Circulating Tumor DNA Analysis Research Articles

2343P Evolution of circulating tumour DNA analysis in France over 5 years

2343P Evolution of circulating tumour DNA analysis in France over 5 years

Immunotherapy response monitoring using personalized circulating tumor DNA analysis in patients with relapsed gynecologic malignancies (2297)

Immunotherapy response monitoring using personalized circulating tumor DNA analysis in patients with relapsed gynecologic malignancies (2297)

A phase II study on the efficacy of regorafenib in treating patients with c-KIT-mutated metastatic malignant melanoma that progressed after previous treatment (KCSG-UN-14-13)

Backgroundc-KIT mutations are found in approximately 15% of patients with malignant melanoma in the Asian population. Regorafenib, an oral multikinase inhibitor, acts against both wild-type and mutant KIT. ObjectiveThis multi-institutional, phase II, single-arm study aimed to evaluate the efficacy of regorafenib against metastatic malignant melanoma harbouring c-KIT mutations. MethodsPatients with metastatic melanoma positive for c-KIT mutations, upon progression after at least one line of systemic treatment, were enroled. Patients received oral regorafenib 160 mg once daily for 3 weeks (4-week cycle). The primary endpoint was disease control rate (DCR), and secondary endpoints were safety, overall response rate (ORR), progression-free survival (PFS), and overall survival (OS). ResultsIn total, 23 patients were enrolled. c-KIT mutations were frequently reported in exon 11 (14/23, 60.9%), followed by exons 13, 17, and 9 in 5 (21.7%), 5 (21.7%), and 2 (8.7%) patients, respectively. DCR at 8 weeks was 73.9%, with 2 patients (8.7%) achieving complete response, 5 (21.7%) achieving partial response, and 10 (43.5%) showing stable disease. ORR was 30.4% (7/23). The median follow-up period was 15.7 months (95% confidence interval [CI], 9.6–21.3), and median OS and PFS were 21.5 months (95% CI, 15.1–27.9) and 7.1 months (95% CI, 5.0–9.2), respectively. Circulating tumour DNA analysis in selected patients showed high c-KIT correlation (85.7%) with tissue-based tumour mutational profiles. The most common adverse events (AEs) were skin reactions, including palmar-plantar erythrodysesthesia (52.2%), and grade 3 AEs were reported in 39.1% (9/23) of the patients. ConclusionRegorafenib in second- or later-line settings demonstrated significant activity in patients with metastatic melanoma harbouring c-KIT mutations.

Circulating Tumor DNA Analysis on Metastatic Prostate Cancer with Disease Progression.

The positivity rate of circulating tumor DNA (ctDNA) next-generation sequencing (NGS) varies among patients with metastatic prostate cancer (mPC), complicating its incorporation into regular practice. This retrospective study analyzed the ctDNA sequencing results of 100 mPC patients from May 2021 to March 2023 to identify the factors associated with positive ctDNA. Three custom gene panels were used for sequencing. Overall, 63% of the patients exhibited tier I/II somatic alterations, while 12% had pathogenic/likely pathogenic germline alterations. The key genes that were altered included AR, TP53, RB1, PTEN, and APC. Mutations in BRCA1/2, either germline or somatic, were observed in 21% of the patients. Among the metastatic castration-resistant prostate cancer (mCRPC) patients, the ctDNA-positive samples generally showed higher median prostate-specific antigen (PSA) levels and were more likely to be at the radiographic and clinical progressive disease stages, although they were not significantly associated with PSA progression. Our results suggest that ctDNA analysis could detect meaningful genetic changes in mPC patients, especially during disease progression.

Leveraging the Full Potential of Sensitive Circulating Tumor DNA Analyses

Leveraging the Full Potential of Sensitive Circulating Tumor DNA Analyses

Circulating tumor DNA analysis detects micrometastatic disease and predicts recurrence in a patient with colon cancer: A case report.

Colorectal cancer (CRC) is one of the most prevalent and deadly cancers worldwide, and approximately 50% of patients with early-stage disease develop metastases. A critical limitation for successful management of CRC is early disease detection and identification of progression. Next-generation sequencing-based circulating tumor DNA (ctDNA) profiling has emerged as a promising biomarker for the assessment of minimal or molecular residual disease in CRC. The patient was initially diagnosed with resectable CRC with uncertain small lung nodules. The patient was diagnosed with sigmoid colon adenocarcinoma placed at 15 to 20 cm above the anal verge (ypT4N1R0). Lung nodules were found in the apical part of the upper lobe of the right lung and the dorsal segment of the lower lobe of the left lung. The patient received systemic therapy and local treatment and plasma ctDNA-MRD detection was performed for monitoring the molecular disease status after surgery. The patient achieved a complete response after treatment. However, he presented with disease recurrence in liver lesions. The postoperative ctDNA detection suggested the possibility of micrometastatic pulmonary disease, and that was confirmed by follow-up examination. Serial ctDNA detection revealed disease relapse ahead of radiologic imaging by a lead time of 9 months. This case demonstrated the potential of ctDNA analysis to be a sensitive and specific tool for the detection of micrometastatic disease and prediction of recurrence.

