Detection Of Tumor DNA Research Articles

The Emerging Applications of Raman Spectroscopy in Clinical Oncology: A Narrative Review Focused on Circulating Tumor DNA Detection and Therapeutic Drug Monitoring

The Emerging Applications of Raman Spectroscopy in Clinical Oncology: A Narrative Review Focused on Circulating Tumor DNA Detection and Therapeutic Drug Monitoring

Feasibility of Circulating Tumor DNA Detection in the Cerebrospinal Fluid of Patients With Central Nervous System Involvement in Large B-Cell Lymphoma.

We explored the utility of cerebrospinal fluid (CSF) circulating tumor DNA (ctDNA) sequencing as a noninvasive diagnostic tool for detecting central nervous system (CNS) involvement in patients with diffuse large B-cell lymphoma (DLBCL). Secondary CNS involvement in DLBCL, although rare (~5% of cases), presents diagnostic and prognostic challenges during systemic disease progression or relapse. Effective treatment is impeded by the blood-brain barrier. This was a prospective cohort study (Samsung Lymphoma Cohort Study III) involving 17 patients with confirmed CNS involvement. High-throughput sequencing was conducted using targeted gene panels designed to detect low-frequency variants and copy number alterations pertinent to lymphomas in ctDNA extracted from archived CSF samples. Despite challenges such as low DNA concentrations affecting library construction, the overall variant detection rate was 76%. Detected variants included those in genes commonly implicated in CNS lymphoma, such as MYD88. The study highlights the potential of CSF ctDNA sequencing to identify CNS involvement in DLBCL, providing a promising alternative to more invasive diagnostic methods such as brain biopsy, which are not always feasible. Further validation is necessary to establish the clinical utility of this method, which could significantly enhance the management and outcomes of DLBCL patients with suspected CNS involvement.

Genomic alterations associated with resistance and circulating tumor DNA dynamics for early detection of progression on CDK4/6 inhibitor in advanced breast cancer.

Combined CDK4/6 inhibitor (CDK4/6i) and endocrine therapy significantly improves outcome for patients with estrogen receptor-positive (ER+) metastatic breast cancer, but drug resistance and thus disease progression inevitably occur. Herein, we aimed to identify genomic alterations associated with combined CDK4/6i and endocrine therapy resistance, and follow the levels of specific mutations in longitudinal circulating tumor DNA (ctDNA) for early detection of progression. From a cohort of 86 patients with ER+ metastatic breast cancer we performed whole exome sequencing or targeted sequencing of paired tumor (N = 8) or blood samples (N = 5) obtained before initiation of combined CDK4/6i and endocrine therapy and at disease progression. Mutations in oncogenic genes at progression were rare, while amplifications of growth-regulating genes were more frequent. The most frequently acquired alterations observed were PIK3CA and TP53 mutations and PDK1 amplification. Longitudinal ctDNA dynamics of mutant PIK3CA or private mutations revealed increased mutation levels at progression in 8 of 10 patients (80%). Impressively, rising levels of PIK3CA-mutated ctDNA were detected 4-17 months before imaging. Our data add to the growing evidence supporting longitudinal ctDNA analysis for real-time monitoring of CDK4/6i response and early detection of progression in advanced breast cancer. Further, our analysis suggests that amplification of growth-related genes may contribute to combined CDK4/6i and endocrine therapy resistance.

Clinical Validation of Human Papilloma Virus Circulating Tumor DNA for Early Detection of Residual Disease After Chemoradiation in Cervical Cancer

Clinical Validation of Human Papilloma Virus Circulating Tumor DNA for Early Detection of Residual Disease After Chemoradiation in Cervical Cancer

Detection of cell-free tumor DNA in cerebrospinal fluid as a diagnostic biomarker for leptomeningeal melanoma metastasis: A case series.

Leptomeningeal melanoma metastases (LMM) are associated with poor survival. Diagnosis is based on clinical presentation, brain MRI and cerebrospinal fluid (CSF) analysis. Inconclusive findings at initial presentation can delay treatment. In this single-center case series, detection of BRAFV600- and NRASQ61-mutant cell-free tumor DNA (cfDNA) in CSF was evaluated as a complementary diagnostic biomarker. In 12 patients with clinical suspicion of LMM, a retrospective analysis of MRI, CSF cytology and cfDNA analysis on 1 mL of CSF using the Idylla® platform was carried out. Nine patients displayed MRI abnormalities suggesting LMM. CSF analysis identified malignant cells in three patients (including one without MRI abnormalities). BRAFV600- or NRASQ61-mutant cfDNA was detected in CSF of nine patients (eight with and one without MRI abnormalities; all patients with positive CSF cytology). Subsequent follow-up confirmed LMM in all patients with positive and in one patient with a negative CSF cfDNA analysis (sensitivity 81.8%; specificity 100%). Our findings suggest that analyzing BRAFV600- and NRASQ61-mutant cfDNA in CSF using the Idylla® platform holds promise as a sensitive and specific complementary diagnostic biomarker for LMM, particularly in case of inconsistency between imaging and CSF cytology. The 110-min analysis can facilitate urgent treatment decisions.

