ctDNA Samples Research Articles

Abstract 972: Non-invasive detection of homologous recombination deficiency in metastatic prostate cancer patients

Abstract Background: The recent endorsement of poly ADP ribose polymerase inhibitors (PARPi) has been a breakthrough in managing prostate cancer (PCa) with homologous recombination deficiency (HRD). However, due to its propensity to metastasize to the bone, HRD assessment in tissue biopsy poses a challenge in advanced PCa. Circulating tumor DNA (ctDNA) as a tumor surrogate may be a promising substitute for pinpointing patients who may benefit from PARPi treatment. Methods: To test whether causes and consequences of HRD can be detected non-invasively in plasma, we pre-selected 139 plasma samples from PCa patients based on aneuploidy screening (mFAST-SeqS). We then applied targeted sequencing using a QIAseq panel including homologous recombination repair (HRR)-related genes as well as genes involved in cell cycle regulation (TP53, RB1, PTEN). Putative, pathogenic germline variants were sequencing in constitutional DNA using Sanger sequencing. Moreover, we performed low pass whole genome sequencing to determine the levels of genomic instability using the shallow HRD (sHRD) algorithm. Results: In our cohort, at least one pathogenic mutation was detected in 68/139 (48.9%) of the patients, of which the majority consisted of alterations in PTEN, TP53 or RB1 (44/139, 31.7%). Pathogenic BRCA1/2 mutations were detected in 13/139 patients (9.4%), the majority of which originated from the germline. In 8/139 patients (5.6%) a pathogenic variant in other HRR genes could be observed and in 3/139 patients (2.2%) CKD12 mutations were detected. As expected, samples with pathogenic HRR mutations and elevated tumor fraction, presented high sHRD scores (<20) in plasma DNA. In contrast, the majority of high ctDNA samples with mutations in PTEN, TP53 or RB1 had sHRD score below the cut-off of 20. However, the detection of genomic instability was clearly depending on tumor fractions. Conclusion: Our study indicates that a non-invasive assessment of root causes and subsequent effects of the HRD phenotype in prostate cancer is feasible, and that mutations in HRR correlate with a high genomic instability. However, to detect and quantify genomic instability in plasma, elevated ctDNA levels are required. Based on in-house data from mFAST-SeqS aneuploidy screening of over 900 plasma samples from advanced prostate cancer, approximately 30% of cfDNA samples would have sufficiently high ctDNA fractions for a combined assessment of causes and consequences of HRD, which might be most informative to direct PARPi treatment in PCa. Citation Format: Georgios Vlachos, Tina Moser, Anna Eberhard, Lisa Glaswitch, Jasmin Blatterer, Emil Bauernhofer, Nina Monsberger, Karl Kashofer, Jochen Geigl, Thomas Bauernhofer, Ellen Heitzer. Non-invasive detection of homologous recombination deficiency in metastatic prostate cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 972.

Abstract 7507: Capturing live single circulating tumor cells platform for comprehensive genomic profiling with paired ctDNA in breast cancer patients

Abstract Background: Single circulating tumor cells (sCTC) capture without cell fixation with no blood contaminants like leukocytes are highly challenging. sCTC genome transcriptomics anticipates new avenues in new discovery, targeted therapies, and inclusion of patients in clinical trials where the tissue is inaccessible. We report, an assay to selectively capture live sCTCs at singularity with NGS-based comprehensive mutational profiling in breast cancer (BC) patients. Further, paired ctDNA outcomes using blood with mutational heterogeneity scores of sCTCs adds comprehensive genomics for establishing an accelerated treatment outcomes and resistance signatures. Methods: Retrospectively, sCTC were isolated from 70 breast cancer (BC) patients using OncoRadar platform consisting affinity-based glass beads mediated by anti EpCAM antibody. CTCs were selectively captured and released without fixing and contamination of any leukocytes. Platform possess cleavable disulfide spacer at pH 8.0, between glass beads (diam. 2 mm, area 12.57 mm2) and a ligand. Sensitivity, specificity, positive predictive value (PPV), negative prediction value (NPV), and accuracy were evaluated using MCF-7 cells and CTCs. Assay to isolate CTC has been developed in 96 well plate, for downstream NGS-based comprehensive gene panel analysis using hybridization-based target enrichment. Interestingly, no mutations detected in blood samples (~20%) for CtDNA versus CTC DNA offered non-chip implicated mutations. Results:. Analytical validation using OncoRadar showed higher cell capture efficiency (99%) with spiked MCF-7 cells/ml of blood. Sensitivity and specificity values were 97% and 98% respect, while PPV was 99% and NPV was 7.5% with the accuracy parameter of 99%. Sensitivity, specificity, PPV, and NPV parameters when assessed for CTC isolation from 70 BC patients. NGS-based mutational analysis, sCTC showed the presence of PIK3CA, ESR1, and NF1 mutations, which were absent from paired ctDNA samples. Conclusion: Detection of ctDNA obscure mutations in paired sCTC samples suggests high sensitivity of sCTC-based genomic assays compared to current standard of practice. Heterogeneity scores amongst inter and intra CTCs with MATH scores offer new dimensions in genomics. Combination of ctDNA and sCTC DNA assay offers a comprehensive realistic genomic outcome for more significant therapy decisions, especially when guideline based options may exhausts. Citation Format: Gowhar Shafi, Atul Bharde, Ganesh Khutale, Saloni Andhari, Richa Deshpande, Bhagwat Jadhav, Sangeeta Prajapati, Moubeen Fauzul, Kanchan Hariramani, Madhura Basavalingegowda, Jayant Khandare. Capturing live single circulating tumor cells platform for comprehensive genomic profiling with paired ctDNA in breast cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7507.

Abstract A083: Personalized targeted circulating tumor DNA (ctDNA) and T-cell responses after combined neoantigen vaccine and immune checkpoint blockade in ovarian cancer

Abstract A083: Personalized targeted circulating tumor DNA (ctDNA) and T-cell responses after combined neoantigen vaccine and immune checkpoint blockade in ovarian cancer

Dynamic monitoring of circulating tumor DNA reveals outcomes and genomic alterations in patients with relapsed or refractory large B-cell lymphoma undergoing CAR T-cell therapy

BackgroundOver 50% of patients with relapsed or refractory large B-cell lymphoma (r/r LBCL) receiving CD19-targeted chimeric antigen receptor (CAR19) T-cell therapy fail to achieve durable remission. Early identification of relapse...