The role of genetic testing in the prognosis and management of solid tumors. A literature review

Abstract Introduction: Cancer is the leading cause of death and an important impediment to increasing life expectancy in every country of the world. During the process of oncogenesis, genetic and epigenetic changes lead to abnormal expression of genes associated with cellular pathways that coordinate extremely important functions such as cell multiplication, cell differentiation, cell death, and cell cycle. Methods: There are over 200 approved biomarker-driven drugs for various types of cancer. Valuable biomarkers are analyzed to establish their importance in specific therapies. Precision medicine for oncological patients has been recognized as a valuable approach to solid tumors. Results: Various genes and their mutations either have a direct pathogenic effect or can give hints to a certain prognosis regarding the oncological pathology. A comprehensive genetic test for a broad molecular profile and complete characterization of tumor genetic heterogenicity should contain genes that are aligned with professional practice, guidelines and clinical trials, full coding region coverage for each gene and targeting of unique emerging and actionable markers. It is useful to use such a comprehensive test when a broad genomic profile identifies treatment options including immunotherapies and targeted drugs for patient enrollment or when relapse or disease progression has occurred after prior therapies. Conclusions: For patients with solid tumors, personalized medicine has been recognized as a successful strategy treatment, but it is not sufficient to seize cancer growth and progression up to a single molecular alteration due to specific hallmarks such as tumor heterogeneity, clonal evolution, and independent resistance mechanisms. Earlier studies have evaluated the effectiveness of using multigene panel screening methods for personalized cancer therapy, with controversial results. Future research in the field of circulating tumor DNA analysis might be the key to overcoming some of these limitations. The liquid biopsy could enable dynamic molecular profiling of all patients diagnosed with solid tumors enhancing accuracy, prognosis, and management

Triaging suspected cancer with a multi-cancer early detection blood test

Notable progress has been made in the field of circulating tumour DNA (ctDNA) analysis over the past decade. Along the spectrum of promising clinical applications of ctDNA across the various stages of cancer, blood-based genotyping in advanced cancer to guide targeted therapies, and more recently, molecular residual disease detection to improve patient selection for adjuvant therapy in stage II colon cancer, are the only indications with sufficient evidence to be integrated into routine clinical care. 1 Pascual J Attard G Bidard FC et al. ESMO recommendations on the use of circulating tumour DNA assays for patients with cancer: a report from the ESMO Precision Medicine Working Group. Ann Oncol. 2022; 33: 750-768 Summary Full Text Full Text PDF PubMed Google Scholar , 2 Tie J Cohen JD Lahouel K et al. Circulating tumor DNA analysis guiding adjuvant therapy in stage II colon cancer. N Engl J Med. 2022; 386: 2261-2272 Crossref PubMed Scopus (137) Google Scholar Among the many other potential applications of ctDNA, a multi-cancer ctDNA test for early detection of multiple cancer types in otherwise healthy individuals, represents the most substantial opportunity to improve cancer survival. Multi-cancer early detection test in symptomatic patients referred for cancer investigation in England and Wales (SYMPLIFY): a large-scale, observational cohort studyThis first large-scale prospective evaluation of an MCED diagnostic test in a symptomatic population demonstrates the feasibility of using an MCED test to assist clinicians with decisions regarding urgency and route of referral from primary care. Our data provide the basis for a prospective, interventional study in patients presenting to primary care with non-specific signs and symptoms. Full-Text PDF Open Access

Whole-genome informed circulating tumor DNA analysis by multiplex digital PCR for disease monitoring in B-cell lymphomas: a proof-of-concept study.