Prognostic value of HPV circulating tumor DNA detection and quantification in locally advanced cervical cancer.

Cervical cancers are mainly caused by an oncogenic HPV. For locally advanced stages, the standard treatment is radio-chemotherapy (RTCT) followed by brachytherapy. Nevertheless, the prognosis remains highly heterogeneous between patients. We investigated the prognostic value of HPV circulating tumor DNA (ctDNA) in locally advanced cervical cancers alongside that of Squamous Cell Carcinoma Antigen (SCC-A). This single-center retrospective study included patients treated in curative intent for an IB3 to IVA squamous cell cervical cancer. Quantification of HPV ctDNA in serum collected at diagnosis was performed using a multiplex digital PCR assay for the simultaneous detection of 8 HPV genotypes. Among the 97 patients included, 76 patients (78.4%) were treated by RTCT, followed by brachytherapy for 57 patients (60%). HPV ctDNA was detected in 59/97 patients at diagnosis (60.8%). This detection was associated with lymph node invasion (p=0.04) but not with tumor stage. A high level of SCC-A at diagnosis was associated with tumor stage (p=0.008) and lymph node invasion (p=0.012). In univariate analysis, better disease-free survival (DFS) was associated with optimal RTCT regimen (p=0.002), exposure to brachytherapy (p=0.0001) and a low SCC-A at diagnosis (continuous analysis, p=0.002). Exploratory analysis revealed that 3/3 patients (100%) whose HPV ctDNA was still detectable at the end of treatment relapsed, while 6/22 patients (27.3%) whose HPV ctDNA was negative at the end of treatment relapsed. HPV ctDNA detection at diagnosis of locally advanced cervical squamous cell carcinomas is frequent and related to node invasion, but not to DFS. The prognostic value of HPV ctDNA detection after treatment warrants specific studies.

Clinical Utility of Tumor-Naïve Presurgical Circulating Tumor DNA Detection in Early-Stage NSCLC

ObjectivesThe use of tumor-informed circulating tumor DNA (ctDNA) testing in patients with early-stage disease before surgery is limited, mainly owing to restricted tissue access and extended turnaround times. This study aimed to evaluate the clinical value of a tumor-naïve, methylation-based cell-free DNA assay in a large cohort of patients with resected NSCLC. MethodWe analyzed presurgical plasma samples from 895 patients with EGFR and anaplastic lymphoma kinase-wild-type, clinical stage I or II NSCLC. The ctDNA status was evaluated for its prognostic significance in relation to tumor volume, metabolic activity, histologic diagnosis, histologic subtypes, and clinical-to-pathologic TNM upstaging. ResultsPresurgical ctDNA detection was observed in 55 of 414 patients (13%) with clinical stage I lung adenocarcinoma (LUAD) and was associated with poor recurrence-free survival (2-year recurrence-free survival 69% versus 91%; log-rank p < 0.001), approaching that of clinical stage II LUAD. Presurgical ctDNA detection was not prognostic in patients with clinical stage II LUAD or non-LUAD. Within LUAD, tumor volume and positron emission tomography avidity interacted to predict presurgical ctDNA detection. Moreover, presurgical ctDNA detection was predictive of the postsurgical discovery of International Association for the Study of Lung Cancer grade 3 tumors (p < 0.001) and pathologic TNM upstaging (p < 0.001). Notably, presurgical ctDNA detection strongly correlated with higher programmed death-ligand 1 expression in tumors (positive rates 28% versus 55%, p < 0.001), identifying a subgroup likely to benefit from anti–programmed death-ligand 1 therapies. ConclusionThese findings support the integration of ctDNA testing into routine diagnostic workflows in early-stage NSCLC without the need for tumor tissue profiling. Furthermore, it is clinically useful in identifying patients at high risk who might benefit from innovative treatments, including neoadjuvant immune checkpoint inhibitors.

