Monitor tumor burden with circulating tumor DNA

Detection of circulating tumor cells and of tumor DNA in plasma during tumor progression in rats

Simple SummaryCtDNA analysis is a promising tool in liquid biopsy for the detection of tumor recurrence and progression, and is increasingly adopted into clinical practice. Still, guidelines for the accurate clinical interpretation of ctDNA analysis results are largely lacking, especially for tumor mutant variants detected at very low frequencies. Here, we show that cutoff determination for the detection and quantification of low-frequency mutant variants enables the accurate prediction of residual disease, tumor recurrence and progression, even before clinical evidence. CtDNA analysis using these cutoffs outperformed cfDNA and CEA level measurements. With these findings, we highlight the need to thoroughly validate each liquid biopsy assay and define the assay-specific limit of blanks (LOB) and limit of quantifications (LOQ) of BRAF p.V600E and KRAS p.G12/p.G13 assays for clinical interpretation. Our approach enables accurate clinical interpretation to support clinical decision making.Circulating tumor DNA (ctDNA) is a promising liquid biopsy (LB) marker to support clinical decisions in precision medicine. For implementation into routine clinical practice, clinicians need precise ctDNA level cutoffs for reporting residual disease and monitoring tumor burden changes during therapy. We clinically validated the limit of blank (LOB) and the limit of quantification (LOQ) of assays for the clinically most relevant somatic variants BRAF p.V600E and KRAS p.G12/p.G13 in colorectal cancer (CRC) in a study cohort encompassing a total of 212 plasma samples. We prove that residual disease detection using the LOB as a clinically verified cutoff for ctDNA positivity is in concordance with clinical evidence of metastasis or recurrence. We further show that tumor burden changes during chemotherapy and the course of disease are correctly predicted using the LOQ as a cutoff for quantitative ctDNA changes. The high potential of LB using ctDNA for accurately predicting the course of disease was proven by direct comparison to the routinely used carcinoembryonic antigen (CEA) as well as the circulating free DNA (cfDNA) concentration. Our results show that LB using validated ctDNA assays outperforms CEA and cfDNA for residual disease detection and the prediction of tumor burden changes.

Introduction: Circulating tumor DNA (ctDNA) is increasingly valuable in cancer care. Early diagnosis of renal cell carcinoma (RCC) significantly improves prognosis. Clear cell RCC (ccRCC), the most prevalent and aggressive subtype, often leads to recurrence in over 20% of localized cases post-nephrectomy. Thus, risk-stratifying tools are crucial for tailored treatment strategies. In this study, we tracked tumor mutations in DNA from plasma (ctDNA) and urine (utDNA) in patients with localized ccRCC to explore their potential as risk-stratifying biomarkers for recurrence. We evaluated ctDNA/utDNA pre-surgery in all RCC patients and conducted longitudinal assessments post-surgery in ccRCC patients. Additionally, for one ccRCC patient with aggressive disease, we analyzed tumor mutations in the plasma of patient- derived xenograft (PDX) replicates. Methodology: RCC patients were recruited from A.C.Camargo Cancer Center. Urine and plasma samples were taken pre-surgery (BL-baseline), and for ccRCC patients, samples were collected at 6-8 weeks and 6, 18 and 30 months post- surgery (M1, M2, M3 and M4, respectively). Patients were monitored for recurrence for up to 6,3 years. We used a customized 28-gene RCC panel and a commercial 409-gene solid tumor panel to identify tumor somatic mutations using Illumina NextSeq 500 and Ion S5 platforms, respectively. Tumor specific mutations were tracked in DNA from patient plasma and urine, and PDX plasma, using the PATS (Personalized amplicon target sequencing) method on Ion S5 Plus platform. Results: Out of 79 RCC patients (58% ccRCC), 57 (72%) had tumor somatic mutations, including 39 (68%) in ccRCC. VHL and PBRM1 were the most frequently mutated genes. Baseline ctDNA/utDNA were analyzed in 51 RCC patients, with 18% (13% plasma, 12% urine) positivity in RCC and 19% (12% plasma, 12% urine) in ccRCC. During ccRCC monitoring, ctDNA/utDNA was positive only in M1 and M3, with 9% (9% plasma, 0% urine) and 18% (12% plasma, 6% urine), respectively. ctDNA-positive baseline plasma was associated to disease progression (p=0.0155) and tumor staging ≥pT3 (p=0.002); these patients also experienced reduced progression-free (p=0.004) and overall (p98%, resembling the patient’s tumor aggressiveness. Conclusions: ccRCC tumors release low levels of tumor DNA in urine and plasma. Pre-surgery plasma positivity for ctDNA appears to indicate a higher risk of recurrence in ccRCC patients. The ctDNA release of PDX tumors replicated that observed in one ccRCC patient with aggressive disease. Citation Format: Ana Carolina Kerekes Miguez, Isabella Tanus Job e Meira, Stephania Martins Bezerra, Adriano de Oliveira Beserra, Walter Henriques da Costa, Tiago Goss dos Santos, Stenio de Cassio Zequi, Giovana Tardin Torrezan, Dirce Maria Carraro. Circulating tumor DNA (ctDNA) in plasma and urine of renal cell carcinoma patients with localized disease [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr A052.