Analyzing liquid biopsies for tumor-specific aberrations can facilitate detection of measurable residual disease (MRD) during treatment and at follow-up. In this study, we assessed the clinical potential of using whole-genome sequencing (WGS) of lymphomas at diagnosis to identify patient-specific structural (SVs) and single nucleotide variants (SNVs) to enable longitudinal, multi-targeted droplet digital PCR analysis (ddPCR) of cell-free DNA (cfDNA). In 9 patients with B-cell lymphoma (diffuse large B-cell lymphoma and follicular lymphoma), comprehensive genomic profiling at diagnosis was performed by 30X WGS of paired tumor and normal specimens. Patient-specific multiplex ddPCR (m-ddPCR) assays were designed for simultaneous detection of multiple SNVs, indels and/or SVs, with a detection sensitivity of 0.0025% for SV assays and 0.02% for SNVs/indel assays. M-ddPCR was applied to analyze cfDNA isolated from serially collected plasma at clinically critical timepoints during primary and/or relapse treatment and at follow-up. A total of 164 SNVs/indels were identified by WGS including 30 variants known to be functionally relevant in lymphoma pathogenesis. The most frequently mutated genes included KMT2D, PIM1, SOCS1 and BCL2. WGS analysis further identified recurrent SVs including t(14;18)(q32;q21) (IGH::BCL2), and t(6;14)(p25;q32) (IGH::IRF4). Plasma analysis at diagnosis showed positive circulating tumor DNA (ctDNA) levels in 88% of patients and the ctDNA burden correlated with baseline clinical parameters (LDH and sedimentation rate, p-value <0.01). While clearance of ctDNA levels after primary treatment cycle 1 was observed in 3/6 patients, all patients analyzed at final evaluation of primary treatment showed negative ctDNA, hence correlating with PET-CT imaging. One patient with positive ctDNA at interim also displayed detectable ctDNA (average variant allele frequency (VAF) 6.9%) in the follow-up plasma sample collected 2 years after final evaluation of primary treatment and 25 weeks before clinical manifestation of relapse. In summary, we demonstrate that multi-targeted cfDNA analysis, using a combination of SNVs/indels and SVs candidates identified by WGS analysis, provides a sensitive tool for MRD monitoring and can detect lymphoma relapse earlier than clinical manifestation.

Tebentafusp (tebe) in a real-world cohort of 72 French metastatic uveal melanoma (UM) patients (pts).

e21583 Background: Up to 50% of UM pts will develop metastases with poor overall survival (OS) and limited treatment options. Tebe, a bispecific T-cell engager binding CD3 and the gp100 protein presented by the HLA A*02-01, recently showed a benefit in overall response rate (ORR), progression-free survival (PFS) and OS in HLA A*02-01pos metastatic UM (mUM) pts in the IMCgp100-202 phase III trial. Prior to the EMA approval, French Health Authorities allowed an early access to tebe in May 2021 to UM metastatic pts. We here report our real-world experience with tebe in metastatic UM pts. Methods: Ongoing ambispective cohort of mUM pts treated with tebe in France. Metastases are evaluated according to RECIST 1.1 with assessments every 12 weeks (liver MRI +/- CT-scan). ORR, PFS, OS and toxicities are retrieved. Results: 72 pts started tebe between May 26th 2021 and December 12th 2022 (29 men and 43 women). Median age was 61 yo (32-78). Thirty, 34 and 7 patients underwent enucleation proton beam therapy or brachytherapy, respectively (one pt did not receive local treatment). The median time to first metastasis was 24 months (0-276). Tebe was prescribed in first-line in 46 patients, in second-line or more in 26 patients. Metastatic sites at tebe initiation were liver, lung, skin, bone and muscle in 71, 4, 2, 3 and 2 patients, respectively. Liver was the sole metastatic site in 63/72 patients (87.5%). With a median follow-up of 44 weeks, patients received a median of 36 weeks of tebe. Thirty patients discontinued tebe because of disease progression, two because of poor health status and none for toxicity. Of 60 assessable pts, 33 (55%) pts showed stable disease and 5 (8%) showed partial response as best response according to RECIST 1.1. Median PFS was 28 weeks (confidence interval 95% [CI95%]: 8-56) in the global cohort. OS at 12 months was 74% ([CI95%] = 0.62-0.89) in the global cohort, 73% ([CI95%] = 0.55-0.99) and 74% ([CI95%] = 0.57-0.97) in 1st and 2nd line and more, respectively. To date, 13 pts died. Circulating tumor DNA analyses and monitoring of peripheral blood leukocytes are ongoing and will be available by June 2023. Conclusions: In this ongoing, real-world, cohort of metastatic UM pts, tebe is associated with similar clinical outcomes as in the IMCgp100-202, phase III trial. Translational studies on blood and tumor samples are ongoing to identify predictive biomarkers of clinical benefit to this drug.

