ctDNA Biomarkers Research Articles

Liquid biopsy: the analysis of circulating tumour DNA

Circulating tumour DNA (ctDNA) fragments found in blood represent a critical source of information about the tumour. However, the analysis of ctDNA is challenging due to the overwhelming presence of DNA from non-malignant cells and requires the development of highly sensitive laboratory techniques. This review discusses the major categories of ctDNA biomarkers, their detection methodologies, and explores the potential of emerging technologies within the liquid biopsy field.

The prognostic role of circulating tumour DNA detected prior to clinical diagnosis of colorectal cancer in the HUNT study

BackgroundToday, the prognostic tools available at the time of diagnosis in colorectal cancer (CRC) are limited. Better prognostic tools are a prerequisite for personalised treatment.This study aimed to investigate whether circulating tumour DNA (ctDNA) markers found in plasma before clinical diagnosis of CRC could contribute to the prediction of poor prognosis.MethodsThis observational cohort study included patients diagnosed with CRC stage I-III within 24 months following participation in the Trøndelag Health Study (n = 85). Known methylated ctDNA biomarkers of CRC were analysed by PCR in plasma. Outcomes were overall survival (OS), recurrence-free survival (RFS) and poor prognosis (PP). Candidate clinical and methylated ctDNA predictors of the outcomes were identified by Cox regression analyses.ResultsMethylated GRIA4 (HR 1.96 (1.06–3.63)), RARB (HR 9.48 (3.00–30.00)), SLC8A1 (HR 1.97 (1.03–3.77)), VIM (HR 2.95 (1.22–7.14)) and WNT5A (HR 5.83 (2.33–14.56)) were independent predictors of OS, methylated RARB (HR 9.67 (2.54–36.81)), SDC2 (HR 3.38 (1.07–10.66)), SLC8A1 (HR 2.93 (1.01–8.51)) and WNT5A (HR 6.95 (1.81–26.68)) were independent predictors of RFS and methylated RARB (HR 6.11 (1.69–22.18)), SDC2 (HR 2.79 (1.20–6.49)) and WNT5A (HR 5.57 (3.04–15.26)) were independent predictors of PP (p < 0.05).ConclusionsPrediagnostic ctDNA markers are promising contributors to predicting poor prognosis in CRC, potentially becoming one of the tools guiding more personalised treatment.

94P A one-tube multiplex methylation-specific droplet digital PCR assay for identification of ctDNA biomarkers in anal squamous cell carcinoma

94P A one-tube multiplex methylation-specific droplet digital PCR assay for identification of ctDNA biomarkers in anal squamous cell carcinoma

Construction of scalable multi-channel DNA nanoplatform for the combined detection of ctDNA biomarkers of ovarian cancer.

Single-level biomarker detection has the limitation of insufficient accuracy in cancer diagnosis. Therefore, the strategy of developing highly sensitive, multi-channel biosensors for high-throughput ctDNAdetermination is critical to improve the accuracy of early diagnosis of clinical tumors. Herein, in order to achieve efficient detection of up to ten targets for early diagnosis of ovarian cancer, a DNA-nanoswitch-based multi-channel (DNA-NSMC) biosensor was built based on the multi-module catalytic hairpin assembly-mediated signal amplification (CHA) and toehold-mediated DNA strand displacement (TDSD) reaction. Only two different fluorescence signals were used as outputs, combined with modular segmentation strategy of DNA-nanoswitch-based reaction platform; the multi-channel detection of up to ten targets was successfully achieved for the first time. The experimental results suggest that the proposed biosensor is a promising tool for simultaneously detecting multiple biomarkers for the early diagnosis of ovarian cancer, offering new strategies for the early screening, diagnosis, and treatment not only for ovarian cancer but also for other cancers.

Early ctDNA kinetics as a dynamic biomarker of cancer treatment response.