Abstract A022: Dissecting patterns of small cell lung cancer evolution using deep whole genome sequencing of circulating tumor DNA

Abstract Background: Small cell lung cancer (SCLC) is the most lethal form of lung cancer. A key driver of this near universal lethality is SCLC’s recalcitrance to therapy. The standard of care for SCLC is a chemotherapy doublet of etoposide and cis/carboplatin in combination with immunotherapy (EP+IO). While most tumors respond to these therapies, >80% of SCLCs progress within one year of treatment. Additionally, the aggressive clinical course of SCLC has historically precluded collection of patient-matched treatment naïve and recurrent tumor tissue traditionally required to study evolution. In lieu of tissue, several groups have used circulating tumor DNA (ctDNA) to study SCLC evolution. However, these studies used targeted sequencing panels that analyze <0.04% of the SCLC genome. Using new methods to comprehensively trace how SCLCs rapidly evolve to therapy resistance is a significant unmet need. Methods: Medical records were reviewed to identify treatment naïve SCLC patients treated at MD Anderson that had both pre- and post-EP+IO liquid biopsies collected under IRB approved protocols. ctDNA was isolated from plasma using a MiniMax High Efficiency Cell-Free DNA Isolation Kit (Apostle Bio). Germline DNA was extracted from buffy coat samples using a QIAamp DNA Blood Midi Kit (Qiagen). Deep whole genome sequencing (WGS) (>100X) of ctDNA and WGS of germline DNA (>60X) was performed using an Illumina NovaSeq X sequencer. Reads were aligned to the hg38 reference genome using BWA-mem. Somatic mutations were called using MuTect2, and clonal and subclonal copy number alterations were identified using Battenberg. DPClust was used to reconstruct cancer cell populations, leveraging mutation and copy number calls. Results: We identified several deleterious genomic alterations impacting TP53 and RB1 tumor suppressor genes, known genetic drivers of SCLC development. We also detected recurrent, whole chromosome arm loss of heterozygosity events impacting many chromosomes in treatment naïve samples, some of which are known to be present in >80% of SCLCs. Additionally, we found that both treatment naïve and recurrent SCLCs were composed of multiple subclones, each defined by dozens to thousands of unique somatic mutations. COSMIC signature analysis identified high activity of tobacco carcinogens, APOBEC, and replicative-based processes across ctDNA samples. We also identified emergence of novel subclones carrying unique copy number alterations following EP+IO recurrence. Importantly, the affected regions encode key effectors that regulate anti-tumor immune responses and cell survival following DNA damage, both of which are intimately related to the mechanism of action of EP+IO. Conclusions: Our data shows that deep WGS of ctDNA recapitulates known genetics of SCLC and allows for sensitive characterization of therapy resistant clones. Using this method, we have captured snapshots of both intrinsic and acquired resistance mechanisms to frontline EP+IO. Deep WGS of ctDNA is a promising approach to comprehensively dissect routes of SCLC evolution and therapy resistance. Citation Format: Benjamin B. Morris, Zhihui Zhang, Simon Heeke, Kyle Concannon, Bingan Zhang, Waree Rinsurongkawong, Vadeerat Rinsurongkawong, J. Jack Lee, Jianjun Zhang, Don L. Gibbons, Ara A. Vaporciyan, Carl M. Gay, Hai T. Tran, John V. Heymach, Lauren A. Byers, Peter Van Loo. Dissecting patterns of small cell lung cancer evolution using deep whole genome sequencing of circulating tumor DNA [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr A022.

Tissue-Matched IgH Gene Rearrangement of Circulating Tumor DNA Shows Significant Value in Predicting the Progression of Diffuse Large B Cell Lymphoma.

Evidence has demonstrated that monitoring of the variable, diversity, and joining gene segments (VDJ) rearrangement of the immunoglobulin (Ig) genes in the circulating tumor DNA (ctDNA) is of value in predicting the outcomes of diffuse large B cell lymphoma (DLBCL). In this study, we investigated the role of VDJ rearrangement proportion in ctDNA for predicting DLBCL progression. Patients diagnosed with newly diagnosed DLBCL were included in this study. The VDJ sequences of IgH were detected using next-generation sequencing (NGS) in formalin-fixed paraffin-embedded tissue and/or peripheral blood. The clonotype of the highest proportion in the peripheral blood was defined as the "dominant circulating clonotype," whilst the clonotype of the highest proportion in matched tissue that is detected in peripheral blood was defined as the "dominant tissue-matched clonotype." The decision tree, a machine learning-based methodology, was used to establish a progression-predicting model through a combination of "dominant tissue-matched clonotype" proportion or "dominant circulating clonotype" proportion, and the clinicopathological information, including age, sex, cell of origin, stage, international prognostic index, lactate dehydrogenase, number of extranodal involvements and β2-microglobulin. A total of 55 patients with eligible sequencing data were used for prognosis analysis, among which 36 patients had matched tissue samples. The concordance rate of "dominant circulating clonotype" and "dominant tissue-matched clonotype" was 19.44% (7/36). The decision tree model showed that the combination of extranodal involvement event and "dominant circulating clonotype" proportion (≥37%) had a clinical value in predicting the prognosis of DLBCL following combined chemotherapy (sensitivity, 0.63; specificity, 0.81; positive prediction value (PPV), 0.59; negative prediction value, 0.83; kappa value, 0.42). Noticeably, the combination of the "dominant tissue-matched clonotype" and extranodal involvement event showed a higher value in predicting the progression (sensitivity, 0.85; specificity, 0.78; PPV, 0.69; kappa value, 0.64). IgH proportion detected in the ctDNA samples traced from tissue samples has a high clinical value in predicting the progression of DLBCL.