Safety and efficacy of trastuzumab biosimilar plus irinotecan or gemcitabine in patients with previously treated HER2 (ERBB2)-positive non-breast/non-gastric solid tumors: a phase II basket trial with circulating tumor DNA analysis

Human epidermal growth factor receptor 2 (HER2) (ERBB2)-directed agents are standard treatments for patients with HER2-positive breast and gastric cancer. Herein, we report the results of an open-label, single-center, phase II basket trial to investigate the efficacy and safety of trastuzumab biosimilar (Samfenet®) plus treatment of physician's choice for patients with previously treated HER2-positive advanced solid tumors, along with biomarker analysis employing circulating tumor DNA (ctDNA) sequencing. Patients with HER2-positive unresectable or metastatic non-breast, non-gastric solid tumors who failed at least one prior treatment were included in this study conducted at Asan Medical Center, Seoul, Korea. Patients received trastuzumab combined with irinotecan or gemcitabine at the treating physicians' discretion. The primary endpoint was the objective response rate as per RECIST version 1.1. Plasma samples were collected at baseline and at the time of disease progression for ctDNA analysis. Twenty-three patients were screened from 31 December 2019 to 17 September 2021, and 20 were enrolled in this study. Their median age was 64 years (30-84 years), and 13 patients (65.0%) were male. The most common primary tumor was hepatobiliary cancer (seven patients, 35.0%), followed by colorectal cancer (six patients, 30.0%). Among 18 patients with an available response evaluation, the objective response rate was 11.1% (95% confidence interval 3.1% to 32.8%). ERBB2 amplification was detected from ctDNA analysis of baseline plasma samples in 85% of patients (n= 17), and the ERBB2 copy number from ctDNA analysis showed a significant correlation with the results from tissue sequencing. Among 16 patients with post-progression ctDNA analysis, 7 (43.8%) developed new alterations. None of the patients discontinued the study due to adverse events. Trastuzumab plus irinotecan or gemcitabine was safe and feasible for patients with previously treated HER2-positive advanced solid tumors with modest efficacy outcomes, and ctDNA analysis was useful for detecting HER2 amplification.

PD-1 blockade plus chemotherapy followed by concurrent SBRT with SIB as preoperative therapy for patients with borderline resectable and locally advanced pancreatic cancer: A biomolecular exploratory, single-arm phase II clinical trial.

4159 Background: Pancreatic cancer is fatal malignant tumor with low resection rate and poor prognosis. We aimed to assess the safety and efficacy of a new mode of preoperative therapy for patients with locally advanced (LAPC) or borderline resectable pancreatic cancer (BRPC). Methods: This is a single arm, exploratory phase II clinical trial (ChiCTR2000032955). Gemcitabine (1000 mg/m2) and nab-paclitaxel (125 mg/m2; AG) were administered to patients with LAPC or BRPC on days 1 and 8, along with tislelizumab (200 mg) on day 1 intravenously (IV) every three weeks. Concurrently, the patients underwent stereotactic body radiotherapy (SBRT) with simultaneous integrated boost (SIB) during the third cycle of treatment. Surgical intervention was reassessed after four cycles of treatment. Objective response rate (ORR), R0 resection rate, median overall survival (mOS), median progression-free survival (mPFS) and safety were analyzed. Multiomics potential predictive biomarkers were investigated as exploratory objectives. Results: Between May 2020 and October 2021, 29 patients were enrolled in the study, 25 of them included in the intention-to-treat analysis. At the end of the last follow-up (November 30, 2022), 15 patients had a best response of partial response, the ORR was 60%. Ten patients underwent resection, and the R0 resection rate was 90% (9/10). The disease control rate (DCR) was 100%. Two of the ten resected patients achieved pathologic complete response and one patient achieved major pathological response. The mPFS, 12-months PFS rate, and 12-months OS rate were 13.7 months (95% CI: 11.7–NR), 64% (95% CI: 47.6%–85.8%), and 72% (95% CI: 56.3%–91.9%), respectively. Grade 3 or higher adverse events are anemia (8%), thrombocytopenia (8%) and jaundice (8%). Biomarker analysis indicated that patients with continuous carbohydrate antigen 19-9 decline and elevated peripheral blood eosinophil counts during treatment exhibited better survival outcomes. Furthermore, circulating tumor DNA analysis reveals that patients with a &gt;50% decline in maximal somatic variant allelic frequency (maxVAF) between the first clinical evaluation and baseline have a longer survival outcome and higher response rate than those who are not (PFS: 20.03 vs. 10.32 months, p = 0.024; OS: not reached vs. 13.47 months, p = 0.024; ORR: 90% vs. 35.7%, p = 0.013). Moreover, maxVAF decline (&gt; 50%) is significantly associated with the surgical rate after preoperative therapy (70.0% vs. 21.4%; p = 0.035). Conclusions: Anti-PD-1 inhibitor tislelizumab plus AG chemotherapy followed by concurrent SBRT with SIB displayed promising antitumor activity and acceptable safety profile for patients with LAPC or BRPC. Multiomics potential predictive biomarkers are identified and warrant further verification. Clinical trial information: ChiCTR2000032955 .