Circulating tumor DNA assays are promising tools for the prediction of cancer treatment response. Here, we build a framework for the design of ctDNA biomarkers of therapy response that incorporate variations in ctDNA dynamics driven by specific treatment mechanisms. We develop mathematical models of ctDNA kinetics driven by tumor response to several therapy classes, and utilize them to simulate randomized virtual patient cohorts to test candidate biomarkers. Using this approach, we propose specific biomarkers, based on ctDNA longitudinal features, for targeted therapy, chemotherapy and radiation therapy. We evaluate and demonstrate the efficacy of these biomarkers in predicting treatment response within a randomized virtual patient cohort dataset. These biomarkers are based on novel proposals for ctDNA sampling protocols, consisting of frequent sampling within a compact time window surrounding therapy initiation - which we hypothesize to hold valuable prognostic information on longer-term treatment response. This study highlights a need for tailoring ctDNA sampling protocols and interpretation methodology to specific biological mechanisms of therapy response, and it provides a novel modeling and simulation framework for doing so. In addition, it highlights the potential of ctDNA assays for making early, rapid predictions of treatment response within the first days or weeks of treatment, and generates hypotheses for further clinical testing.

Recent Advancements in the Application of Circulating Tumor DNA as Biomarkers for Early Detection of Cancers.

Early detection of cancer is vital for increasing patient survivability chances. The three major techniques used to diagnose cancers are instrumental examination, tissue biopsy, and tumor biomarker detection. Circulating tumor DNA (ctDNA) has gained much attention in recent years due to advantages over traditional technology, such as high sensitivity, high specificity, and noninvasive nature. Through the mechanism of apoptosis, necrosis, and circulating exosome release in tumor cells, ctDNA can spread throughout the circulatory system and carry modifications such as methylations, mutations, gene rearrangements, and microsatellite instability. Traditional gene-detection technology struggles to achieve real-time, low-cost, and portable ctDNA measurement, whereas electrochemical biosensors offer low cost, high specificity alongside sensitivity, and portability for the detection of ctDNA. Therefore, this review focuses on describing the recent advancements in ctDNA biomarkers for various cancer types and biosensor developments for real-time, noninvasive, and rapid ctDNA detection. Further in the review, ctDNA sensors are also discussed in regards to their selections of probes for receptors based on the electrode surface recognition elements.

Pembrolizumab for advanced urothelial carcinoma: exploratory ctDNA biomarker analyses of the KEYNOTE-361 phase 3 trial

Circulating tumor DNA (ctDNA) is emerging as a potential biomarker in early-stage urothelial cancer, but its utility in metastatic disease remains unknown. In the phase 3 KEYNOTE-361 study, pembrolizumab with and without chemotherapy was compared with chemotherapy alone in patients with metastatic urothelial cancer. The study did not meet prespecified efficacy thresholds for statistical significance. To identify potential biomarkers of response, we retrospectively evaluated the association of pre- and posttreatment ctDNA with clinical outcomes in a subset of patients who received pembrolizumab (n = 130) or chemotherapy (n = 130) in KEYNOTE-361. Baseline ctDNA was associated with best overall response (BOR; P = 0.009), progression-free survival (P < 0.001) and overall survival (OS; P < 0.001) for pembrolizumab but not for chemotherapy (all; P > 0.05). Chemotherapy induced larger ctDNA decreases from baseline to treatment cycle 2 than pembrolizumab; however, change with pembrolizumab (n = 87) was more associated with BOR (P = 4.39 × 10−5) and OS (P = 7.07 × 10−5) than chemotherapy (n = 102; BOR: P = 1.01 × 10−4; OS: P = 0.018). Tumor tissue-informed versions of ctDNA change metrics were most associated with clinical outcomes but did not show a statistically significant independent value for explaining OS beyond radiographic change by RECIST v.1.1 when jointly modeled (pembrolizumab P = 0.364; chemotherapy P = 0.823). These results suggest distinct patterns in early ctDNA changes with immunotherapy and chemotherapy and differences in their association with long-term outcomes, which provide preliminary insights into the utility of liquid biopsies for treatment monitoring in metastatic urothelial cancer. Clinical trial registration: NCT02853305.