<div>Abstract<p>The ability to consistently detect cell-free tumor-specific DNA in peripheral blood of patients with metastatic breast cancer provides the opportunity to detect changes in tumor burden and to monitor response to treatment. We developed cMethDNA, a quantitative multiplexed methylation-specific PCR assay for a panel of ten genes, consisting of novel and known breast cancer hypermethylated markers identified by mining our previously reported study of DNA methylation patterns in breast tissue (103 cancer, 21 normal on the Illumina HumanMethylation27 Beadchip) and then validating the 10-gene panel in The Cancer Genome Atlas project breast cancer methylome database. For cMethDNA, a fixed physiologic level (50 copies) of artificially constructed, standard nonhuman reference DNA specific for each gene is introduced in a constant volume of serum (300 μL) before purification of the DNA, facilitating a sensitive, specific, robust, and quantitative assay of tumor DNA, with broad dynamic range. Cancer-specific methylated DNA was detected in training (28 normal, 24 cancer) and test (27 normal, 33 cancer) sets of recurrent stage IV patient sera with a sensitivity of 91% and a specificity of 96% in the test set. In a pilot study, cMethDNA assay faithfully reflected patient response to chemotherapy (<i>N</i> = 29). A core methylation signature present in the primary breast cancer was retained in serum and metastatic tissues collected at autopsy two to 11 years after diagnosis of the disease. Together, our data suggest that the cMethDNA assay can detect advanced breast cancer, and monitor tumor burden and treatment response in women with metastatic breast cancer. <i>Cancer Res; 74(8); 2160–70. ©2014 AACR</i>.</p></div>

Individual bulk tumor biopsies are invasive and may fail to capture clonal heterogeneity within primary tumors and metastatic sites of disease. Further, analyses of subclonal variants are often hindered by background error rates related to tissue preservation methods (e.g. FFPE) and sequencing artifact. Use of plasma-only ultrasensitive liquid biopsy approaches may allow for noninvasive inference of clonality and dynamically track changes in tumor burden. We previously developed MRD-EDGE, a tumor-informed machine learning classifier for ultrasensitive liquid biopsy monitoring of single nucleotide variants (SNVs) and copy number variants (CNVs) using standard plasma whole genome sequencing. For SNVs, MRD- EDGE uses a novel machine learning framework to classify individual cell free DNA (cfDNA) fragments as circulating tumor DNA or cfDNA sequencing artifact. We demonstrated the potential of plasma-only MRD-EDGE to identify SNVs in advanced melanoma and monitor tumor burden throughout treatment with immune checkpoint inhibiton. In tumor-informed settings, MRD-EDGE was used to identify minimal residual disease at tumor fractions (TFs) of 1:100,000 and below. Accurate SNV classification is a function of classifier performance and background error rate. To reduce error rates, we combined MRD-EDGE SNV with paired plus- minus sequencing (ppmSeq) from Ultima Genomics. ppmSeq is a PCR-free approach that leverages the hydrogen bonds of complementary DNA to carry matched native strands directly into sequencing, enabling scalable duplex sequencing. Use of MRD-EDGE SNV together with ppmSeq enables ultrasensitive tracking of early-stage non-small cell lung cancer throughout neoadjuvant immunotherapy. Plasma-only MRD-EDGE is therefore poised to enable dynamic monitoring of tumor burden and clonal composition outside the scope of tumor-informed approaches, including the comparison of SNV composition in cancer recurrence with preoperative disease. Citation Format: Adam Widman, Alexandre P. Cheng, John Zinno, Srinivas Rajagopalan, Ashish Saxena, Nasser Altorki, Dan A. Landau. Plasma-only ultrasensitive liquid biopsy to monitor tumor burden and clonal evolution [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr IA021.