A randomized, open-label, phase II/III efficacy and safety study of atezolizumab in combination with FLOT versus FLOT alone in patients with gastric cancer and adenocarcinoma of the oesophagogastric junction and high immune responsiveness: The IKF-S633/DANTE trial, a trial of AIO in collaboration with SAKK.

TPS4177 Background: Perioperative FLOT chemotherapy has become a standard of care for locally advanced, resectable esophagogastric adenocarcinoma (EGA). However, patient outcomes are still unsatisfactory. Immune checkpoint inhibitors combined with chemotherapy have proven activity in advanced Her2 negative EGA with PD-L1 expression (KEYNOTE-590, Checkmate-649). Atezolizumab is a PD-L1 inhibitor with established efficacy and tolerability profiles and will be evaluated in this study in the perioperative treatment of potentially resectable EGA in combination with FLOT. As shown at ASCO 2022 for the phase II part of DANTE, adding atezolizumab to FLOT led to improved tumor downsizing and pCR (24% vs 15%). Of note, regression rates further improved with higher PD-L1 expression (33% vs 12% in tumors with CPS ≥10) or in MSI-high tumors (63% vs 27%). Prompted by these results, we decided to transition this trial from the initial phase II to a phase III design. Methods: This is a multinational, prospective, randomized, investigator-initiated, open label phase II/III trial. Patients (pts) with locally advanced, potentially resectable EGA (≥cT2 and/or N-positive) without distant metastases are enrolled. Based on the subgroup analyses of the phase II trial, we decided to limit the future enrollment to pts with high immune responsiveness, i.e. either of the following: MSI-high, PD-L1 CPS≥1, TMB ≥10/MB or EBV+. Eligibility status is centrally evaluated. Pts are randomized 1:1 to 4 pre-operative 2-week cycles (8 weeks) of FLOT (Docetaxel 50 mg/m²; Oxaliplatin 85 mg/m²; Leucovorin 200 mg/m²; 5-FU 2600 mg/m²) plus 840 mg atezolizumab q2w followed by surgery and 4 additional cycles of FLOT/atezolizumab, followed by a total of 8 additional cycles of atezolizumab at 1200 mg every 3 weeks as monotherapy (arm A) or FLOT alone (arm B). Primary endpoint is event-free survival (EFS) as assessed by the Kaplan-Meier-Method. An estimated HR of 0.72 would correspond to a median EFS of 41.67 months for the experimental Arm A. This difference is considered clinically relevant. A total of 556 pts (318 events) will be randomized. As 177/295 pts with PD-L1 positive or MSI status were already enrolled into the phase II portion, additional 379 pts will be enrolled into phase III. Main secondary endpoints are rates of locally assessed pathological regression (complete and nearly complete pathological regression), OS, OS and EFS in the subgroup of pts with PD-L1 CPS ≥5 and ≥10 and pts with MSI, R0 resection, and safety. In addition, a prospective biomarker study including serial circulating tumor DNA analysis before and during treatment will be performed. Recruitment started 2018 and continues for phase III in 2023. Clinical trial information: NCT03421288 .

Association of cachexia with loss of function mutations in STK11/LKB1 for NSCLC.

e15099 Background: Cancer cachexia (CC), a wasting syndrome of muscle and adipose tissue resulting in weight loss, occurs in 50% of non-small cell lung cancer (NSCLC) patients. Management of CC is limited by the absence of biomarkers and knowledge of molecules that drive its phenotype. The evolving landscape of increased genomic testing of human tumors and derived cell lines has further given us an opportunity to leverage these findings to identify a genetic biomarker that regulates CC development through a novel in vivo human NSCLC cachexia screen. Methods: To identify such molecules, we injected 54 human non-small cell lung cancer (NSCLC) lines into immunodeficient mice, 17 of which produced an unambiguous phenotype of cachexia (n = 10) or non-cachexia (n = 7). Whole exome sequencing of tumors was conducted to identify candidate cachexia-associated genes and gene variant analysis was conducted to identify gene variants that associated with NSCLC-associated CC. CRISPR/Cas9 targeted gene silencing in human NSCLC and mouse cancer lines verified if target genes conferred the cachexia phenotype. Circulating tumor DNA analysis of a 246 NSCLC patient cohort was used to confirm candidate gene variants association with cancer-related weight loss. Results: Whole exome sequencing revealed that 8 of 10 cachexia lines, but none of the non-cachexia lines, possessed mutations in STK11/LKB1 (p = 2x10-12), a regulator of nutrient sensor AMP kinase. Silencing of STK11/LKB1 in human NSCLC and murine colorectal carcinoma lines conferred a cachexia phenotype after cell transplantation into immunodeficient and immunocompetent models, respectively. This host wasting was associated with an alteration in the immune cell repertoire of the tumor microenvironments that led to increases in local mRNA expression and serum levels of CC-associated cytokines resulting in host adipose and muscle tissue wasting. Mutational analysis of circulating tumor DNA from 246 NSCLC patients identified 89% concordance between STK11/LKB1 mutations and weight loss at cancer diagnosis (OR = 17 ± 1, p = 0.004). Conclusions: The current data provides evidence that tumor STK11/LKB1 loss of function is a driver of CC in NSCLC, simultaneously serving as the first genetic biomarker for this wasting syndrome.