Neoadjuvant sintilimab plus chemotherapy in EGFR-mutant NSCLC: Phase 2 trial interim results (NEOTIDE/CTONG2104)

The clinical efficacy of neoadjuvant immunotherapy plus chemotherapy remains elusive in localized epidermal growth factor receptor (EGFR)-mutant non-small cell lung cancer (NSCLC). Here, we report interim results of a Simon's two-stage design, phase 2 trial using neoadjuvant sintilimab with carboplatin and nab-paclitaxel in resectable EGFR-mutant NSCLC. All 18 patients undergo radical surgery, with one patient experiencing surgery delay. Fourteen patients exhibit confirmed radiological response, with 44% achieving major pathological response (MPR) and no pathological complete response (pCR). Similar genomic alterations are observed before and after treatment without influencing the efficacy of subsequent EGFR-tyrosine kinase inhibitors (TKIs) invitro. Infiltration and Tcell receptor (TCR) clonal expansion of CCR8+ regulatory T (Treg)hi/CXCL13+ exhausted T (Tex)lo cells define a subtype of EGFR-mutant NSCLC highly resistant to immunotherapy, with the phenotype potentially serving as a promising signature to predict immunotherapy efficacy. Informed circulating tumor DNA (ctDNA) detection in EGFR-mutant NSCLC could help identify patients nonresponsive to neoadjuvant immunochemotherapy. These findings provide supportive data for the utilization of neoadjuvant immunochemotherapy and insight into immune resistance in EGFR-mutant NSCLC.

Longitudinal circulating tumor DNA monitoring for detection of molecular residual disease in patients with advanced germ cell tumors.

e17022 Background: Germ cell malignancies, commonly manifesting as testicular cancer, is one of the most common malignancies in men 15 to 45 years of age, with the incidence doubling over the past 40 years. When identified promptly and treated with a multidisciplinary approach, germ cell tumors have an excellent prognosis with cure rate &gt;90% and 5-year survival rate &gt;95%. Treatment involves radical orchiectomy for diagnostic and therapeutic purposes. Further management includes active surveillance, adjuvant chemotherapy, retroperitoneal lymph node dissection (RLND), and radiation therapy. While AFP, B-HCG, and LDH are good biomarkers, they are not sensitive or specific for detecting molecular residual disease (MRD). B-HCG is detected in &lt;30% of individuals with seminoma and B-HCG and AFP are detected in 50–60% of patients with non-seminomatous tumors. We describe the use of circulating tumor DNA (ctDNA) for detection of MRD in advanced germ cell malignancy, especially when baseline biomarkers are negative. Methods: This is a retrospective analysis of 20 patients with testicular cancer treated at Rush University Medical Center who monitored closely for MRD. Signatera (Natera Inc.), a personalized tumor-informed ctDNA assay, was utilized for detection and quantification of ctDNA in patients’ plasma samples, measured at MRD (1-12 weeks post-orchiectomy) and regular intervals thereafter, regardless of treatment modality. Event free survival (EFS) was determined, defined as the period from radical orchiectomy to date of radiographic progression of disease. Results: There was a total of 20 patients (35% seminoma, 65% non-seminoma) with 2 of the patients having extragonadal disease. The mean age was 32.2 years old with IQR (28-36). Post operatively, 20% underwent RLND, 10% were on surveillance, 53% received post-orchiectomy chemotherapy, 6.7% of patients underwent autologous stem cell transplant. The median follow up time is 1.14 years. Two patients had positive ctDNA despite negative baseline traditional biomarkers. There were 23.3% (7/30) of patients that had evidence of radiographic progression. Of the patients with progression, serial ctDNA monitoring had high rates of concordance (85%, 6/7) of ctDNA positivity with biomarker positivity and radiographic progression. Conclusions: Overall, ctDNA correlated with, and sometimes even preceded, traditional biomarkers and radiographic findings of disease progression. The ctDNA positivity of 2 patients in this cohort despite negative baseline AFP, B-HCG, and LDH, highlights the sensitivity and specificity of ctDNA for MRD compared to more traditional biomarkers. Serial monitoring of ctDNA offers valuable insights into germ cell tumor disease status, including presence of MRD, and there is a need for prospective studies to guide treatment escalation and de-escalation in germ cell tumors.

Monitoring ctDNA dynamics in early breast cancer using a novel ultra-sensitive tumor-informed structural variant approach combining whole-genome sequencing and multiplex dPCR.

