scan. Based on these results, ctDNA can be used to specifically clarify disease status of patients with metachronous cancers.ConclusionsUsing cancer-specific mutational targets, we report here for the first time the efficacy of ctDNA to accurately provide a comprehensive outlook of the tumour status of two different cancers within one patient. Thus, ctDNA analysis has a potential clinical utility to delineate clinical information in patients with multiple cancer types.

Genomic Profiling of Circulating Tumor DNA Reveals Patterns of Response and Refractoriness in Aggressive B-Cell Lymphoma - a Nordic Lymphoma Group Correlative Study

Introduction Sequencing of circulating cell-free tumor DNA (ctDNA) has opened a diagnostic avenue for the patients with B-cell neoplasias, including diffuse large B-cell lymphoma (DLBCL). Treatment refractoriness and disease relapse after first-line therapy are associated with dismal survival. We sought to assess the clinical feasibility and prognostic value of ctDNA detection in prospectively collected samples from young high-risk patients treated uniformly in a Nordic phase II study. Materials and Methods The patients were treated in a phase II trial with dose-dense chemoimmunotherapy (biweekly R-CHOEP) and early systemic CNS prophylaxis with high-dose methotrexate (NLG-LBC-05; Leppä et al., 15-ICML; ClinicalTrials.gov NCT01325194). Longitudinal plasma samples from all trial centers were gathered and the plasma purified for cell-free DNA (cfDNA) in Helsinki, Finland (Figure 1A). We designed a 225 kb custom panel targeting most commonly mutated genomic drivers, regions of aberrant somatic hypermutation and immunoglobulin genes. Next-generation sequencing was performed on longitudinal cfDNA samples and primary tumor samples together with matched germline controls from the first 32 patients in the study. Sequencing was completed on Hiseq2500 platform and depth after duplicate removal with unique molecular identifiers was on average 1,926x (ctDNA), 3,073x (primary tumors) and 2,171x (germline controls). Multi-tumor variant calling was performed by Mutect2. Results cfDNA was successfully extracted from 96 patients (Figure 1B). Among the patients with completed sequencing and bioinformatics pipeline, we identified a median of 87 traceable somatic mutations in 97% of the patients. In plasma samples, ctDNA was detectable in 93% of the patients prior to treatment. Compellingly, we observed that the levels of total cfDNA and ctDNA were higher at baseline in the patients who relapsed. We evaluated the concordance between pretreatment ctDNA and primary tumor biopsy mutations in patients with available material. The percentage of shared somatic mutations ranged between 14 - 100%, suggesting substantial spatial heterogeneity in some cases. While the mutations in known lymphoma genes were mostly shared between the baseline ctDNA and the diagnostic tumor biopsy, some lymphomas displayed vast discordance mostly in the immunoglobulin loci, suggesting active somatic hypermutation processes upon clonal divergence in these lymphomas (Figure 1C). In all longitudinally analyzed plasma samples, the levels of ctDNA dropped after the first three treatment courses. At the end of therapy, the levels of ctDNA were undetectable in most of the patients with durable remissions (Figure 1D #1). However, in the patients with progressive disease, the ctDNA levels increased at the end of the therapy (Figure 1D #2). In the patients with late relapse (>12 months progression free survival), we observed the appearance of a subset of the mutations that were identified at diagnosis, suggesting clonal selection (Figure 1D #3). Conclusion Our findings elucidate the biology of ctDNA in B-cell lymphomas, and the ctDNA kinetics in homogeneously treated patients with primary high-risk DLBCL. Figure 1. A) Collection of cfDNA samples in the CHIC trial. B) Swimmers plot of the patients with extracted cfDNA in the liquid biopsy cohort. C) Concordance between primary tumor and ctDNA mutations at diagnosis. CHIC_100: high concordance. CHIC_88: low concordance. D) Kinetics of ctDNA in patients with different diseases courses. Figure 1 Disclosures Jørgensen: Roche: Membership on an entity's Board of Directors or advisory committees; Gilead: Membership on an entity's Board of Directors or advisory committees. Jerkeman:Janssen: Honoraria, Research Funding; Gilead: Honoraria, Research Funding; Acerta: Honoraria, Research Funding; Celgene: Honoraria, Research Funding; Roche: Honoraria, Research Funding. Holte:Novartis: Honoraria, Other: Advisory board. Leppa:Celgene: Consultancy; Bayer: Research Funding; Roche: Consultancy, Honoraria, Research Funding; Takeda: Consultancy, Research Funding; Janssen: Consultancy, Research Funding.