Plasma ctDNA biomarker study in patients with non-small cell lung cancer with EGFR exon 20 insertion mutation treated with sunvozertinib.

8563 Background: There are limited reports on biomarker studies of non-small cell lung cancer (NSCLC) with epidermal growth factor receptor (EGFR) exon 20 insertion mutation (exon20ins). Sunvozertinib (DZD9008), an oral, potent, irreversible and selective EGFR tyrosine kinase inhibitor (TKI), has been granted conditional approval in China for the treatment of NSCLC with EGFR exon20ins in the ≥ second-line setting. Here we report biomarker analysis of EGFR exon20ins in large sample size, by pooling data from WU-KONG series of studies. Methods: Serial plasma ctDNA samples were collected from baseline until progressive disease (PD). Next generation sequencing was used to assess EGFR exon20ins in baseline plasma ctDNA, and to analyze genetic alterations in baseline and PD plasma ctDNA to identify potential resistance mechanisms to sunvozertinib. Droplet digital PCR was used to dynamically monitor the quantity of EGFR exon20ins during treatment. In addition, association between baseline EGFR exon20ins and disease characteristics as well as antitumor activity of sunvozertinib was analyzed. Furthermore, in vitro and in vivo experiments were performed to explore potential approach which may overcome the resistance to sunvozertinib. Results: A total of 121 patients were included in this biomarker analysis, among them 81 out of 121 (66.9%) had detectable EGFR exon20ins in baseline plasma ctDNA. There was a positive correlation between detectable EGFR exon20ins and higher number of metastasis sites. In addition, higher EGFR exon20ins abundance was positively correlated with more metastasis sites and brain metastasis. Patients with EGFR exon20ins negative in plasma ctDNA achieved a higher objective response rate (ORR) (68.0% vs. 45.8%) and longer median progression free survival (PFS) (7.4 months vs. 5.5 months) with sunvozertinib treatment. In patients with baseline detectable EGFR exon20ins, the mutant allele decreased over time with treatment in majority of patients (12/14, 85.7%), and the earliest clearance of EGFR exon20ins occurred after one week of treatment. In patients who developed disease progression, 12 of 18 (66.7%) maintained EGFR exon20ins at PD, and among them, 3 concurrently acquired EGFR C797S, all in cis with exon20ins. In addition, EGFR G724S and other genetic aberrations in EGFR downstream signaling pathway, were also detected. Exploratory work on overcoming resistance to sunvozertinib suggests that combination of golidocitinib, a selective JAK1 inhibitor, with chemotherapy could be a potential approach. Conclusions: This study showed that positive EGFR exon20ins in plasma ctDNA is associated with advanced disease characteristics. Sunvozertinib can effectively clear EGFR exon20ins in plasma ctDNA, confirming its direct effect on EGFR pathway. The resistance to sunvozertinib can be through EGFR-dependent and EGFR-independent mechanisms.

Abstract PO4-05-07: Differential dynamics of fragmentomic and epigenetic circulating tumor DNA (ctDNA) features in first-line Palbociclib and Ribociclib treatment for Hormone Receptor (HR) positive, HER2 negative metastatic breast cancer (MBC)