<div>AbstractPurpose:<p>To investigate the use of plasma and urine DNA mutation analysis for predicting neoadjuvant chemotherapy (NAC) response and oncological outcome in patients with muscle-invasive bladder cancer.</p>Experimental Design:<p>Whole-exome sequencing of tumor and germline DNA was performed for 92 patients treated with NAC followed by radical cystectomy (RC). A custom NGS-panel capturing approximately 50 mutations per patient was designed and used to track mutated tumor DNA in plasma and urine. A total of 447 plasma samples, 281 urine supernatants, and 123 urine pellets collected before, during, and after treatment were analyzed. Patients were enrolled from 2013 to 2019, with a median follow-up time of 41.3 months after RC.</p>Results:<p>We identified tumor DNA before NAC in 89% of urine supernatants, 85% of urine pellets, and 43% of plasma samples. Tumor DNA levels were higher in urine supernatants and urine pellets compared with plasma samples (<i>P</i> < 0.001). In plasma, detection of circulating tumor DNA (ctDNA) before NAC was associated with a lower NAC response rate (<i>P</i> < 0.001). Detection of tumor DNA after NAC was associated with lower response rates in plasma, urine supernatant, and urine pellet (<i>P</i> < 0.001, <i>P</i> = 0.03, <i>P</i> = 0.002). Tumor DNA dynamics during NAC was predictive of NAC response and outcome in urine supernatant and plasma (<i>P</i> = 0.006 and <i>P</i> = 0.002). A combined measure from plasma and urine supernatant tumor DNA dynamics stratified patients by outcome (<i>P</i> = 0.003).</p>Conclusions:<p>Analysis of tumor DNA in plasma and urine samples both separately and combined has a potential to predict treatment response and outcome.</p></div>

Background: Increased levels of CTC and a persistent elevated level after just one cycle of chemotherapy are very strong and independent markers of worse progression-free survival (PFS) and overall survival (OS) in patients (pts) with metastatic breast cancer (MBC) (Bidard et al, Lancet Oncol 2014). ctDNA can be used to detect mutation associated with resistance to treatment. It has also been shown that dynamic changes in ctDNA levels closely reflect changes in tumor burden. We prospectively monitored CTC and ctDNA early variations during first line chemotherapy for MBC. Patients & methods: The French cohort COMET is a prospective study including first line HER2 negative patients (pts) receiving weekly paclitaxel and bevacizumab according to EMA approved combination. The aim of this cohort is to evaluate clinical, biological and radiological parameters associated with pts outcome (CTC, serum markers, ctDNA, pharmacogenomic polymorphisms, metabolomic parameters, visceral fat, serum estradiol level and quality of life). We present here the first planned analysis on pts evaluated for CTC (CellSearch) and ctDNA using targeted sequencing (Roche SeqCap technology) of a panel of 46 genes and 8 promoters, using unique molecular identifiers to increase ctDNA detection sensitivity. Blood samples were obtained at baseline (BL) and before the second cycle of chemotherapy (C2). Results: From 09/2012 to 5/2014, 218 pts were included in this substudy. Median age was 55 years and 22% of pts had triple negative BC. At BL, 70% of pts had ≥1 detectable CTC per 7.5 ml of blood (median 4 CTC, range 1- 30,000) and 37% at C2. With a threshold of ≥5 CTC, 47% of pts were positive at BL and 22% at C2. For ctDNA, out of the first 141 pts analyzed, 105 had at least one somatic mutation detected in plasma (74%). The average number of mutations per pt was 2.7 and most commonly mutated genes were TP53 and PIK3CA. ESR1 was found mutated in 9% of all cases and restricted to the ER+ subgroup. Median Allelic Frequency was 10% (range 0.6-83%). Only 33% of pts had detectable ctDNA at C2. At BL, CTC and ctDNA levels were correlated (r=0.46, p<0.0001). Despite no complete overlap, 11% of pts had no CTC nor ctDNA detected. Median follow-up was 53 months and median OS was 32 months. Increased level of CTC and ctDNA were significantly associated with decreased PFS and OS. At C2, ≥5 CTC or still detectable ctDNA were strong markers of reduced OS: HR 4.6 (CI95 3.1-7) and HR 3.2 (CI95 1.8 – 5.5), respectively (both p< 0.0001). At multivariate analysis for PFS, detectable ctDNA at C2 and triple negative status were the only significant prognostic factors. None of serum marker level at BL or their early variations had prognostic value. Conclusion: This is the largest prospective cohort assessing the respective prognostic values of early CTC and ctDNA changes in homogenously treated first line MBC patients. Analysis of mutations profile variations and comparison with primary tumor and metastasis biopsies are ongoing and may reveal early mechanisms of resistance. Citation Format: Pierga J-Y, Silveira A, Lorgis V, Tanguy M-L, Tredan O, Dubot C, Jacot W, Goncalves A, Debled M, Levy C, Ferrero J-M, Jouannaud C, Luporsi E, Mouret-Reynier M-A, Dalenc F, Lemonnier J, Berger F, Proudon C, Bidard F-C. Circulating tumor DNA (ctDNA) and circulating tumor cells (CTC) predictive value in HER2 negative metastatic breast cancer patients treated with first line weekly paclitaxel and bevacizumab: Results of a prospective cohort from the French Breast Cancer InterGroup Unicancer (UCBG): COMET study [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr PD2-03.