Utility of circulating tumor DNA (ctDNA) for the detection of minimal residual disease (MRD) after curative-intent therapy for patients with localized pancreatic adenocarcinoma (PDAC): A single institution series and meta-analysis.

695 Background: PDAC is associated with a high recurrence rate even after curative-intent surgical resection and perioperative chemotherapy. Detection of MRD in this setting can inform prognosis and may be actionable for innovative targeted therapies or additional chemotherapy to improve outcomes. While CA19-9 may detect disease before it is clinically apparent, it lacks specificity and up to 20% of patients (pts) are non-producers. ctDNA has been shown to be useful for MRD detection in other cancers but its utility in PDAC is not established. Methods: Pts with PDAC who had a commercial ctDNA assay (Natera) after completion of all curative-intent therapy (surgery and chemotherapy) in the MRD setting were included. Recurrence and survival data were correlated with the end-of-treatment (EOT) ctDNA result. Published literature and abstracts for studies examining ctDNA for MRD detection in PDAC using the same testing platform were identified. Available data were pooled to determine EOT ctDNA positivity rate, positive and negative predictive values (PPV, NPV), and lead time from a positive ctDNA to documented recurrence. Results: A total of 33 pts had EOT ctDNA samples collected at our institution. At EOT, ctDNA was + in 30.3% (n = 10). At a median follow-up time of 14.3 months, median recurrence free survival (RFS) for + vs negative ctDNA was 3.6 vs 25.1 months (HR = 15.8 [4.7-53.4], p < 0.001). Correlation of +ctDNA with recurrence showed a sensitivity of 52% (10/19), specificity of 100% (14/14), PPV of 100% (10/10) and NPV of 61% (14/23). Our institutional data were then combined with 138 pts reported in 3 prior publications/abstracts, for a total of 171 pts. Median follow-up ranged from 11.9-14.3 months and the overall EOT+ rate was 39% in the pooled cohort. The pooled sensitivity was 67% (49/73), specificity was 83% (81/98), PPV was 74% (49/66) and NPV was 77% (81/105). In each study as well as the pooled analysis, an EOT+ ctDNA was associated with significantly shorter RFS (HR = 8.1-120.5). Among 10 pts at our institution with recurrence, a + ctDNA test was detected after the recurrence 90% of the time, with a median lag-time of 4.70 months after recurrence (range -2.2 to 16.67 months). In the pooled cohort, among the 73 pts with recurrences, the ctDNA test was + before, at the time of, or after the recurrence in 23 (32%), 9 (12%) and 17 (23%) pts respectively; the ctDNA was negative despite recurrence in the remaining 24 (33%) pts. Conclusions: A tumor-informed positive ctDNA test after EOT shows high specificity and PPV for recurrence and is associated with significantly worse RFS in the MRD setting, while sensitivity of the test remains low. When positive, ctDNA assessment provides an opportunity for innovative therapies in the adjuvant setting to improve outcomes for localized PDAC.

Concordance of circulating tumor DNA and matched formalin-fixed paraffin-embedded tumor tissue in gastric cancer as a predictor of recurrence.

Combined analysis of the variant composition of circulating tumor DNA (ctDNA) from cell-free plasma and DNA from tumor tissue could provide insight into the implications of the genetic alterations responsible for the intratumoral and intertumoral heterogeneity of gastric cancer. We aimed to evaluate the usefulness of this approach in these patients. Cell-free plasma and formalin-fixed paraffin-embedded tumor tissue samples from 46 patients with gastric cancer were examined. Targeted deep sequencing was performed using a commercially available kit. The cell-free DNA (cfDNA) concentration was higher in stage II-IV versus stage I patients and in larger versus smaller tumors. Only 12 of the 36 (33.3%) alterations in the tumor tissue samples were in concordance with those in the ctDNA samples. Two variants were in concordance in stage I samples and 10 in stage II-IV samples. Actionable variants that were detected in concordance were in the stage II-IV samples. Preoperative ctDNA positivity of actionable variants was significantly associated with cfDNA concentration, lymphatic invasion, N stage, and TNM stage. Cancer recurrence was significantly associated with tumor size, lymphatic/vascular invasion, TNM stage, and ctDNA-tumor tissue variant concordance. Preoperative ctDNA genetic analysis using a multigene panel offers substantial clinical benefits when performed in conjunction with targeted deep sequencing of tumor tissue. Concordance between preoperative ctDNA and tumor tissue mutations may serve as a prognostic indicator in patients with gastric cancer.

Abstract B153: Resistance mechanisms to mobocertinib in treating NSCLC with EGFR exon 20 insertion mutations

Abstract Background: Mobocertinib is an oral epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) that received FDA accelerated approval for non-small cell lung cancer (NSCLC) with EGFR exon 20 insertion (ex20ins) mutations, based on data from a pivotal phase 1/2 study of mobocertinib (NCT02716116). In platinum-pretreated patients (pts) with EGFR ex20ins NSCLC (N=114), the overall response rate (ORR) was 28%, median duration of response was 17.5 months, and median progression-free survival was 7.3 months. Despite this encouraging clinical activity, de novo and acquired resistant mechanisms to mobocertinib remain largely unknown. Methods: Tumor samples and circulating tumor DNA (ctDNA) samples were obtained from platinum-pretreated pts with EGFR ex20ins+ NSCLC treated with mobocertinib (NCT02716116) and subjected to next-generation sequencing (NGS) analyses. CtDNA was collected at baseline, cycle 3 day 1 (C3D1) and progression per protocol. Tumor growth assay was performed in BaF3 cells and patient-derived xenograft models to evaluate efficacy of combination therapies to overcome resistance. Results: At baseline, in tumor (n=56), the combined presence of BRAF and PIK3CA mutations alone (n=9) or together with copy number gains (CNV) in EGFR, MYC, CDK4, or CCND1 (n=19) was significantly associated with inferior ORR to mobocertinib with odd ratios of ‘infinity’ (p=0.045) and 13.21 (p=0.0047), respectively. Individual co-occurring gene mutations and CNV were not significantly associated with differential clinical outcomes. Longitudinal analysis of paired tumor-blood samples at baseline and C3D1 showed that 22 out of 55 pts (40%) achieved clearance at C3D1, including 81.2% (13/16) of PR pts, 50% of SD pts, and 20% of PD pts. CtDNA was also used to assess emerging mutations after mobocertinib progression after at least 5 months of treatment (n=18). TP53 (n=11) and acquired secondary EGFR (n=5) were the most common genes with emerging variants, including EGFR T790M (n=4) and D379E (n=1). With this observation, T790M was engineered in Ba/F3 cells in the context of EGFR ex20ins mutations (H773_V774insNPH and 769_D770insASV). T790M did confer resistance to mobocertinib in vitro, and to all EGFR TKIs tested including osimertinib. In patient-derived xenograft models (H773_V774insNPH and 769_D770insASV), the combination of mobocertinib plus the bispecific monoclonal antibody amivantamab demonstrated greater antitumor activity than either agent alone. Conclusions: Our results indicate that bypass pathway alterations are associated with de novo resistance whereas T790M emergence mediates acquired resistance to mobocertinib. Future research is warranted to determine the potential clinical benefits of combination strategies in patients with EGFR ex20ins+ NSCLC. Citation Format: Xiuning Le, Monique Nilsson, Sampurna Chatterjee, Zhenqiang Su, Junqin He, Hibiki Udagawa, Xiaoxing Yu, Alissa Poteete, Qian Huang, John V Heymach, Sylvie Vincent. Resistance mechanisms to mobocertinib in treating NSCLC with EGFR exon 20 insertion mutations [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr B153.