Abstract Background: Cyclin-dependent kinase inhibitors (CDK4/6i) in combination with endocrine therapy (ET) represent the cornerstone for the management of HR positive, HER2 negative MBC. However, the lack of prospective cohorts comparing the distinctions among palbociclib (PAL), ribociclib (RIB) and abemaciclib (ABE) poses a significant clinical knowledge gap. The aim of this ancillary analysis was to explore the differential clinical impact of CDK4/6i by leveraging new ctDNA biomarkers in a prospective clinical study. Methods: A total of 114 patients (pts) with HR positive, HER2 negative MBC were prospectively enrolled in the multicenter MAGNETIC.1 study (CRO-2018-56) from January 2018 to January 2023. At baseline (BL) and every 3 months (mos.), ctDNA samples were collected concurrently with radiological restaging. The samples were then analyzed through methylation-specific (MS) droplet digital PCR (ddPCR), ddPCR fragmentomics, and next generation sequencing. Matched pairs of variations were tested through Wilcoxon signed rank test, and survival was analyzed by log-rank test. Results: Out of the 114 pts enrolled, 59 received PAL, 48 RIB, and 16 ABE. In the de novo subgroup, 51.4 % of pts were treated with PAL, 42.9% with RIB, and 5.7% with ABE. Among the pts who received PAL, 7 harbored an ESR1 mutation at BL (D538G: 2, H377R: 1, Y537N: 1, Y537S: 3). Additionally,12 pts had PIK3CA mutations, and 2 pts had AKT1 mutations. In the RIB group, 5 and 2 pts, respectively, had a PIK3CA- and AKT-mutated MBC, while no ESR1 mutations were detected. When comparing matched pairs of variations, it was found that at BL, at first radiological restaging (T1), and at 6 mos. after initiation of CDK4/6i (T2), only PAL showed significantly higher levels of promoter A and B methylation (promA and promB) at T1 (P = 0.0005 and P = 0.0056, respectively for promA and promB), A significant decrease in promA and promB levels was detected at T2 for PAL (P = 0.0005 and P &amp;lt; 0.0001 respectively for promA and promB) but not for RIB. Both PAL and RIB demonstrated a significant decrease in ctDNA short fragments at T1 (P = 0.0263 for PAL and P = 0.0001 for RIB), However, PAL showed a significant rebound at T2, with an increase in 80% of samples (P = 0.0014). The same was not seen with RIB. After a median follow-up of 34.8 mos., there were no significant differences between PAL and RIB in terms of PFS (P= 0.2573) and OS (P= 0.3783). The PFS rates at 12 and 24 mos. were 69% and 48% for PAL, and 76% and 64% for RIB. The OS rates at 12 and 24 mos. were 94% and 84% for PAL, compared to 97% and 82% of RIB, respectively. Conclusions This analysis of MAGNETIC.1 highlighted significant differences in ctDNA biomarkers between palbociclib and ribociclib, suggesting their potential impact on the development of endocrine resistance. Further biomarker-driven clinical trials leveraging this concept are needed to refine the sequencing algorithms for CDK4/6i. Citation Format: Claudia Noto, Linda Cucciniello, Elisabetta Molteni, Silvia Bolzonello, Alessandra Franzoni, Lucia Da Ros, Silvia Buriolla, Arianna Dri, Lorenzo Foffano, Simon Spazzapan, Stefania Russo, Brenno Pastò, Giulia Cudia, Giada Targato, Serena Della Rossa, Marta Bonotto, Alessandro Marco Minisini, Giuseppe Damante, Barbara Belletti, Lorenzo Gerratana, Fabio Puglisi. Differential dynamics of fragmentomic and epigenetic circulating tumor DNA (ctDNA) features in first-line Palbociclib and Ribociclib treatment for Hormone Receptor (HR) positive, HER2 negative metastatic breast cancer (MBC) [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-05-07.

Abstract 5145: Association of a ctDNA biomarker of treatment response with clinical outcomes in a real-world pan-cancer cohort treated with tyrosine kinase inhibitors