Circulating cell-free DNA (cfDNA) is now under investigation as a "liquid biopsy" in the real time management of cancer. In The New England Journal of Medicine Dawson et al. reported a proof of concept investigation of tumour specific alterations in cfDNA and demonstrate that this fraction termed "circulating tumour DNA" (ctDNA) shows greater correlation with changes in tumour burden than two other circulating biomarkers (CA 15-3 and circulating tumor cell counts) in individuals with metastatic breast cancer receiving therapy.

To examine the effects of the surgical manipulation of tumors on the hematogenous dissemination of tumors, we compared rates of detection of tumor-derived DNA in the buffy coat and in plasma from tumor-bearing rats before and after tumor resection. We injected DHD/K12-PROb cells subcutaneously into BD-IX rats. Three weeks later, we removed the tumors surgically. Group PERI was sacrificed 3 hours after surgery, group POST-2 was sacrificed 2 weeks later, group POST-4 was sacrificed another 2 weeks later, and group POST-LONG was sacrificed when rats were close to death. In group PERI, four perioperative blood samples were taken. In the other groups, only one blood sample was taken per rat, immediately before euthanasia. We used polymerase chain reaction to detect tumor-derived DNA in buffy-coat, plasma, and lung samples. In group PERI, tumor DNA in plasma was more frequent than circulating tumor cells at all perioperative time points. The difference was statistically significant 3 hours after surgery (P = .035). In group POST-2, there was no detectable metastasis or tumor DNA in blood samples. There were lymphatic and lung metastases in most animals in group POST-4 and in all animals in group POST-LONG. In the last two groups, the frequencies of tumor DNA in the buffy coat and in plasma were similar. In our animal model, the hematogenous dissemination of tumors due to surgery seemed to be more closely related to tumor-derived cell-free DNA than to circulating tumor cells. In addition, the surgical resection of primary tumors did not inhibit the development of metastases.