Circulating Tumor DNA in the Peripheral Blood As Early Predictor of Clinical Outcome in Relapsed/ Refractory Multiple Myeloma

Introduction: Treatment of multiple myeloma (MM) has improved over the last decade. Although long-term survival is noted in some patients, emergence of resistant disease still prevents cures. The objective of this study was to define "liquid biopsy" parameters that identify patients who do not benefit from a particular treatment before relapse becomes evident by serological markers. Having such parameters at hand will potentially inform changes in treatment. Methods: Here, we apply low-pass whole genome sequencing to profile a uniform cohort of 45 relapsed and refractory MM (RRMM) patients who have been treated in a multicenter phase II trial evaluating the combination of elotuzumab, pomalidomide, bortezomib and dexamethasone (elo-PVd; NCT02718833). Peripheral blood plasma samples were acquired for circulating tumor DNA (ctDNA) evaluation at four different timepoints (screening, cycle 3 day 1 (C3D1), cycle 5 day 1 and end of treatment). The concentration, relative fraction and copy number profile of myeloma-derived ctDNA were determined across all timepoints. Results: At the time of this preliminary analysis, 17 patients (35%) continue on treatment whereas 28 patients (58%) have developed progressive disease (PD). Our data suggest that ctDNA levels at screening and C3D1 strongly correlate with progression-free survival (PFS). Patients with available follow-up samples (n=40) were stratified according to ctDNA levels at C3D1 of treatment. Patients with a residual ctDNA level <10% showed a significantly longer PFS (median 17.6 months (95% CI: 1.4-6.5)) as compared to those with ctDNA levels ≥10% (median 5.9 months (95% CI: 0.2-0.7), log-rank Mantel-Cox test P=0.0006). The kinetics of ctDNA were largely concordant with the course of M protein and serum-free light chains (SFLC). To test our hypothesis that ctDNA assessment could be particularly useful for patients with inconclusive serological markers (minimal response (MR)/ stable disease (SD) by IMWG criteria), we performed a subgroup analysis of all patients with MR/SD at first follow-up (C3D1). In this group of 19 patients a residual ctDNA fraction ≥10% translated into a significantly shorter median PFS (1.6 months, 95% CI: 0.1-0.8) as compared to ctDNA levels <10% (5.8 months, 95% CI: 1.2-11.4, P=0.02). Conclusions: These data indicate that "liquid biopsy" evaluation of ctDNA may refine prognostication and provide added predictive value over serological markers alone. While in the large majority of cases ctDNA has excellent concordance with M protein and SFLC for monitoring of MM disease progression, ctDNA may identify patients where relapse is imminent before it can be detected by serological parameters. This approach may therefore complement our framework for treatment decisions. Notably, this approach is highly scalable, cost-efficient and provides information about the clonal evolution of MM without the need for a bone marrow biopsy. Disclosures Yee: Adaptive: Consultancy; Amgen: Consultancy, Honoraria; Takeda: Consultancy; Celgene: Consultancy, Honoraria, Research Funding; Karyopharm: Consultancy; Bristol-Myers Squibb: Consultancy, Research Funding. Lipe:amgen: Research Funding; Celgene: Consultancy; amgen: Consultancy. O'Donnell:Sanofi: Consultancy; Amgen: Consultancy; Celgene: Consultancy; BMS: Consultancy; Takeda: Consultancy. Munshi:Abbvie: Consultancy; Amgen: Consultancy; Celgene: Consultancy; Abbvie: Consultancy; Amgen: Consultancy; Adaptive: Consultancy; Adaptive: Consultancy; Janssen: Consultancy; Celgene: Consultancy; Takeda: Consultancy; Janssen: Consultancy; Oncopep: Consultancy; Takeda: Consultancy; Oncopep: Consultancy. Richardson:Bristol-Myers Squibb: Research Funding; Takeda: Membership on an entity's Board of Directors or advisory committees, Research Funding; Celgene: Membership on an entity's Board of Directors or advisory committees, Research Funding; Oncopeptides: Membership on an entity's Board of Directors or advisory committees, Research Funding; Karyopharm: Membership on an entity's Board of Directors or advisory committees; Sanofi: Membership on an entity's Board of Directors or advisory committees; Amgen: Membership on an entity's Board of Directors or advisory committees; Janssen: Membership on an entity's Board of Directors or advisory committees. Anderson:OncoPep: Other: Scientific founder ; Sanofi-Aventis: Other: Advisory Board; Janssen: Other: Advisory Board; C4 Therapeutics: Other: Scientific founder ; Gilead Sciences: Other: Advisory Board. Raje:Celgene Corporation: Consultancy; Amgen Inc.: Consultancy; Merck: Consultancy; Takeda: Consultancy; Janssen: Consultancy; Bristol-Myers Squibb: Consultancy. Lohr:T2 Biosystems: Honoraria; Celgene: Research Funding. OffLabel Disclosure: This abstract reports on the quadruple regimen elotuzumab, pomalidomide, bortezomib and dexamethasone which is not yet approved for the treatment of multiple myeloma in the United States.