Abstract Clinical evidence suggests that early changes in circulating tumor DNA tumor fraction (ctDNA TF) is predictive of patient response to immune checkpoint inhibitors, but the extent to which this approach can be used for patients on Tyrosine Kinase Inhibitors (TKIs) is not known. Here, we use xF Monitor to estimate ctDNA TF in patients that received TKIs and show that changes in circulating TF correlate with outcomes in a real-world pan-cancer cohort. Tempus xF Monitor is a ctDNA assay that measures quantitative molecular changes in ctDNA TF by utilizing diverse genomic events, dynamically weighting somatic variant allele frequencies and copy number variants, while using germline information to inform these estimates and providing single nucleotide variant (SNV) results on 105 genes. Molecular responders (MR) were defined as patients with ≥50% reduction in ctDNA TF between baseline and on-treatment time points, consistent with our previously established threshold. Deidentified patient records from the Tempus multimodal database were analyzed if patients had an xF test ≤ 15 weeks prior to the start of their first TKI regimen and an xF test 15 -180 days post-TKI initiation. Patients received TKI agents as classified in the Tempus Medical Ontology, which assigns a unique ID to key clinical concepts, validated and harmonized across industry standard terminologies. The TKI list was further validated using the NCI Metathesaurus (https://ncim.nci.nih.gov/ncimbrowser/) TKI concept (NCI Code C1967). Clinical endpoints were defined from TKI start to the first progression event or death (rwPFS) or death (rwOS), both censored on the last follow-up in event-free patients. Kaplan Meier analysis and Cox proportional hazard models were fitted to compare MR status and survival outcomes on TKI. The evaluable pan-cancer cohort N=69, median age = 61.5 yo, advanced/metastatic disease = 72%, 65% were female, consisted of &amp;gt; 10 cancer diagnoses (35% NSCLC, 26% BC), 41% 1L. In this cohort, 49% of patients received a TKI combination regimen, 21% with CT, 18% with ICI. 68% of patients with NGS testing received matched targeted mutation therapies based on NCCN guidelines. Patients classified as MR based on xF Monitor results had improved survival outcomes with a median rwOS of 951 days (vs 439 days for non-MRs). MR patients had significantly longer rwPFS (HR = 0.383, p = 0.005, CI = 0.12 - 0.75) and rwOS (HR = 0.205, p = 0.004, CI = 0.07 - 0.61) than non-MRs. xF Monitor is a novel tumor naive serial quantitative ctDNA TF algorithm off the Tempus xF assay that has the potential to be used clinically as a monitoring biomarker to stratify patients who are likely to benefit from TKI therapy. xF monitor can be used as a strategy to identify patients at a high risk of progression who could benefit from early switch or intensifying therapy. Results need to be prospectively validated in a larger cohort. Citation Format: Akash Mitra, John Guittar, Regina Schwind, Terri Driessen, Matthew Berginski, Christine Lo, Michelle M. Stein, Jonathan Freaney, Seung Won Hyun, Chithra Sangli, Kate Sasser, Halla Nimeiri, Aadel Chaudhuri. Association of a ctDNA biomarker of treatment response with clinical outcomes in a real-world pan-cancer cohort treated with tyrosine kinase inhibitors [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 5145.

Abstract 3670: Reducing the patient burden for ctDNA biomarkers: Advancing small volume home-based collection technologies

Abstract There is broad consensus from regulatory agencies, clinicians and patients for the need to move to decentralized trials while focusing on patient-centric approaches with the COVID-19 pandemic being the catalyst. This requires the development of new sample collection capabilities and workflows to ensure that the necessary biomarkers can be measured. Circulating tumor DNA (ctDNA) has become an increasingly important biomarker for cancer detection and genetics, and monitoring patients during treatment. Typical measurements of ctDNA involve venous draws of &amp;gt;10mls of whole blood that require patients to be in clinic. Here, we test the feasibility of using a new collection device, Tasso+, to collect capillary blood for ctDNA analysis using the Guardant360 panel. A pilot of whole blood microsamples (&amp;lt; 1 mL) with a cfDNA yield of 0.7-1.4 ng/ml spiked to 0.5% MAF with Seraseq ctDNA reference material. This resulted in detection of ~20% of the total expected variants across variant classes showing the feasibility of using the G360 panel to detect low volume/low MAF samples. Initial testing of Tasso+ collected samples revealed a 5-10x increase in high MW gDNA compared to traditional venipuncture. SPRI bead-based size selection was used in the extraction protocol to remove &amp;gt;95% of the high MW DNA, resulting in a 35% loss of target cfDNA fraction. Traditional venipuncture samples and Tasso+ samples were collected from 5 cancer patients and run using the G360 platform. Microsamples detected 75% of the variants across all variant classes found in venipuncture samples. Tasso+ lost sensitivity of variants when the MAF was &amp;lt;0.5%. To expand usage of Tasso+ to at-home collection of blood for ctDNA analysis, we sought to determine if lyophilization of the Streck DNA BCT RUO tube reagent could still provide stability to samples and a potential framework for at-home collections. Venipuncture and Tasso+ samples were collected from control patients, pooled and spiked with Seraseq cfDNA reference material. Samples were aliquoted into standard liquid Streck tubes or tubes with lyophilized reagent at the concentration per manufacturer’s directions and evaluated for stability over time. The Tasso+ samples with a target MAF between 0.5%-2.0% detected ~26% of all variants compared to the standard samples with a similar MAF. Lyophilization of the Streck reagent had minimal effect (&amp;lt;20% reduction in variants detected) on the reagent’s performance as there were approximately an equal number of total variants detected when comparing liquid and lyophilized samples for both the standard tubes and Tasso+ samples. Overall, these results provide support and a framework for using a home-based patient-centric sampling approach for monitoring ctDNA from cancer patients in clinical development. Citation Format: Brad R. Evans, Robert J. Foley, Steven M. Townson, Emily J. Welch, Kevin P. Bateman. Reducing the patient burden for ctDNA biomarkers: Advancing small volume home-based collection technologies [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 3670.