568 Background: Persistent circulating cell-free tumor DNA (ctDNA) detection during neoadjuvant treatment of early-breast cancer (EBC) indicates high-risk disease. Detection of ctDNA post-resection of EBC (molecular residual disease, MRD) indicates occult metastatic disease and impending disease relapse. For ctDNA to be integrated into EBC management, accessible and scalable diagnostic tools are required. Here, we apply a highly sensitive, personalized tumor-informed approach to ctDNA evaluation predicated on analyses of structural variants (SVs) using a novel digital PCR (dPCR) SV technology. Methods: 170 patients with EBC and eligible for neoadjuvant therapy (NAT) were recruited through the prospective SCAN-B study (NCT02306096) between Dec 2014 and Mar 2019 (25.8% TNBC, 47.1% HR+/HER2- and 24.1% HER2+). Interim results are presented for the first 46 consecutive patients (comprising 567 plasma samples) where minimum QC criteria were met (10% tumor content and 10x sequencing depth). Whole genome sequencing (WGS) was performed on tumor material and personalized multiplex dPCR assays designed tracking up to 8 SVs for use in ctDNA analyses. Plasma samples were collected at baseline, during NAT, pre- and post-surgery and at 6-monthly intervals during follow up. Clinical characteristics and recurrence outcomes were recorded. Results: ctDNA was detected at one or more timepoints prior to surgery in 43/46 (93%) patients across all breast cancer subtypes, at a median variant allele frequency (VAF) of 0.14% (range 0.0002% - 27.6%). ctDNA levels remained detectable at the end of NAT in 24% patients (11/46); 5/11 (45%) ctDNA positive patients experienced disease relapse versus 1/35 (3%) ctDNA negative patients (P=0.002, Fisher’s exact test). At one or more post-operative timepoints, ctDNA was detected in 6/6 (100%) patients who experienced clinical recurrence, with lead times up to 52 months (median 11.8 months, range 3.5 to 52 months). In 40 patients without presentation of clinical recurrence to date, ctDNA was undetectable across 285/287 (99.3%) plasma timepoints collected post-surgery. Post-operative detection of ctDNA associated with poor overall survival (OS) compared to absence of ctDNA (log-rank P&lt;0.0001). Conclusions: In this interim analysis of an ongoing prospective study in patients with EBC receiving NAT, we analyzed plasma for ctDNA using a novel tumor-informed dPCR assay tracking patient-specific SVs. ctDNA detection post-neoadjuvant therapy, prior to surgery associated with high-risk of disease relapse. Postoperative ctDNA detection was observed in 100% patients with clinical recurrence, and associated with poorer OS and long lead-times. Our data demonstrate the feasibility of SVs as an MRD analyte and provide evidence for high levels of clinical sensitivity achievable with this approach in EBC. Clinical trial information: NCT02306096 .

A pilot study on ultra-sensitive circulating tumor DNA detection with a novel methylation amplifier probe in colorectal cancer.

10547 Background: Liquid biopsy is extensively researched for detecting cancer-related methylation markers. However, detecting ultra-low methylation signals in liquid biopsies is extremely challenging. In early-stage cancer patients, less than 1% of circulating cell-free DNA (cfDNA) is tumor tissue-derived DNA (ctDNA), presenting a low signal-to-noise ratio for effective tumor marker detection. Methods: Here, we introduce Methylation Amplifier Probe for Low-signal Enrichment (MAPLE), a method for designing ultra-short hybrid capture probes (25-55 nt). By reducing the length of the probes, MAPLE enhances their intolerance to DNA base mismatches, thereby significantly improving their ability to specifically bind and enrich the targeted methylation haplotypes. A panel consisting of 13,218 CRC-related methylation haplotypes was constructed for validation. 42 samples from patients with cancer and 43 gender/age matched control samples were processed for the panel validation. All the DNA samples underwent bisulfite conversion, library preparation and parallelly hybridized with two capture panels composed with conventional probes (120 nt) or the MAPLE probes, demonstrating its effectiveness in increasing cancer signal-to-noise ratio in the final NGS data. Results: With MAPLE, in the final NGS data, ratio of CRC-related methylation haplotypes reads (signal) in patient’s plasma samples increased from 7% (conventional) to 28% (MAPLE). At 20M total raw reads (1000x sequencing depth), the MAPLE panel detects over four times the targeted haplotype fragments compared to the conventional panel. For a cohort including 42 patients (I-III:24, IV:18) with CRC and 43 gender/age matched controls, the MAPLE panel aided by a machine-learning classifier detected patients with a sensitivity of 0.83 and a specificity of 0.95. Conclusions: This pilot study highlights the potential of ultra-short probes in capturing cancer-related methylation haplotypes, advancing towards an early detection test for pan-cancer.

A multi-assay liquid biopsy approach to improve detection of bone and soft tissue sarcomas.