Real-World Utility of an Amplicon-Based Next-Generation Sequencing Liquid Biopsy for Broad Molecular Profiling in Patients With Advanced Non–Small-Cell Lung Cancer

PURPOSETo assess the feasibility and utility of circulating tumor DNA (ctDNA) by amplicon-based next-generation sequencing (NGS) analysis in the daily clinical setting in a cohort of patients with advanced non–small-cell lung cancer (NSCLC), as an alternative approach to tissue molecular profiling.PATIENTS AND METHODSIn this single-center prospective study, treatment-naïve and previously treated patients with advanced NSCLC were enrolled. Clinical validation of ctDNA using amplicon-based NGS analysis (with a 36-gene panel) was performed against standard-of-care tissue molecular analysis in treatment-naïve patients. The feasibility, utility, and prognostic value of ctDNA as a dynamic marker of treatment efficacy was evaluated. Results of tissue molecular profile were blinded during ctDNA analysis.RESULTSOf 214 patients with advanced NSCLC who were recruited, 156 were treatment-naïve patients and 58 were pretreated patients with unknown tissue molecular profile. ctDNA screening was successfully performed for 91% (n = 194) of all patients, and mutations were detected in 77% of these patients. Tissue molecular analysis was available for 111 patients (52%), and tissue somatic mutations were found for 78% (n = 87) of patients. For clinically relevant variants, concordance agreement between ctDNA and tumor tissue analysis was 95% among 94 treatment-naïve patients who had concurrent liquid and tumor biopsy molecular profiles. Sensitivity and specificity were 81% and 97%, respectively. Of the 103 patients with no tissue available, ctDNA detected potential actionable mutations in 17% of patients; of these, 10% received personalized treatment. ctDNA kinetics correlated with response rate and progression-free survival in 31 patients treated with first-line platinum-based chemotherapy.CONCLUSIONThese real-world data from a prospective study endorse ctDNA molecular profile by amplicon-based NGS as an accurate and reliable tool to detect and monitor clinically relevant molecular alterations in patients with advanced NSCLC.

Repeated mutKRAS ctDNA measurements represent a novel and promising tool for early response prediction and therapy monitoring in advanced pancreatic cancer

BackgroundThe presence of mutated KRAS (mutKRAS ctDNA) in plasma samples has been consistently shown to be a negative prognostic indicator in pancreatic cancer (PC). Only small pilot studies have evaluated the value of serial mutKRAS ctDNA-measurements in PC. Patients and methodsThe aim of the present study was to explore the potential of repeated mutKRAS ctDNA measurements for response prediction and therapy monitoring in advanced PC patients. We used the BEAMing technology to determine levels of mutKRAS ctDNA, CA 19-9, CEA and CYFRA 21-1 in 284 plasma samples of 54 patients with advanced PC receiving gemcitabine-based chemotherapy. Absolute levels and kinetics of mutKRAS ctDNA, CA 19-9, CEA and CYFRA 21-1 were correlated to radiological response, progression-free and overall survival. ResultsmutKRAS ctDNA was present in a majority of advanced PC patients (n = 36/54, 67%) and indicated tissue KRAS mutation status with a high sensitivity (75%) and specificity (100%). The presence of mutKRAS ctDNA, as well as higher levels of CA 19-9, CEA and CYFRA 21-1 before initiation of the first-line chemotherapy, was significantly correlated to an adverse overall survival. During therapy, changes in mutKRAS ctDNA levels were more rapid and pronounced than changes in protein-based tumor markers. A decrease in mutKRAS ctDNA levels during therapy was an early indicator of response to therapy, while there was no significant correlation between kinetics of CA 19-9, CEA or CYFRA 21-1 and response to chemotherapy during the first four weeks of treatment. Repeated mutKRAS ctDNA measurements during follow-up appeared to be superior to protein-based tumor markers in detecting progressive disease (sensitivity: 83%, specificity: 100%). ConclusionmutKRAS ctDNA kinetics appear to be a powerful and highly specific tool in early response prediction and therapy monitoring of advanced PC patients receiving chemotherapy.

HPV-16 ctDNA kinetics predict for pathologic persistent disease in oropharyngeal cancer patients treated with deintensified chemoradiation

HPV-16 ctDNA kinetics predict for pathologic persistent disease in oropharyngeal cancer patients treated with deintensified chemoradiation