Abstract 3706: Single cell and cell-free nucleic acid analyses of liquid biopsy specimens from a blood collection tube using a new droplet digital PCR system

Abstract Introduction: Liquid biopsy-based testing has increasingly been adopted by oncologists for biomarker-driven diagnostics, therapy selection, and patient monitoring. Unlike tissue-based approaches, the target analytes in blood specimens are often rare events that must be discriminated from a background of non-tumor derived material. Droplet digital PCR (ddPCR) is an ideal platform for detection of rare nucleic acid markers in the clinic, because it is highly sensitive and specific, robust, and quantitative. Additionally, the workflow is simple to adopt and execute. The QX600 System is a new ddPCR instrument designed for advanced multiplexing which enables simultaneous detection of up to 6 unique fluorophores in a single well. This capability can decrease the sub-sampling needed for detection of multiple analytes. The objective of our study was to develop multiplexed ddPCR assays for detection of cell-based and cell-free circulating biomarkers from a single tube of whole blood. Methods: Tumor cells were enriched from the buffy coat fraction of whole blood collected in fixative-containing cfDNA BCT based on size and morphology using a microfluidics-based system. Enriched tumor cells were enumerated by immunofluorescence (DAPI+/Pan-CK+/CD45-), and gene expression was measured using the QX600 for a panel of cytokeratins (CK) and PD-L1 in CTC negative, NSCLC donor specimens (n=8). Results were compared to CTC positive, contrived specimens (whole blood spiked with breast tumor cell line MCF7 cells; n=5). For ctDNA analysis of the plasma fraction, a multiplexed ddPCR assay was designed to test for five actionable mutations prevalent in NSCLC, including EGFR del19, L858R, T790M, KRAS G12C, BRAF V600E, and wildtype EGFR. To evaluate performance of the multiplexed assay, concordance evaluation was conducted using cfDNA from 8 mutation-positive NSCLC donors on the QX600 and compared to single assays run on the QX200 system. Results: CK8 and CK19 were differentially expressed in the cells enriched from the CTC negative NSCLC cohort as compared to the contrived positives (p=0.0058, and p=0.0049, respectively). All the NSCLC cfDNA samples were positive for the reference variant, and linear regression analysis of the minor variant frequency for ctDNA biomarkers showed good concordance between QX systems (R2=0.8847). Conclusions: These studies demonstrate proof of concept for single cell and cell-free analysis from a single blood draw into a cfDNA BCT using the QX600 system. Liquid biopsy analysis of CTCs and ctDNA can enable minimally invasive, comprehensive decision making in the diagnostic workup of patients. Future studies will focus on further optimizing the cell enrichment methodology from cfDNA BCT and development of additional multiplexed ddPCR assays for NSCLC-relevant biomarkers on the QX600. Citation Format: Leisa Jackson, Colin Cochran, Claire Gould, Sarah Kreston, Jazmin Bello, Brittany D’Alessio, Janice Riley, Alisa Tubbs, Gary A. Pestano. Single cell and cell-free nucleic acid analyses of liquid biopsy specimens from a blood collection tube using a new droplet digital PCR system [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 3706.