BackgroundAccurate measurement of tumor burden in breast cancer disease is essential to improve the clinical management of patients. In this study, we evaluate whether the fluctuations in the fraction of PIK3CA mutant allele correlates with tumor response according to RECIST criteria and tumor markers quantification.MethodsEighty six plasma samples were analyzed by digital PCR using Rare Mutation Assays for E542K, E545K and H1047R. Mutant cfDNA and tumor markers CA15-3 and CEA were compared with radiographic imaging.ResultsThe agreement between PIK3CA mutation status in FFPE samples and circulating tumor DNA (ctDNA) was moderate (K = 0.591; 95% IC = 0.371–0.811). Restricting the analysis to the metastatic patients, we found a good agreement between PIK3CA mutation status assessed in liquid and solid biopsy (K = 0.798 95%; IC = 0.586–1). ctDNA showed serial changes with fluctuations correlating with tumor markers 15.3 and CEA in 7 out of 8 cases with Pearson correlation coefficients ranging from 0.99 to 0.46 and from 0.99 to 0.38 respectively. Similarly, fluctuations in the fraction of PIK3CA mutant allele always correlated with changes in lesion size seen on images, although in two cases it did not correlate with treatment responses as defined by RECIST criteria.Conclusiononcogenic mutation quantification in plasma samples can be useful to monitor treatment outcome. However, it might be limited by tumor heterogeneity in advanced disease and it should be evaluated together with radiographic imaging.

<div>AbstractPurpose:<p>Double inhibition of epidermal growth factor receptor (EGFR) using a tyrosine kinase inhibitor plus a monoclonal antibody may be a novel treatment strategy for non–small cell lung cancer (NSCLC). We assessed the efficacy and toxicity of afatinib + cetuximab versus afatinib alone in the first-line treatment of advanced <i>EGFR</i>-mutant NSCLC.</p>Patients and Methods:<p>In this phase II, randomized, open-label study, patients with stage III/IV <i>EGFR</i>-positive NSCLC were randomly assigned (1:1) to receive afatinib (group A) or afatinib + cetuximab (group A + C). Oral afatinib 40 mg was given once daily; cetuximab 250 mg/m² was administered intravenously on day 15 of cycle 1, then every 2 weeks at 500 mg/m² for 6 months. The primary endpoint was time to treatment failure (TTF) rate at 9 months. Exploratory analysis of <i>EGFR</i> circulating tumor DNA in plasma was performed.</p>Results:<p>Between June 2016 and November 2018, 59 patients were included in group A and 58 in group A + C. The study was ended early after a futility analysis was performed. The percentage of patients without treatment failure at 9 months was similar for both groups (59.3% for group A vs. 64.9% for group A + C), and median TTF was 11.1 (95% CI, 8.5–14.1) and 12.9 (9.2–14.5) months, respectively. Other endpoints, including progression-free survival and overall survival, also showed no improvement with the combination versus afatinib alone. There was a slight numerical increase in grade ≥3 adverse events in group A + C. Allele frequency of the <i>EGFR</i> gene mutation in circulating tumor DNA at baseline was associated with shorter PFS, regardless of the treatment received.</p>Conclusions:<p>These results suggest that addition of cetuximab to afatinib does not warrant further investigation in treatment-naïve advanced <i>EGFR</i>-mutant NSCLC.</p></div>

152 Background: Circulating tumor DNA in plasma (ctDNA) is an emerging resource for detecting genomic alterations in various cancers. However, the characteristics and clinical utility of ctDNA are not fully elucidated, especially in patients with genitourinary (GU) cancers. Methods: In April 2019, SCRUM-Japan started the MONSTAR-SCREEN project, which evaluates the ctDNA from patients with various advanced solid tumors. We collected plasma and tumor samples from patients with advanced prostate cancer (PC), urothelial carcinoma (UC), and renal cell carcinoma (RCC). Plasma ctDNA and tissue genomic DNA were analyzed using NGS-based cell-free DNA assay, a modified version of FoundationOne Liquid (F1L) including blood tumor mutational burden (TMB) analysis, and tissue-based panel, FoundationOne CDx (F1CDx), respectively. Success rate of ctDNA was defined as the percentage of patients whose sample quality control status was “pass” or “qualified”. Level of ctDNA was defined as the maximum allele fraction (AF) for all known somatic alterations detected. Results: As of June 18, 2020, ctDNA analysis results were available for 470 of 540 patients with advanced solid tumors. Among them, we analyzed 70 advanced GU cancers (35 PC, 17 UC, and 18 RCC) and 400 non-GU cancers. The success rate of ctDNA was significantly lower in GU cancers than in non-GU cancers (81.4% vs. 91.5%, P = 0.016). The levels of ctDNA in PC and UC were similar to those in non-GU cancers. RCC had the second lowest ctDNA level (median 0.13%) after that in malignant melanoma. The median TMB, as estimated by ctDNA, was 4.40, 0.88 and 0.44 mutations/Mb in UC, PC and RCC, respectively. The most frequently altered genes were TP53 (34%), AR (11%), BRCA2 (11%), ATM (8.6%), and CDK12 (8.6%) in PC, TP53 (59%), TERT (41%), and CHEK2 (18%) in UC, and TP53 (22%), ATM (11%), and MTOR (11%) in RCC. The mutation rate in genes related to DNA damage response (DDR) pathways was significantly higher in GU cancers compared to that in non-GU cancers (30.0% vs. 18.0%, P = 0.033). However, other pathways were less frequently altered in GU cancers versus non-GU cancers, including Wnt (5.7% vs. 16.8%, P = 0.017), PI3K (8.6% vs. 19.0%, P = 0.039) and RAS/MAPK (8.6% vs. 29.5%, P < 0.001). Conclusions: Our results reveal the genomic landscape of ctDNA in several advanced solid tumors, and highlight the differences between tumor types. Comprehensive analysis of ctDNA using the F1L assay reveled alterations in DDR-associated genes were significantly more frequent in GU cancers than in non-GU cancers. Clinical trial information: UMIN000036749.