10019 Background: Bone and soft tissue sarcomas are among the most common extra-cranial solid tumors of childhood, yet advances in liquid biopsies lag behind what has been achieved across adult cancers. Solid tumors that lack recurrent genetic mutations or translocations, such as bone and soft tissue sarcomas, are more difficult to detect in circulation using established assays, such as ddPCR. We have developed a pipeline to analyze cell-free DNA (cfDNA) using two molecular profiling techniques that we hypothesized would improve detection of circulating tumor DNA at diagnosis for patients with bone and soft tissue sarcomas. Methods: cfDNA was isolated from plasma of patients with osteosarcoma (OS) (n = 36) and fusion-negative rhabdomyosarcoma (FN-RMS) (n = 7) at multiple timepoints. Methods for detecting tumor DNA in cfDNA included ultra-low coverage whole genome sequencing (ULC-WGS, 0.5x) and ultra-deep targeted sequencing (UDP, ~1000x) using a panel of 11 and 22 tumor-associated genes for OS and FN-RMS, respectively. ULC-WGS data underwent ichorCNA analysis to define percent tumor content of each sample. UDP analysis identified somatic variants through variant callers, Mutect2, Lancet, strelka, and DELLY2, with ClinVar to annotate and define tumor-specific variants in each sample. Combining ULC-WGS and UDP data, an integrated tumor score was developed and assessed in diagnostic samples. Results: 136 OS and 30 FN-RMS cfDNA samples were collected during the patients’ disease courses. Circulating tumor material was detected in 18/23 (78%) OS and7/7 (100%) FN-RMS samples at diagnosis. The most frequent copy number aberrations were seen in the region of chromosome 8q containing the cMYC gene. cMYC amplification was found in 11/23 (48%) of diagnostic OS samples and 2/7 (29%) of diagnostic FN-RMS samples. UDP analysis identified variants in 17/23 (73%) and 7/7 (100%) of diagnostic OS and FN-RMS samples respectively. The most commonly detected variants included TP53, BRCA2, MET, and BRAF. Of the 23 diagnostic OS samples, four had TP53 translocations. The integrated tumor score detected the presence of tumor associated material within diagnostic samples with a sensitivity of 25/30 (83%), compared to the sensitivity of ULC-WGS or UDP alone, which was 15/30 (50%) and 24/30 (80%) respectively. Conclusions: A multi-assay liquid biopsy has promise to improve disease detection and monitoring for patients with solid tumors that lack recurrent driver mutations. We plan to integrate additional molecular profiling technologies to improve the sensitivity and specificity of our cfDNA assays and aim to adapt our pipeline across additional cancers.

Prognostic implication of methylation-based circulating tumor DNA detection prior to surgery in stage I non-small cell lung cancer

BackgroundCirculating tumor DNA (ctDNA) positivity at diagnosis, which is associated with worse outcomes in multiple solid tumors including stage I–III non-small cell lung cancer (NSCLC), may have utility to guide (neo)adjuvant therapy. MethodsIn this retrospective study, 260 patients with clinical stage I NSCLC (180 adenocarcinoma, 80 squamous cell carcinoma) were allocated (2:1) to high- and low-risk groups based on relapse versus disease-free status ≤5 years post-surgery. We evaluated the association of preoperative ctDNA detection by a plasma-only targeted methylation-based multi-cancer early detection (MCED) test with NSCLC relapse ≤5 years post-surgery in the overall population, followed by histology-specific subgroup analyses. ResultsAcross clinical stage I patients, preoperative ctDNA detection did not associate with relapse within 5 years post-surgery. Sub-analyses confined to lung adenocarcinoma suggested a histology-specific association between ctDNA detection and outcome. In this group, ctDNA positivity tended to associate with relapse within 2 years, suggesting prognostic implications of MCED test positivity may be histology- and time-dependent in stage I NSCLC. Preoperative ctDNA detection was associated with upstaging of clinical stage I to pathological stage II–III NSCLC. ConclusionsOur findings suggest preoperative ctDNA detection in patients with resectable clinical stage I NSCLC using MCED, a pan-cancer screening test developed for use in an asymptomatic population, has no detectable prognostic value for relapse ≤5 years post-surgery. MCED detection may be associated with early adenocarcinoma relapse and increased pathological upstaging rates in stage I NSCLC. However, given the exploratory nature of these findings, independent validation is required.

Integrating Imaging and Circulating Tumor DNA Features for Predicting Patient Outcomes.