Use of circulating tumor DNA analysis to predict recurrence and need for adjuvant chemotherapy in stage I-IV colorectal cancer.

e15537 Background: Circulating tumor DNA (ctDNA) has emerged as a biomarker that can define the risk of recurrence after curative-intent surgery for patients with colorectal cancer (CRC). However, beyond the predictive power of postoperative ctDNA detection, the efficacy and potential limitations of ctDNA detection urgently need to be fully elucidated in a large cohort of CRC. Methods: We enrolled 309 patients with stages Ⅰ to Ⅳ CRC who underwent definitive surgery. Tumor tissues from those patients were sequenced by a custom-designed next-generation sequencing (NGS) panel to identify somatic mutations, and plasma was analyzed using ctDNA-based molecular residual disease (MRD) assay which integrated tumor genotype–informed and tumor genotype–naïve ctDNA analysis. Results: ctDNA was detected after surgery in 5.4%, 13.8%, 15% and 30% of patients with stage Ⅰ, Ⅱ, Ⅲ and Ⅳ disease, respectively, and in 17.5% of all longitudinal samples. Detection of MRD after surgery and in serial plasma samples during follow-up were associated with shorter disease-free survival (DFS) (hazard ratio [HR], 13.17; P &lt; 0.0001 and HR, 14.44; P &lt; 0.0001, respectively) independent of tumor site, stage, and MSI status. Within the population, only 13 patients (6.6%) with longitudinal undetectable MRD recurred, resulting in a negative predictive value of 93.4%. Correspondingly, the positive predictive value of longitudinal detectable MRD was 79.6%, with a median lead time of 10.1 months. Further subgroup analyses revealed that adjuvant therapy did not confer a superior survival for patients with undetectable or detectable MRD. Moreover, lung-only and peritoneal metastases were less detectable by MRD. Conclusions: Postoperative ctDNA status is a strong predictor of recurrence independent of stage and MSI status. Longitudinal undetectable MRD could be used to define the potentially cured population in CRC patients undergoing curative-intent surgery.

Mutational evolution after chemotherapy-progression in metastatic colorectal cancer revealed by circulating tumor DNA analysis.

Emerging new mutations after treatment can provide clues to acquired resistant mechanisms. Circulating tumor DNA (ctDNA) sequencing has enabled noninvasive repeated tumor mutational profiling. We aimed to investigate newly emerging mutations in ctDNA after disease progression in metastatic colorectal cancer (mCRC). Blood samples were prospectively collected from mCRC patients receiving palliative chemotherapy before treatment and at radiological evaluations. ctDNA from pretreatment and progressive disease (PD) samples were sequenced with a next-generation sequencing panel targeting 106 genes. A total of 712 samples from 326 patients were analyzed, and 381 pretreatment and PD pairs (163 first-line, 85 second-line and 133 later-line [≥third-line]) were compared. New mutations in PD samples (mean 2.75 mutations/sample) were observed in 49.6% (189/381) of treatments. ctDNA samples from later-line had more baseline mutations (P = .002) and were more likely to have new PD mutations (adjusted odds ratio [OR] 2.27, 95% confidence interval [CI]: 1.40-3.69) compared to first-line. RAS/BRAF wild-type tumors were more likely to develop PD mutations (adjusted OR 1.87, 95% CI: 1.22-2.87), independent of cetuximab treatment. The majority of new PD mutations (68.5%) were minor clones, suggesting an increasing clonal heterogeneity after treatment. Pathways involved by PD mutations differed by the treatment received: MAPK cascade (Gene Ontology [GO]: 0000165) in cetuximab and regulation of kinase activity (GO: 0043549) in regorafenib. The number of mutations revealed by ctDNA sequencing increased during disease progression in mCRC. Clonal heterogeneity increased after chemotherapy progression, and pathways involved were affected by chemotherapy regimens.