Clinical Utility of Circulating Tumor (ct)DNA Quantity and Kinetics in Patients Undergoing CAR T-Cell Therapy for Relapsed/Refractory Aggressive B-Cell Lymphoma

Background: CD19-targeted CAR T-cells are approved for relapsed and/or refractory (RR) aggressive B-cell lymphomas. While some patients experience durable remissions, others do not respond or relapse. Improved patient selection and early identification of patients who may need additional therapies are thus necessary. ctDNA is a promising biomarker for prognostication in DLBCL and has the potential to guide therapeutic decisions. We aimed to explore the possible clinical utility of ctDNA quantitation in patients with aggressive B-cell lymphomas undergoing CAR T-cell therapy. Methods: Twenty-eight patients undergoing CAR T-cell therapy as part of standard of care pathways for RR aggressive B-cell lymphoma were included. Pre- and post-CAR T-cell infusion ctDNA samples were retrospectively analyzed with a panel of over 400 genes relevant to B-NHL using a modified version of the AVENIO ctDNA analysis workflow (Roche; Research Use Only) based on the previously described CAPP-Seq workflow (Kurtz, J Clin Oncol 2018). Peripheral blood was used as a source of germline DNA to allow selection of tumor-specific variants in the ctDNA. ctDNA levels were expressed as mean mutant molecules per mL (MMPM) and ctDNA clearance was determined using a detection cutoff of p = 0.005. ctDNA results were correlated with clinical findings and outcomes including response rate, PFS and OS. Results: Eighteen male and 10 female patients were included in the analysis (median age 63). Sixteen (57%) patients had a diagnosis of DLBCL while the remainder had transformed FL or MZL (n=6), HGBL (n=4) and PMBL (n=2). Seventeen patients were treated with tisagenlecleucel and 11 with axicabtagene ciloleucel. Twenty-five (89%) patients had stage III or IV disease and 15 (54%) patients had ≥3 lines of prior therapy. The median number of tumor-specific variants in baseline ctDNA samples was 31 (range 1-252). ctDNA levels correlated with metabolic tumor volumes across all time points (Spearman r=0.69, p<0.0001). There was a greater reduction in ctDNA quantity observed in those who achieved CR/PR (n=21) at day 28 vs those who progressed (n=7) (median MMPM log-fold reduction 1.3 vs -0.9). Baseline ctDNA quantity was significantly higher in those with an elevated LDH pre-lymphodepletion compared to those with a normal LDH (median MMPM 228.5 vs 7.6, p = 0.0003). Survival also correlated with baseline ctDNA measurement with patients with a ctDNA quantity above the median of the cohort having a significantly shorter OS compared to those below the median (median OS 6.7 mo vs not reached, p=0.0012). Four patients had no detectable ctDNA at day 28 post CAR T-cell infusion including 1 patient with pseudoprogression on imaging (SUVMax 10) who had no evidence of lymphoma on biopsy and remained in CR. Of the 4 patients who were ctDNA negative at day 28, 3 remained in long-term remission. In summary, measurement of ctDNA quantity and kinetics shows promising clinical utility in the context of CAR T-cell treatment for aggressive B-cell lymphoma including prediction of outcome and resolving radiological pseudoprogression. Larger prospective cohorts and standardized methodological approaches are required to optimize predictive thresholds for clinical outcomes.

Optimizing Circulating Tumor DNA Limits of Detection for DLBCL during First Line Therapy