Biomarkers for evaluating tumor response to therapy and estimating the risk of disease relapse represent tremendous areas of clinical need. To evaluate treatment efficacy, tumor response is routinely assessed using different imaging modalities like positron emission tomography/computed tomography or magnetic resonance imaging. More recently, the development of circulating tumor DNA detection assays has provided a minimally invasive approach to evaluate tumor response and prognosis through a blood test (liquid biopsy). Integrating imaging- and circulating tumor DNA-based biomarkers may lead to improvements in the prediction of patient outcomes. For this mini-review, we searched the scientific literature to find original articles that combined quantitative imaging and circulating tumor DNA biomarkers to build prediction models. Seven studies reported building prognostic models to predict distant recurrence-free, progression-free, or overall survival. Three discussed building models to predict treatment response using tumor volume, pathologic complete response, or objective response as endpoints. The limited number of articles and the modest cohort sizes reported in these studies attest to the infancy of this field of study. Nonetheless, these studies demonstrate the feasibility of developing multivariable response-predictive and prognostic models using regression and machine learning approaches. Larger studies are warranted to facilitate the building of highly accurate response-predictive and prognostic models that are generalizable to other datasets and clinical settings.

Ultrasensitive and Rapid Circulating Tumor DNA Liquid Biopsy Using Surface-Confined Gene Amplification on Dispersible Magnetic Nano-Electrodes.

Circulating tumor DNA (ctDNA) detection has been acknowledged as a promising liquid biopsy approach for cancer diagnosis, with various ctDNA assays used for early detection and treatment monitoring. Dispersible magnetic nanoparticle-based electrochemical detection methods have been proposed as promising candidates for ctDNA detection based on the detection performance and features of the platform material. This study proposes a nanoparticle surface-localized genetic amplification approach by integrating Fe3O4-Au core-shell nanoparticles into polymerase chain reactions (PCR). These highly dispersible and magnetically responsive superparamagnetic nanoparticles act as nano-electrodes that amplify and accumulate target ctDNA in situ on the nanoparticle surface upon PCR amplification. These nanoparticles are subsequently captured and subjected to repetitive electrochemical measurements to induce reconfiguration-mediated signal amplification for ultrasensitive (∼3 aM) and rapid (∼7 min) metastatic breast cancer ctDNA detection in vitro. The detection platform can also detect metastatic biomarkers from in vivo samples, highlighting the potential for clinical applications and further expansion to rapid and ultrasensitive multiplex detection of various cancers.

Metal-Graphene Hybrid Terahertz Metasurfaces for Circulating Tumor DNA Detection Based on Dual Signal Amplification.

Terahertz (THz) spectroscopy has impressive capability for label-free biosensing, but its utility in clinical laboratories is rarely reported due to often unsatisfactory detection performances. Here, we fabricated metal-graphene hybrid THz metasurfaces (MSs) for the sensitive and enzyme-free detection of circulating tumor DNA (ctDNA) in pancreatic cancer plasma samples. The feasibility and mechanism of the enhanced effects of a graphene bridge across the MS and amplified by gold nanoparticles (AuNPs) were investigated experimentally and theoretically. The AuNPs serve to boost charge injection in the graphene film and result in producing a remarkable change in the graded transmissivity index to THz radiation of the MS resonators. Assay design utilizes this feature and a cascade hybridization chain reaction initiated on magnetic beads in the presence of target ctDNA to achieve dual signal amplification (chemical and optical). In addition to demonstrating subfemtomolar detection sensitivity and single-nucleotide mismatch selectivity, the proposed method showed remarkable capability to discriminate between pancreatic cancer patients and healthy individuals by recognizing and quantifying targeted ctDNAs. The introduction of graphene to the metasurface produces an improved sensitivity of 2 orders of magnitude for ctDNA detection. This is the first study to report the combined application of graphene and AuNPs in biosensing by THz spectroscopic resonators and provides a combined identification scheme to detect and discriminate different biological analytes, including nucleic acids, proteins, and various biomarkers.

CtDNA as an Adjunct to Posttreatment PET for Head and Neck Cancer Recurrence Risk Assessment.

Circulating tumor DNA (ctDNA) detection is an emerging technique that identifies minimal residual disease in patients with solid tumors. ctDNA can act as an adjunct method to help overcome the limitations of positron emission tomography (PET) and select patients who are at high risk for recurrence. Retrospective Single Institutional Study. University Hospital Setting. Twenty-nine patients who underwent definitive treatment for squamous cell carcinoma of the head and neck (HNSCC) from 8/2021 to 01/2023 had ctDNA levels analyzed at 1 to 3, 6, 9, and 12 months after definitive treatment. A personalized, tumor-informed, multiplex polymerase chain reaction (PCR) next-generation sequencing (NGS) assay was used to detect the ctDNA levels. The primary outcome was recurrence-free probability (RFP), and the secondary outcomes were overall survival (OS), sensitivity, specificity, and the test's negative (NPV) and positive predictive values (PPV). The median age of patients was 65 years (interquartile range: 56-69), with majority being males (n = 22, 76%). The primary sites were larynx (n = 12), oropharynx (n = 10), and oral cavity (n = 6). Posttreatment ctDNA was detected in 7 patients, all of whom had disease recurrence. ctDNA detection after definitive treatment was associated with a higher risk of disease recurrence (hazard ratio: 9.94, 95% confidence interval: 1.56-63.3, P = .015). ctDNA identified recurrence with 100% specificity and 78% sensitivity. The NPV and PPV were 91% and 100%. PET had 78% sensitivity but only 68% specificity with 86% NPV, and 54% PPV. Based on our data, ctDNA can be an excellent adjunct test for posttreatment PET and can help guide physicians in cases where PET results are inconclusive and difficult to interpret.