Circulating tumor DNA and its role in detection, prognosis and therapeutics of hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is considered the fifth most prevalent cancer among all types of cancers and has the third most morbidity value. It has the most frequent duplication time and a high recurrence rate. Recently, the most unique technique used is liquid biopsies, which carry many markers; the most prominent is circulating tumor DNA (ctDNA). Varied methods are used to investigate ctDNA, including various forms of polymerase chain reaction (PCR) [emulsion PCR (ePCR), digital PCR (dPCR), and bead, emulsion, amplification, magnetic (BEAMing) PCR]. Hence ctDNA is being recognized as a potential biomarker that permits early cancer detection, treatment monitoring, and predictive data on tumor burden are subjective to therapy or surgery. Numerous ctDNA biomarkers have been investigated based on their alterations such as 1) single nucleotide variations (either insertion or deletion of a nucleotide) markers including TP53, KRAS, and CCND1; 2) copy number variations which include markers such as CDK6, EFGR, MYC and BRAF; 3) DNA methylation (RASSF1A, SEPT9, KMT2C and CCNA2); 4) homozygous mutation includes ctDNA markers as CDKN2A, AXIN1; and 5) gain or loss of function of the genes, particularly for HCC. Various researchers have conducted many studies and gotten fruitful results. Still, there are some drawbacks to ctDNA namely low quantity, fragment heterogeneity, less stability, limited mutant copies and standards, and differential sensitivity. However, plenty of investigations demonstrate ctDNA's significance as a polyvalent biomarker for cancer and can be viewed as a future diagnostic, prognostic and therapeutic agent. This article overviews many conditions in genetic changes linked to the onset and development of HCC, such as dysregulated signaling pathways, somatic mutations, single-nucleotide polymorphisms, and genomic instability. Additionally, efforts are also made to develop treatments for HCC that are molecularly targeted and to unravel some of the genetic pathways that facilitate its early identification.

Abstract 222: High frequency of structural variants in FFPE colorectal cancer tissue detected by targeting selected common fragile site genes and LINE transposable elements