Background: Circulating tumor DNA (ctDNA) assessment is effective in diffuse large B-cell lymphoma (DLBCL) monitoring and risk stratification, with prognostic utility throughout first-line (1L) therapy. DLBCL ctDNA assays vary in analytical sensitivity, or limit of detection (LOD), which range from parts per thousand to below 1 part per million (1 in 10 6). With differing assays and time-points assessed in DLBCL studies, the relationship between analytical and clinical sensitivity for outcome prediction remains unclear. We assessed the prognostic ability of ctDNA at various LODs and used modeling strategies to project the efficacy of assays for minimal residual disease (MRD) detection. Methods: We previously reported a DLBCL dataset assessing plasma ctDNA before, during and after curative-intent 1L anthracycline-based treatment from multiple prospective studies, including RCHOP or EP[O]CH with acalabrutinib, lenalidomide, obinutuzumab, and polatuzumab (Roschewski et al. ASH 2022). In this study, ctDNA was evaluated by Phased Variant Enrichment Detection and Sequencing (PhasED-Seq, Foresight Diagnostics), a ctDNA MRD assay with LOD below 1 in 10 6. Samples from this study and a prospective DLBCL cohort treated with standard 1L therapy at Samsung Medical Center were considered in this analysis. We assessed the prognostic ability of ctDNA detection, considering LODs from 1 in 100 (10 2)to 1 in 10 6 to predict progression free survival (PFS) before, during and after 1L treatment. We assessed the desired sensitivity for ctDNA MRD during treatment by generating patient-specific log-linear models assuming exponential decay. We projected the distribution of variant allele frequencies (VAFs) during therapy from cycles 2 to 5 for patients who progressed to determine the minimal acceptable analytical sensitivity. Results: We included 230 patients consisting of 588 ctDNA samples, with 201 before therapy, 71 at C2D1, 101 at C3D1, 70 at C4D1 and 145 at end of therapy (EOT). Median follow-up was 17.5 months and 62 patients (27%) progressed. To evaluate the impact of LOD at treatment milestones, we applied a threshold for ctDNA positivity ranging from 1 in 10 2 to 1 in 10 6. Increased LOD had no effect on the performance of ctDNA before therapy (Figure A & B). At C2D1, if the LOD was at least 1 in 10 4, there was no difference in MRD prognostic performance. Starting at C3D1, improving the LOD for ctDNA positivity down to 1 in 10 6 showed superior predictive power for PFS at 24 months. The power of ctDNA to predict PFS at 24 months improved later in therapy, with area under the receiver operator curves (AUROCs) for PFS24 of 0.68, 0.73, 0.77, 0.88, and 0.86, at pretreatment, C2D1, C3D1, C4D1, and EOT time-points respectively (Figure A). To further understand the desired LOD for ctDNA MRD, we developed personalized models of ctDNA VAFs. Exponential models fit the data well in 43/44 cases with ≥ 3 MRD-detectable samples through C4D1, with a median correlation of 0.91, confirming their utility for modeling ctDNA. We generated log-linear models for 106 patients with ≥ 2 MRD-detectable samples, and used log-fold change in VAF per cycle (i.e. the slope) to compare patients by progression. Median log-fold change in VAF per cycle was worse for patients who progressed at -1.1 (IQR -1.4, -0.7) compared to those who remained disease-free with median -1.5 (IQR -2.0, -1.1) (p<0.0001). Patients with primary refractory DLBCL on EOT imaging had less robust log-fold change per cycle with median of -0.9 (IQR -1.3, -0.5) compared to those who relapsed after CR with median -1.3 (IQR -1.7, -0.9) (p=0.0004). We used the distribution of slopes to project VAFs for cycles 2 to 5 for patients who progressed to determine the LODs that provide acceptable clinical sensitivity. We found the analytical sensitivity for detecting DLBCL extended lower for each cycle, demonstrating the need for a LOD at least 1 in 10 6 for robust MRD detection at late time-points during 1L treatment. Conclusion: When using an ultrasensitive assay, MRD assessment at later timepoints better predicts PFS than at early timepoints. While the technical LOD does not affect disease burden assessment before therapy, using more sensitive assays during and after therapy improves disease detection and outcome prediction. Utilizing the most sensitive ctDNA MRD assays in 1L DLBCL therapy will maximize the efficacy of MRD-driven therapeutic strategies and MRD as a surrogate endpoint in future trials.

ESR1 F404 Mutations and Acquired Resistance to Fulvestrant in ESR1-Mutant Breast Cancer.

Novel F404 ESR1 mutations may be acquired to cause overt resistance to fulvestrant when combined with preexisting activating ESR1 mutations. Novel combinations of mutations in the ER ligand binding domain may cause drug-specific resistance, emphasizing the potential of similar drug-specific mutations to impact the efficacy of oral ER degraders in development. This article is featured in Selected Articles from This Issue, p. 201.

PATH-27. DROPLET DIGITAL PCR ENHANCES DETECTION OF HOTSPOT MUTATIONS IN CIRCULATING TUMOR DNA FROM CEREBROSPINAL FLUID OF PATIENTS WITH HIGH-GRADE GLIOMA

Abstract Molecular profiling of circulating tumor DNA (ctDNA) from cerebrospinal fluid (CSF) has the potential to enhance diagnosis, prognosis, and longitudinal monitoring for glioma patients through a minimally invasive approach. We previously detected somatic mutations from gliomas in CSF samples using MSK-IMPACT™, a 505-gene FDA-authorized next-generation DNA sequencing panel, and detected tumor-derived mutations in 50% of samples of patients with high-grade gliomas (HGG). To investigate whether we could enhance sensitivity of CSF ctDNA profiling and biomarker detection, we tested MSK-IMPACT™ pre-capture NGS residual DNA libraries from 43 CSF ctDNA samples by droplet digital PCR (ddPCR) for detection of key recurrent alterations in IDH1, BRAF, TERT, H3F3A, and TP53 using previously validated probes. Residual libraries contained a median of 18.0ng of DNA library (range, 0.0153-18.0ng). Of the 7 samples positive for IDH1 R132H, TERT C228T, or TERT C250T mutations in MSK-IMPACT™, we found that ddPCR accurately detected all mutations (7/7, 100%), confirming sensitivity of ddPCR in CSF ctDNA. We also tested 36 mutation-negative samples by MSK-IMPACT™ for the corresponding undetected mutations, of which 7 were tested for two mutations. Overall, ddPCR detected 41.9% (18/43) of previously undetected mutations. Specifically, we found that ddPCR rescued hotspot mutations such as BRAF V600E (2/3, 66.7%), IDH1 R132G/H (3/8, 37.5%), TERT C228T (11/26, 42.3%), and TERT C250T (2/4, 50.0%). Collectively, our results suggest that a combined-modality approach involving MSK-IMPACT™ and ddPCR enables comprehensive assessment of limited CSF ctDNA samples with high sensitivity and provides a minimally invasive methodology to molecularly profiling glioma.