Circulating tumour DNA in colorectal cancer management.

Circulating tumour DNA analysis can be performed using two opposing paradigms: tumour-informed and tumour-agnostic approaches. The first requires sequencing data from the primary tumour sample to identify tumour DNA in circulation, whereas the latter occurs without previous primary tumour genetic profiling. Several preanalytical and laboratory considerations need to be taken into account before proceeding with in-house circulating tumour DNA analysis. Detection of circulating tumour DNA after curative resection is associated with a significant risk of recurrence. For those with stage II disease and detectable postoperative circulating tumour DNA, administration of adjuvant chemotherapy results in a reduction in the number of patients receiving chemotherapy while providing non-inferior recurrence-free survival compared with standard histopathological decision-making algorithms. Monitoring circulating tumour DNA during post-treatment surveillance may provide a significantly earlier diagnosis of recurrence.

Circulating tumor DNA analysis of the phase III VOYAGER trial: KIT mutational landscape and outcomes in patients with advanced gastrointestinal stromal tumor treated with avapritinib or regorafenib

The current treatment paradigm of imatinib-resistant metastatic gastrointestinal stromal tumor (GIST) does not incorporate KIT/PDGFRA genotypes in therapeutic drug sequencing, except for PDGFRA exon 18-mutant GIST that is indicated for avapritinib treatment. Here, circulating tumor DNA (ctDNA) sequencing was used to analyze plasma samples prospectively collected in the phase III VOYAGER trial to understand how the KIT/PDGFRA mutational landscape contributes to tyrosine kinase inhibitor (TKI) resistance and to determine its clinical validity and utility. VOYAGER (N = 476) compared avapritinib with regorafenib in patients with KIT/PDGFRA-mutant GIST previously treated with imatinib and one or two additional TKIs (NCT03465722). KIT/PDGFRA ctDNA mutation profiling of plasma samples at baseline and end of treatment was assessed with 74-gene Guardant360® CDx. Molecular subgroups were determined and correlated with outcomes. A total of 386/476 patients with KIT/PDGFRA-mutant tumors underwent baseline (pre-trial treatment) ctDNA analysis; 196 received avapritinib and 190 received regorafenib. KIT and PDGFRA mutations were detected in 75.1% and 5.4%, respectively. KIT resistance mutations were found in the activation loop (A-loop; 80.4%) and ATP-binding pocket (ATP-BP; 40.8%); 23.4% had both. An average of 2.6 KIT mutations were detected per patient; 17.2% showed 4-14 different KIT resistance mutations. Of all pathogenic KIT variants, 28.0% were novel, including alterations in exons/codons previously unreported. PDGFRA mutations showed similar patterns. ctDNA-detected KIT ATP-BP mutations negatively prognosticated avapritinib activity, with a median progression-free survival (mPFS) of 1.9 versus 5.6 months for regorafenib. mPFS for regorafenib did not vary regardless of the presence or absence of ATP-BP/A-loop mutants and was greater than mPFS with avapritinib in this population. Secondary KIT ATP-BP pocket mutation variants, particularly V654A, were enriched upon disease progression with avapritinib. ctDNA sequencing efficiently detects KIT/PDGFRA mutations and prognosticates outcomes in patients with TKI-resistant GIST treated with avapritinib. ctDNA analysis can be used to monitor disease progression and provide more personalized treatment.