Circulating tumor DNA (ctDNA) from the blood of cancer patients is a promising biomarker of certain types of colorectal cancer, with potential use in screening, treatment selection, therapy response monitoring, minimal residual disease detection, and surveillance. We present results demonstrating that the OnTarget ctDNA detection assay can be used as an indicator of the presence of genomic variants associated with colorectal cancer in patients prior to treatment. The study includes three cohorts of individuals: young normal controls, age-matched normal controls, and colorectal cancer patients whose blood was drawn prior to treatment or surgery, and whose diagnosis confirms the presence of a colorectal tumor. Tissue from the primary tumor biopsy was also collected and analyzed with the OnTarget assay. Using Boreal Genomics' OnTarget 46-mutation panel, we find high correlation between the tumor mutational profile and the plasma mutation profile even for early stage patients demonstrating high sensitivity (88% plasma-tissue concordance to date) of the assay. By applying the same assay in the normal population we demonstrate extremely low false positive rates, highlighting the potential of the assay as a tool for therapy monitoring, surveillance, or screening. The OnTarget assay is capable of single molecule sensitivity, specificity to ≤0.01% mutation abundance versus wild-type, and multiplexing of over 100 mutations in a single test from a single plasma sample. The OnTarget technology employs a combination of Next Generation DNA Sequencing and a proprietary target selection process that removes wild-type DNA prior to amplification to greatly improve signal to noise and reduce the error rate of sequencing. We present an overview of the technology and results from an ongoing study to demonstrate the potential clinical utility of ctDNA as an effective biomarker to guide management of colorectal cancer. Citation Format: Matthew Wiggin, Jaryn Perkins, Laura Mai, Valentina Vysotskaia, Andre Marziali. Highly sensitive detection of circulating tumor DNA in plasma as a biomarker of colorectal cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1886. doi:10.1158/1538-7445.AM2014-1886