Plasma Circulating Tumor DNA (ctDNA) as an Alternative to Tissue DNA for Genotyping of DLBCL: Results from the POLARIX Study

Introduction: In the POLARIX study (NCT03274492), polatuzumab vedotin in combination with rituximab plus cyclophosphamide, doxorubicin, and prednisone (Pola-R-CHP) demonstrated prolonged progression-free survival (PFS) versus rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) in patients with previously untreated diffuse large B-cell lymphoma (DLBCL; Tilly et al. N Eng J Med 2022); the PFS benefit was maintained with longer follow-up (Herrera et al. Blood 2022). We previously validated the prognostic value of ctDNA at baseline, on treatment, and at the end of treatment in POLARIX (Herrera et al. Blood 2022). Here, we assess and compare the mutation landscape and molecular subtyping of DLBCL by plasma ctDNA versus tissue DNA using the LymphGen classifier. Methods: Baseline plasma ctDNA single nucleotide variants (SNVs) were identified using the AVENIO ctDNA NHL assay (Research Use Only) with an allelic frequency (AF) of 0.5% (Stokowski et al. Blood 2022). Tissue SNVs at baseline were determined by whole exome sequencing (WES) with an AF cutoff of 5%. Plasma-depleted whole blood at baseline was used as a source of germline DNA to filter non-tumor-specific variants for both ctDNA and WES assays. Mutation landscapes in tissue DNA and plasma ctDNA were compared, focusing on genomic regions covered by both assays and variants within the coding regions. LymphGen uses genetic mutations, copy number data, and BCL2/BCL6 rearrangements to classify samples into at least one of seven genetic subtypes (Wright et al. Cancer Cell 2020). Genetic subtypes were defined by the LymphGen classifier using tissue and ctDNA SNVs, per the following: A53 ( TP53 and TP53BP1 mutations), BN2 ( BCL6 translocations and NOTCH2 mutations), EZB ( EZH2 mutations and BCL2 translocations), MCD ( MYD88L265P and CD79B mutations), N1 ( NOTCH1 mutations), and ST2 ( SGK1 and TET2 mutations). Hazard ratios (HR) were adjusted for International Prognostic Index score (2 vs 3-5) and age (≤60 vs >60 years). Results: At baseline, 443 patients had both WES and ctDNA data. When comparing mutation landscapes between tissue DNA and ctDNA, a median 82% (lower quartile: 0.5, upper quartile: 1.0) of tissue SNVs per patient were also found in their matched ctDNA samples. In total, tissue and ctDNA SNVs were found in 163 and 202 genes, respectively. Among these genes, 154 had SNVs in both tissue and ctDNA samples, representing 96% and 78% of mutated genes identified in tissue and ctDNA, respectively. Eleven genes showed statistically significant differences in distribution between tissue and ctDNA (Fisher's exact test, false discovery rate<0.01; Benjamini and Hochberg. J R Stat Soc 1995), including MEF2BNB-MEF2B, MEF2B, BCL10, BNC2, TNFAIP3, RIMS2, CDH19, KIF2B, BCL6, KMT2D and MYC; all but one ( MEF2B) showed higher mutation frequencies in ctDNA than in tissue. The distribution of molecular subtypes is listed in Table 1; due to a lack of information on copy number alterations, the A53 subtype was not included. Based on the tissue SNV data, LymphGen was able to determine the molecular subtypes of 442 patients. Using LymphGen results from tissue SNVs as a reference, 333 (75.3%) patients had the same subtype designation by tissue and ctDNA SNVs, and 109 (24.7%) had different designations ( Table 2). Among the 109 patients, 9 (8.2%) were assigned to a different molecular subtype by ctDNA, 50 (45.9%) patients with tissue SNV-defined molecular subtype were assigned to the undetermined subtype by ctDNA SNVs, and 50 (45.9%) patients with undetermined status by tissue SNVs were classified into distinctive genetic subtypes by ctDNA variants. In a pooled analysis, the 2-year PFS estimates of individual subtypes by tissue versus ctDNA SNVs were consistent ( Table 1). Conclusion: Our analyses demonstrated that the mutation landscape of ctDNA in DLBCL characterized by the AVENIO ctDNA NHL assay resembles that of tumor tissue determined by WES. Patients with molecular subtypes defined by WES or ctDNA had similar PFS outcomes. Overall, these findings support the use of plasma ctDNA as an alternative to tumor tissue for the genotyping of DLBCL.

Extensive mutational ctDNA profiles reflect High-grade serous cancer tumors and reveal emerging mutations at recurrence

ObjectiveCirculating tumor DNA (ctDNA) offers a minimally-invasive alternative to study genomic changes in recurrent malignancies. With a high recurrence rate, the overall survival in high-grade serous ovarian carcinoma (HGSC) has remained low. Our objectives were to determine whether ctDNA from plasma adequately represents HGSC, and to find mutational changes at relapse suggesting therapy options that could alter patient outcome. MethodsWe collected 152 longitudinal plasma and 92 fresh tissue samples from 29 HGSC patients, sequencing and detecting mutations with a gene panel of more than 700 cancer-related genes. Tumor content was measured using TP53 VAF. We analyzed the concordance between the mutations in tissue and plasma samples and calculated correlations to patient outcomes. We also searched for novel mutations appearing at relapse. ResultsThe concordance rate between mutations in plasma compared to tumor tissue was 83 % at diagnosis and 90 % at relapse. CtDNA was released similarly from the tubo-ovarian tumors, intra-abdominal metastases and ascites. CtDNA release was high when CA-125 level was elevated. The TP53 VAF in ctDNA from plasma samples before the third cycle of primary chemotherapy showed a negative correlation to patient outcome. At relapse, 19 novel, pathogenic DNA mutations appeared, suggesting possible actionable alterations and biological mechanisms related to chemoresistance. ConclusionRelapse ctDNA samples reflect tissue samples well and longitudinal sampling provides a timely source for mutational profiling. The emerging genetic mutations at recurrence propose that ctDNA accurately represents the widespread disease and provides possibilities for personalized therapy options.