Abstract LB105: Sensitive urothelial cancer detection via high volume urine DNA analysis

Abstract Background: The detection of cancer-associated DNA in urine samples has significant potential in urothelial cancer (UC) detection and surveillance. Every year millions of patients with urinary symptoms undergo cystoscopy, an examination of the bladder using a flexible scope. Only 10% of these invasive examinations result in a cancer diagnosis. Cystoscopy is also used in post-operative surveillance, with many UC patients requiring life-long cystoscopies. Methods: We developed a high-volume urine DNA collection kit and laboratory platform and prospectively analyzed 433 urine samples collected from diagnostic and post-operative timepoints from 167 UC patients and 95 negative controls from January 2021 to September 2023. We used a hybridization capture assay targeting the coding regions of 21 commonly mutated genes in urothelial tumors, as well as 8 frequently copy number altered loci. Samples were sequenced using Illumina NovaSeq instruments. Mutations, copy number alterations, and chromosomal rearrangements were computationally identified. Key Findings: In the diagnostic settings our assay achieved a sensitivity of 100% for pT1+ bladder cancer, 97% for pTa bladder cancer, and 91% for upper tract urothelial cancer (UTUC) (100% for pT1+ or high grade) in an all-comers UC cohort, at a specificity of 93%. Post-operative urine DNA surveillance informed by preoperative urine mutations detected 28/30 (93%) residual cancer cases found in cystoscopy or surgery, with two pTa low grade recurrences missed. Using a secondary, highly stringent urine tumor DNA detection threshold (100% specificity for UC), we show that urine DNA testing in the diagnostic setting may allow up to 68% of UC patients to be scheduled directly to operating room procedures, reducing hospital workload and expediting care. In addition, we demonstrate the feasibility of urine DNA for detecting underlying Lynch syndrome in UC patients by identifying three UTUC patients who carried germline defects in mismatch repair genes MSH2 or MSH6, indicative of Lynch syndrome. In two of these patients our assay also found a somatic second hit and high mutation load. Conclusions and Clinical Implications: These results show promise in urine DNA based cancer diagnostics even in patients with low grade tumors. The assay is designed to offer a non-invasive and cost-effective alternative for cystoscopies. Citation Format: Jussi Nikkola, Lauri Ryyppö, Juuso Vuorinen, Heini Kallio, Hanna Selin, Pyry Jämsä, Jonne Åkerla, Tarmo Pekkarinen, Antti Kaipia, Matti Nykter, Thea Veitonmäki, Matti Annala. Sensitive urothelial cancer detection via high volume urine DNA analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB105.

Abstract 3656: Target enrichment of methylated circulating tumor DNA for colorectal cancer detection

Abstract Aberrant DNA methylation changes are one of the earliest signatures of cancer development. Methylation profiling of circulating tumor DNA (ctDNA) from plasma has emerged as a promising approach for early cancer detection (ECD). However, the set of methylation targets that can successfully distinguish cancer through liquid biopsy will vary depending on cancer type and subtype. Here, we explored a methylation target enrichment workflow and developed a methylation-based classification model to distinguish between patients with colorectal cancer (CRC) and healthy individuals. First, CRC-specific CpG targets were identified by comparing the methylation landscape of CRC and normal samples (tissue and blood) available in The Cancer Genome Atlas (TCGA) database and Gene Expression Omnibus (GEO) datasets. This analysis resulted in &amp;gt;800 CRC-specific CpG targets for initial evaluation. To develop and test the classification model, CRC patients and healthy individuals with plasma samples were included. A machine learning model was used to evaluate the highest performing CpG targets that effectively discriminated between CRC patients with detected ctDNA (“CRC ctDNA-positive”) and healthy individuals. Correlation between methylation levels of the high performing CpG targets and the variant allele frequency (VAF) among CRC ctDNA-positive patients was calculated. In total, 86 patients were included in this proof of concept study (mean age, 62 ±12 years; male, 55%). 50 CRC ctDNA-positive patients (24% stage I, 40% stage II, 24% stage III, and 12% stage IV) and 36 healthy normals were included in the analysis. We investigated this cohort to identify the highest performing CpG targets among the &amp;gt;800 potential CpG targets that provided effective discrimination between CRC patients and healthy individuals. Using the highest performing CpG targets, observed methylation level was correlated with VAF of single nucleotide variants detected by ctDNA testing (R2: 0.8). In summary, we developed a cost-effective methylation target enrichment workflow and utilized machine-learning algorithms to demonstrate the potential use of ctDNA methylation markers in early detection. Additional studies are needed to confirm that these and other markers can accurately distinguish between patients with CRC and healthy individuals. Citation Format: Hsiao-Yun Huang, Ravi Vijaya Satya, Wen-Ching Chan, Esha Atolia, Joshua Babiarz, Bernhard Zimmermann, Trupti Kawli. Target enrichment of methylated circulating tumor DNA for colorectal cancer detection [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 3656.