Background: Detection of circulating tumour DNA (ctDNA) in plasma predicts future recurrence in early breast cancer (EBC). Previous studies have relied on tumour-informed approaches with personalised assays. In this study, we performed orthogonal testing on plasma samples collected prospectively in the c-TRAK-TN study to compare a tissue-free assay with digital droplet PCR (ddPCR) for ctDNA analysis. Methods: c-TRAK-TN recruited 161 patients with early triple negative breast cancer (TNBC) deemed clinically high risk of relapse. Patients underwent ctDNA analysis by ddPCR starting within 4 weeks of completion of treatment and continuing every 3 months for up to 2 years. ddPCR tracked 1 or 2 patient specific variants as previously described. We further analysed 1062 timepoints from a total of 159 patients (median 7 per patient, range 1-11) using Guardant Reveal assay, a tissue-free approach that exploits differential methylation patterns in breast cancer compared with normal tissue. Results: Samples were successfully analysed from 95.3% (1012/1062) timepoints from 159 patients with the tissue-free Reveal assay. CtDNA was detected in 34.0% (54/159) of patients in at least 1 timepoint, with a median methylation tumour fraction of 0.266% (range 0.002 to 51.0%). Detection of ctDNA with the tumour agnostic assay strongly associated with future risk of relapse (HR 20.62, p<0.0001; logrank). Of patients who relapsed by 24 months follow up, 89.5% (34/38) of relapses were detected by prior ctDNA analysis. There were 159 patients available for comparison between ddPCR and the tissue-free assay (Reveal), in 1005 timepoints (median 7 per patient, range 1-11). Concordant test results were observed in 950/1005 timepoints with an overall agreement rate of 94.5%. In this cohort, 63.5% (101/159) of patients did not have ctDNA detected by either assay; 26.4% (42/159) had ctDNA detected by both assays and 10.1% (16/159) had discordant results. Of those detected, 44.8% (26/58) were detected by the tissue-free assay first and 6.9% (4/58) by ddPCR (p<0.0001, Fisher exact test). The median time from first detection of ctDNA to relapse for the tissue-free assay was 7.9 months (95% confidence interval (CI): 5.7-10.5 months) compared to ddPCR assay with 5.7 months (95% CI: 2.9-9.7 months) (HR = 0.6, p=0.0574; mixed effects cox model). Conclusion: Detection of ctDNA with a tissue-free assay anticipated relapse with high accuracy, in patients with early TNBC. The tissue-free assay frequently detected ctDNA at an earlier timepoint than ddPCR, trending towards a longer lead time from detection of ctDNA to relapse. Tissue-free approaches might offer simpler workflows for ctDNA analysis than tumour-informed approaches, and further assessment in clinical trials is warranted. Citation Format: N. Cunningham, R. J. Cutts, C. Swift, K. Dunne, M. Dewan, L. Kilburn, K. Goddard, P. Hall, C. Harper-Wynne, T. Hickish, I. Macpherson, A. Okines, A. Wardley, S. Waters, C. Palmieri, M. Winter, J. Bliss, D. Dustin, M. Ellis, I. Garcia- Murillas, N. C. Turner. Tissue-free circulating tumour DNA detection in patients with early triple negative breast cancer from the c-TRAK-TN trial [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr RF3-05.

Pancreatic ductal adenocarcinoma (PDAC) frequently presents as hypo- or iso-dense masses with poor contrast delineation from surrounding parenchyma, which decreases reproducibility of manual dimensional measurements obtained during conventional radiographic assessment of treatment response. Longitudinal registration between pre- and post-treatment images may produce imaging biomarkers that more reliably quantify treatment response across serial imaging. Thirty patients who prospectively underwent a neoadjuvant chemotherapy regimen as part of a clinical trial were retrospectively analyzed in this study. Two image registration methods were applied to quantitatively assess longitudinal changes in tumor volume and tumor burden across the neoadjuvant treatment interval. Longitudinal registration errors of the pancreas were characterized, and registration-based treatment response measures were correlated to overall survival (OS) and recurrence-free survival (RFS) outcomes over 5-year follow-up. Corresponding biomarker assessments via manual tumor segmentation, the standardized response evaluation criteria in solid tumors (RECIST), and pathological examination of post-resection tissue samples were analyzed as clinical comparators. Average target registration errors were for a biomechanical image registration algorithm and for a diffeomorphic intensity-based algorithm, corresponding to 1-2 times voxel resolution. Cox proportional hazards analysis showed that registration-derived changes in tumor burden were significant predictors of OS and RFS, while none of the alternative comparators, including manual tumor segmentation, RECIST, or pathological variables were associated with consequential hazard ratios. Additional ROC analysis at 1-, 2-, 3-, and 5-year follow-up revealed that registration-derived changes in tumor burden between pre- and post-treatment imaging were better long-term predictors for OS and RFS than the clinical comparators. Volumetric changes measured by longitudinal deformable image registration may yield imaging biomarkers to discriminate neoadjuvant treatment response in ill-defined tumors characteristic of PDAC. Registration-based biomarkers may help to overcome visual limits of radiographic evaluation to improve clinical outcome prediction and inform treatment selection.