Circulating Tumor DNA Analysis Associates with Progression-Free Survival (PFS) with Odronextamab Monotherapy in Relapsed/Refractory (R/R) Follicular Lymphoma (FL) and Diffuse Large B-Cell Lymphoma (DLBCL): Identification of Minimal Residual Disease Status and High-Risk Subgroups from the Phase 2 ELM-2 Study

Background Molecular characterization of B-cell non-Hodgkin lymphoma (B-NHL), through circulating tumor DNA (ctDNA) assessment of minimal residual disease (MRD) has been proposed as a tool to predict clinical outcome. Odronextamab, a CD20×CD3 bispecific antibody, demonstrated deep and durable responses and a generally manageable safety profile in patients (pts) with R/R FL or DLBCL in the Phase 2 ELM-2 study (NCT03888105; Kim TM et al. and Kim WS et al. ASH. 2022). In the overall populations, 12-month PFS rates were 64% and 29%, respectively. Using ctDNA from ELM-2, we show that these assessments associate with clinical outcomes following odronextamab treatment. Methods In ELM-2, pts received IV odronextamab in 21-day cycles, with step-up dosing in Cycle (C) 1, 80 mg (FL)/160 mg (DLBCL) QW in C2-4, then 160 mg (FL)/320 mg (DLBCL) Q2W until disease progression or unacceptable toxicity. Baseline (BL) ctDNA and tumor biopsies were used for molecular profiling. BL and on-treatment ctDNA were used for MRD determination in the biomarker population (BP; pts required ≥1 available plasma biomarker sample to be included in the BP). The first post-BL ctDNA sample was collected on C5 Day (D) 1, at the time of positron emission tomography-computed tomography (PET-CT). A modified AVENIO ctDNA analysis workflow (Roche; research only) was used for next-generation sequencing, based on the cancer personalized profiling by deep sequencing technique (Kurtz et al. J Clin Oncol. 2018). Whole blood cell pellets were used to filter out germline allele variants. MRD negativity was reported when the P value for variant allele frequency was >0.005. Results The BP comprised 53 FL pts and 63 DLBCL pts; at BL, all FL pts and all but one DLBCL pt were MRD(+). Pts remaining on study until C5D1 had similar PFS regardless of whether they were in the BP or overall population (FL, n=111; DLBCL, n=83). Pts who were MRD(-) at C5D1 had significantly longer PFS vs. those who remained MRD(+) (FL: HR 0.27 [95% CI 0.09-0.84], P=0.024 [Fig. 1a]; DLBCL: HR 0.29 [95% CI 0.12-0.71], P=0.007). In pts with FL achieving complete response (CR) by PET-CT at C5D1, a trend for prolonged PFS was observed in those who were MRD(-) (n=26) at this timepoint vs. those who were MRD(+) (n=17; HR 0.29 [95% CI 0.07-1.1], P=0.072). Pts with DLBCL who were MRD(-) at C5D1 (n=20) had similar PFS benefit regardless of PET-CT CR status (HR 0.56 [95% CI 0.10-3.11], P=0.511). Four DLBCL pts who were MRD(-) and did not achieve CR by PET-CT at C5D1 (partial response, n=3; stable disease, n=1) went on to achieve PET-CT CR at a later timepoint. Mutational analyses of BL ctDNA identified TP53 as the most frequent mutation (FL, n=34/53 [64%] mutation-evaluable pts; DLBCL, n=44/58 [76%]). In FL pts, TP53 mutations were associated with MRD(+) status at C5D1 (Fisher's exact test, P=0.002) and predicted significantly shorter PFS (HR 3.57 [95% CI 1.01-12.69]; P=0.049); this association was not observed in DLBCL. LymphGen classification (Wright et al. Cancer Cell. 2020) of BL ctDNA in pts with DLBCL identified mostly MCD and EZB subtypes (MCD, n=15; EZB, n=14; ST2, n=1; BN2, n=1; other, n=26). EZB-subtype pts treated with odronextamab had significantly longer PFS compared with MCD-subtype pts (HR 0.23 [95% CI 0.07-0.83]; P=0.025 [Fig. 1b]). Using BL ctDNA, cell of origin was determined in 43/58 pts with DLBCL; odronextamab treatment led to similar PFS in higher-risk non-germinal-center B-cell-like (non-GCB, n=18 [42%]) pts vs. GCB pts (n=25 [58%]; HR 1.62 [95% CI 0.72-3.62]; P=0.244). Further molecular assessment focused on gene fusions in DLBCL pts in the BP (39 with local laboratory gene fusion and ctDNA analyses, 24 with only ctDNA analyses). Odronextamab led to similar PFS in pts with double-hit (n=15) or triple-hit (n=5) fusions compared to those without (n=43; P=0.343 and P=0.140, respectively). Conclusions This study is among the first to analyze ctDNA in pts with R/R FL and DLBCL in a pivotal trial. This non-invasive method allows molecular characterization of pts with no available tissue, enabling identification of high-risk subgroups. CtDNA MRD status at C5D1 of odronextamab treatment was highly associated with PFS in pts with FL and DLBCL and in the future could form the basis of response-directed treatment paradigms. Molecular characterization in tumor biopsies, including CD20, will be presented. Ongoing monitoring of ctDNA may serve as an important early progression marker in R/R FL and DLBCL.

Early Identification of Refractory/Relapsed Diffuse Large B Cell Lymphoma with Serial Ctdna Sampling