MP55-02 CIRCULATING TUMOR DNA ANALYSIS ON METASTATIC PROSTATE CANCER WITH DISEASE PROGRESSION

You have accessJournal of UrologyCME1 Apr 2023MP55-02 CIRCULATING TUMOR DNA ANALYSIS ON METASTATIC PROSTATE CANCER WITH DISEASE PROGRESSION Sungun Bang, Hyun Ho Han, Kang Su Cho, Jae Won Park, Young Deuk Choi, Saeam Shin, and Dong Ju Won Sungun BangSungun Bang More articles by this author , Hyun Ho HanHyun Ho Han More articles by this author , Kang Su ChoKang Su Cho More articles by this author , Jae Won ParkJae Won Park More articles by this author , Young Deuk ChoiYoung Deuk Choi More articles by this author , Saeam ShinSaeam Shin More articles by this author , and Dong Ju WonDong Ju Won More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000003308.02AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: Circulating tumor DNA (ctDNA) can be a reliable source of genomic information of the metastatic prostate cancer (mPC) tumors. In particular, next-generation sequencing (NGS) of the ctDNA may provide clinically relevant genomic alterations such as androgen receptor (AR) aberrations, homologous recombination repair (HRR) genes, and mismatch repair (MMR) genes. Yet, the positivity rate of ctDNA NGS varies between 30-70% in patients with mPC, making it challenging to incorporate the test as a regular practice. We recently started ctDNA NGS in clinic. We aimed to analyze factors associated with ctDNA NGS positive results basd on our initial experience. METHODS: We retrospectively analyzed ctDNA NGS results of mPC patients in our institute, from May 2021 to July 2022. We used a custom panels of 101 genes known to be detected in malignant tumors. Samples were read by position indexed sequencing using Nova 6000 sequencer. Interpretation of the variants were based on the four-tier system guidelines of Association of Molecular Pathology (AMP), American Society of Clinical Oncology (ASCO), and College of American Pathologists (CAP). Test positivity of ctDNA was determined by detection of Tier 1 or 2 genomic alteration(s) associated with prostate cancer. RESULTS: We analyzed 74 mPC ctDNA samples. We found somatic alterations from cell-free DNA as well as germline alterations from white blood cell fraction. Within somatic alterations, frequently altered genes include AR(16.2%), TP53(14.7%), RB1(9.6%) and CDK12(4.4%). Mutations of HRR genes (BRCA1/2, ATM - 9.6%) and MMR genes (MSH2, MSH6 – 4.4%) were also found. ctDNA-positive samples (n=46) had higher serum PSA than negative samples (n=28)( 42.3ng/mL vs 28ng/mL, p=0.006) at the time of sampling. Also, samples of radiographic progression were more likely to be ctDNA-positive (36 of 46 (78.3%) vs 14 of 28 (50%), p=0.02), and samples of clinical progression were more likely to be ctDNA-positive (23 of 46 (50%) vs 6 of 28 (21.4%), p=0.026). CONCLUSIONS: Circulating tumor DNA analysis may detect clinically relevant genetic alterations in patients with mPC especially at the time of disease progression. Source of Funding: none © 2023 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 209Issue Supplement 4April 2023Page: e763 Advertisement Copyright & Permissions© 2023 by American Urological Association Education and Research, Inc.MetricsAuthor Information Sungun Bang More articles by this author Hyun Ho Han More articles by this author Kang Su Cho More articles by this author Jae Won Park More articles by this author Young Deuk Choi More articles by this author Saeam Shin More articles by this author Dong Ju Won More articles by this author Expand All Advertisement PDF downloadLoading ...

Plasma-only circulating tumor DNA analysis detects minimal residual disease and predicts early relapse in hepatocellular carcinoma patients undergoing curative resection.

Minimal residual disease (MRD) is considered an essential factor leading to relapse within 2 years (early relapse) after radical surgery, which is challenging to be detected by conventional imaging. Circulating tumor DNA (ctDNA) provides a novel approach for detecting MRD and predicting clinical outcomes. Here, we tried to construct a fixed panel for plasma-only ctDNA NGS to enable tumor-uninformed MRD detection in hepatocellular carcinoma (HCC). Here, we performed the followings: (i) profiling genomic alteration spectrum of ctDNA from the Chinese HCC cohort consisting of 493 individuals by NGS; (ii) screening of MRD monitoring genes; and (iii) performance evaluation of MRD monitoring genes in predicting early relapse in the ZJZS2020 cohort comprising 20 HCC patients who underwent curative resection. A total of 493 plasma samples from the Chinese HCC cohort were detected using a 381/733-gene NGS panel to characterize the mutational spectrum of ctDNA. Most patients (94.1%, 464/493) had at least one mutation in ctDNA. The variants fell most frequently in TP53 (45.1%), LRP1B (20.2%), TERT (20.2%), FAT1 (16.2%), and CTNNB1 (13.4%). By customized filtering strategy, 13 MRD monitoring genes were identified, and any plasma sample with one or more MRD monitoring gene mutations was considered MRD-positive. In the ZJZS2020 cohort, MRD positivity presented a sensitivity of 75% (6/8) and a specificity of 100% (6/6) in identifying early postoperative relapse. The Kaplan-Meier analysis revealed a significantly short relapse-free survival (RFS; median RFS, 4.2 months vs. NR, P=0.002) in the MRD-positive patients versus those with MRD negativity. Cox regression analyses revealed MRD positivity as an independent predictor of poor RFS (HR 13.00, 95% CI 2.60-69.00, P=0.002). We successfully developed a 13-gene panel for plasma-only MRD detection, which was effective and convenient for predicting the risk of early postoperative relapse in HCC.