Abstract 5071: Minimal residual disease (MRD) status by peripheral blood mononuclear cells (PBMCs) and circulating tumor DNA (ctDNA) demonstrates rapid, deep, and sustained response in patients (Pts) with relapsed/refractory follicular lymphoma (R/R FL) treated with subcutaneous (SC) epcoritamab monotherapy in the pivotal phase 1/2 EPCORE™ NHL-1 trial

Abstract Introduction: Outcomes in high-risk R/R FL are poor. Epcoritamab SC, a CD3xCD20 bispecific antibody, demonstrated promising efficacy with a manageable safety profile in pts with R/R FL after ≥2 prior lines of therapy (phase 1/2 EPCORE NHL-1; NCT03625037). Here we evaluated MRD with PBMCs and ctDNA in pts with R/R FL and correlated the results with clinical findings. Methods: Adults with R/R FL 1-3A enrolled in EPCORE NHL-1 received epcoritamab SC in 28-day cycles. MRD analysis was performed on longitudinal plasma and PBMC samples collected at prespecified timepoints (clonoSEQ assay, Adaptive Biotechnologies). Screening tumor biopsies were used to identify trackable tumor clones; samples were quantified as tumor clones detected per mL plasma for ctDNA and per one million nucleated cells for PBMC. Overall response and progression-free survival (PFS) were assessed using Lugano criteria by independent review committee. Results: Of 128 pts in the R/R FL 1-3A cohort, 91 with PBMC data and 100 with ctDNA data were MRD evaluable. Overall MRD negativity was achieved in 67.0% [95% CI: 56.4-76.5] of pts per PBMC and 68.0% [95% CI: 57.9-77.0] of pts per ctDNA. Concordance of subject-level MRD status was high (79 of 89 with PBMC and ctDNA data; 88.8%). In most pts, MRD negativity was reached prior to radiographic complete response (PBMC, 76.4%; ctDNA 58.5%). MRD negativity by PBMC preceded ctDNA (median days to MRD negativity, 28 [PBMC] vs 57 [ctDNA]), suggesting a difference in methodology in detecting tumor DNA. Pts who became MRD negative had prolonged PFS (median not reached). Baseline MRD levels were not associated with clinical outcomes (PBMC; Wilcoxon P=0.59, ctDNA P=0.39). PFS was similar in pts achieving MRD negative status (median not reached, PBMC and ctDNA), independent of high-risk/difficult-to-treat disease (≥4 prior lines, Ann Arbor stage III-IV, bulky disease, double refractory, FLIPI 3-5, and POD24). The overall MRD negativity rate was also similar in high-risk pts, except those with ≥4 prior lines of therapy. Conclusions: Based on the EPCORE-NHL-1 study, one of the first pivotal studies to report MRD in pts with R/R FL, epcoritamab drives rapid, deep, and sustained responses as supported by MRD assessment by both PBMC and ctDNA. MRD results correlate with clinical outcome, and achieving MRD negativity is associated with longer PFS. PFS was similar among all pts who achieved MRD negativity, including those with high-risk disease. Citation Format: David Soong, Işıl Altıntaş, John Karavitis, Kim M. Linton, Wojciech Jurczak, Catherine Thieblemont, Kevin Zhao, Edith Szafer-Glusman, Daniela Hoehn, Elena Favaro, Mariana Sacchi, Maria Jure-Kunkel. Minimal residual disease (MRD) status by peripheral blood mononuclear cells (PBMCs) and circulating tumor DNA (ctDNA) demonstrates rapid, deep, and sustained response in patients (Pts) with relapsed/refractory follicular lymphoma (R/R FL) treated with subcutaneous (SC) epcoritamab monotherapy in the pivotal phase 1/2 EPCORE™ NHL-1 trial [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 5071.