Background: Diffuse Large B Cell Lymphoma (DLBCL) is an aggressive lymphoma that is curable in 60% of patients with chemoimmunotherapy. Outcomes are poor for those experiencing relapsed or refractory disease (rrDLBCL), particularly for patients with primary refractory disease (REFR, < 9 months from diagnosis) and early relapse (ER, 9 months to 2 years from diagnosis). Some of these patients would be candidates for chimeric antigen receptor T cell therapy (CART) in second line, where outcomes are superior when the disease burden is low. Therefore, exploring strategies to identify these high-risk patients early is important. Plasma circulating tumor DNA has been shown to be prognostic in various DLBCL cohorts. Method: We developed a custom panel of 170 genes to identify early treatment failure in a cohort of 171 patients that had profiling performed on 323 plasma samples. Plasma samples were taken serially starting at diagnosis and as patients progressed through frontline treatment. All plasma samples underwent DNA extraction, library preparation and subsequent sequencing using a panel of DLBCL related genes at high read depth (~1000x). Single nucleotide variant (SNV) calling was carried out using a custom pipeline including paired normal DNA for improved somatic variant detection. ctDNA fraction was estimated based on the highest variant allele fraction detected, using a loss of heterozygosity somatic model. Our ctDNA analysis focused on samples at diagnosis, cycle 2 of therapy, and end of treatment in order to identify early determinants of refractory disease. Changes in ctDNA levels between time points were represented as log2 ratio of ctDNA fraction. Results: rrDLBCL cases were separated into 3 categories based on the time between diagnosis and progressive disease (PD): 47 REFR, 34 ER, and 31 late relapse (LR, >24 months). The remaining patients were disease free after frontline therapy for over 24 months (CR, n=59), resulting in a cohort enriched for rrDLBCL (65% of cases). The average international prognostic index (IPI) of each group at diagnosis was REFR=3.38, ER=2.87, LR=2.81, and CR=2.41. Cell of Origin, as determined by Hans algorithm, showed a higher number of non-GCB samples in ER and LR groups (53% and 60%, respectively) while REFR and CR displayed increased GCB cases (63% and 66%, respectively). The REFR patients were significantly more likely to be of a 4/5 IPI score at diagnosis than other groups (p=0.0203). Progression-free survival (PFS2) at relapse therapy for REFR (median=0.29 years) was shorter when compared to both ER (p=0.0104, median=0.44 years) and LR (p=0.0012, median=0.80 years). Using the diagnostic plasma sample, there was no significant difference in ctDNA fraction in any of the three groups. When the sample with the highest ctDNA fraction was compared between patients, REFR had significantly higher levels than LR and CR, consistent with a higher overall tumor burden (p=0.001 and 0.026, respectively). There was a trend towards higher ctDNA fraction at the end of treatment in both REFR and ER groups. As ctDNA dynamics are known to be informative of molecular response, we compared patients using the change in ctDNA fraction at cycle 2 of therapy (log2 ratio). This value was significantly different in REFR patients (p=0.0073 vs ER), consistent with a lower rate of molecular response to treatment. Conclusions: While refractory and later relapsed DLBCL have similar ctDNA features at diagnosis, we find they have distinct ctDNA dynamics during treatment. REFR had higher maximal ctDNA levels across time points and both REFR and ER patients exhibited higher levels of ctDNA at end of treatment. Moreover, patients with minimal change in ctDNA levels at cycle 2 of therapy are at a high risk of treatment failure and refractory disease. Further exploration of the specific mutational patterns is ongoing. These results could enable the earlier identification of rrDLBCL and facilitate the prioritization of approaches for therapeutic intervention in rrDLBCL.

NGS Testing on Plasma-based ctDNA Samples at Key Clinical Timepoints in Advanced NSCLC: Handling of Blood Samples and Real-World Experience

NGS Testing on Plasma-based ctDNA Samples at Key Clinical Timepoints in Advanced NSCLC: Handling of Blood Samples and Real-World Experience

Circulating tumor DNA-based copy-number profiles enable monitoring treatment effects during therapy in high-grade serous carcinoma

Circulating tumor DNA (ctDNA) analysis has emerged as a promising tool for detecting and profiling longitudinal genomics changes in cancer. While copy-number alterations (CNAs) play a major role in cancers, treatment effect monitoring using copy-number profiles has received limited attention as compared to mutations. A major reason for this is the insensitivity of CNA analysis for the real-life tumor-fraction ctDNA samples. We performed copy-number analysis on 152 plasma samples obtained from 29 patients with high-grade serous ovarian cancer (HGSC) using a sequencing panel targeting over 500 genes. Twenty-one patients had temporally matched tissue and plasma sample pairs, which enabled assessing concordance with tissues sequenced with the same panel or whole-genome sequencing and to evaluate sensitivity. Our approach could detect concordant CNA profiles in most plasma samples with as low as 5% tumor content and highly amplified regions in samples with ∼1% of tumor content. Longitudinal profiles showed changes in the CNA profiles in seven out of 11 patients with high tumor-content plasma samples at relapse. These changes included focal acquired or lost copy-numbers, even though most of the genome remained stable. Two patients displayed major copy-number profile changes during therapy. Our analysis revealed ctDNA-detectable subclonal selection resulting from both surgical operations and chemotherapy. Overall, longitudinal ctDNA data showed acquired and diminished CNAs at relapse when compared to pre-treatment samples. These results highlight the importance of genomic profiling during treatment as well as underline the usability of ctDNA.

Clinical utility of plasma ctDNA sequencing in metastatic urothelial cancer

BackgroundGenomic stratification may help improve the management of patients with metastatic urothelial cancer (mUC), given the recent identification of targetable alterations. However, the collection of tissue samples remains challenging. Here, we assessed the clinical utility of plasma circulating tumour DNA (ctDNA) sequencing in these patients. MethodsPatients with mUC were prospectively enroled in the STING trial (NCT04932525), in which ctDNA was profiled using the Foundation One Liquid CDx Assay (324 genes, blood tumour mutational burden [bTMB], microsatellite instability status). Each genomic report was reviewed by a multidisciplinary tumor board (MTB). ResultsBetween January 2021 and June 2022, 140 mUC patients underwent molecular profiling. The median time to obtain the assay results was 20 days ((confidence interval) CI95%: [20,21]). The ctDNA analysis reproduced the somatic genomic landscape of previous tissue-based cohorts. Concordance for serial ctDNA samples was strong (r = 0.843 CI95%: [0.631–0.938], p < 0.001). At least one actionable target was detected in 63 patients (45%) with a total of 35 actionable alterations, including bTMB high (≥10 mutations/Mb) (N = 39, 21.1%), FGFR3 (N = 20, 10.8%), and Homologous recombination deficiency (HRD) alterations (N = 14, 7.6%). MTB recommended matched therapy in 63 patients (45.0%). Eight patients (5.7%) were treated, with an overall response rate of 50% (CI95%: 15.70–84.30) and a median progression-free survival (PFS) of 5.2 months (CI95%: 4.1 - NR). FGFR3 alterations were associated with a shorter PFS in patients treated with immunotherapy. ConclusionOverall, we demonstrated that genomic profiling with ctDNAs in mUC is a reliable and feasible approach for the timely initiation of genotype-matched therapies.