Abstract Introduction: Structural variants (SVs) caused by chromosomal rearrangements or LINE retrotranspositions are a highly prevalent type of somatic DNA alterations in colorectal cancer (CRC). Studies about the function of SVs in tumor biology and their putative application as biomarkers are currently hampered by the need for fresh frozen tumor material to detect SVs by long-read or deep whole genome sequencing. This impedes the identification of SVs in retrospective cohorts and implementation in routine diagnostics (where only formalin-fixed paraffin-embedded (FFPE) tissue is available). In this study, we explored the applicability of FFPE-Targeted Locus Capture (FFPE-TLC) as a novel technology for targeted detection of SVs in CRC. Materials and methods: We defined the regions most frequently presenting SVs in CRC and included these in a customized capture panel. FFPE-TLC followed by targeted sequencing was performed on primary tumors of 29 metastatic CRC patients and eight patient-matched normal colon tissues. SV-specific droplet digital PCR (ddPCR) assays were designed for orthogonal validation of SVs in tumor tissue and detection of SVs in cell-free plasma circulating tumor DNA (ctDNA). Results: The regions associated with most SVs in metastatic CRC were four common fragile site (CFS) genes; MACROD2, PARK2, FHIT, WWOX, and three LINE source elements, and were included in a 2.7 Mb targeted panel. After filtering for germline variation, we identified 168 somatic SVs in 26/29 patients (90%), median SVs per patient: 3, range: 1-22. 110 SVs were found in CFS genes in 19/29 patients (66%), 12 of them presenting SVs in MACROD2. 58 SVs were caused by LINE integrations in 19/29 patients (66%), with different LINE behaviors observed: one source LINE generated 19 SVs in 13 patients, whilst another LINE caused 33 SVs in 5 patients. For selected cases, the tumor-specific origin of SVs was verified and its applicability as a plasma ctDNA biomarker demonstrated. Discussion: This study demonstrates, for the first time, the feasibility of targeted detection of SVs in CFS genes and SVs caused by LINE retrotransposition in routinely obtained FFPE tissue without prior knowledge of the breakpoint location. The high prevalence of SVs offers opportunities to detect many somatic alterations by targeting few genes and LINEs, e.g. for translation into ctDNA biomarker assays. We conclude that FFPE-TLC enables the investigation of SV mutations in retrospective cohorts and opens new avenues for mutation analysis in routine diagnostics. Citation Format: Carmen Rubio-Alarcon, Ellen Stelloo, Daan C. Vessies, Iris van ‘t Erve, Nienke Mekkes, Joost Swennenhuis, Soufyan Lakbir, Elise van Bree, Marianne Tijssen, Pien Delis-van Diemen, Mirthe Lanfermeijer, Theodora C. Linders, Daan van den Broek, Cornelis J. Punt, Jaap Heringa, Gerrit A. Meijer, Sanne Abeln, Harma Feitsma, Remond J. Fijneman. High frequency of structural variants in FFPE colorectal cancer tissue detected by targeting selected common fragile site genes and LINE transposable elements [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 222.

Lesion Shedding Model: unraveling site-specific contributions to ctDNA.

Sampling circulating tumor DNA (ctDNA) using liquid biopsies offers clinically important benefits for monitoring cancer progression. A single ctDNA sample represents a mixture of shed tumor DNA from all known and unknown lesions within a patient. Although shedding levels have been suggested to hold the key to identifying targetable lesions and uncovering treatment resistance mechanisms, the amount of DNA shed by any one specific lesion is still not well characterized. We designed the Lesion Shedding Model (LSM) to order lesions from the strongest to the poorest shedding for a given patient. By characterizing the lesion-specific ctDNA shedding levels, we can better understand the mechanisms of shedding and more accurately interpret ctDNA assays to improve their clinical impact. We verified the accuracy of the LSM under controlled conditions using a simulation approach as well as testing the model on three cancer patients. The LSM obtained an accurate partial order of the lesions according to their assigned shedding levels in simulations and its accuracy in identifying the top shedding lesion was not significantly impacted by number of lesions. Applying LSM to three cancer patients, we found that indeed there were lesions that consistently shed more than others into the patients' blood. In two of the patients, the top shedding lesion was one of the only clinically progressing lesions at the time of biopsy suggesting a connection between high ctDNA shedding and clinical progression. The LSM provides a much needed framework with which to understand ctDNA shedding and to accelerate discovery of ctDNA biomarkers. The LSM source code has been available in the IBM BioMedSciAI Github (https://github.com/BiomedSciAI/Geno4SD).

Abstract PD13-04: PD13-04 Exploratory subgroup and biomarker analyses of acelERA Breast Cancer: Phase II study of giredestrant (GDC-9545) vs physician’s choice of endocrine therapy for previously treated, estrogen receptor+, HER2– advanced breast cancer

Abstract BACKGROUND Endocrine therapy (ET) is the mainstay for management of estrogen receptor (ER)+ advanced breast cancer (aBC). Giredestrant is a highly potent, nonsteroidal, oral selective ER antagonist and degrader (SERD) that achieves robust ER occupancy. The Phase II randomized, open-label acelERA BC study (NCT04576455) evaluated giredestrant vs physician’s choice of ET (PCET) in the second- or third-line ER+, HER2– aBC setting. While the study did not reach statistical significance for its primary endpoint of investigator-assessed progression-free survival (INV-PFS), the giredestrant arm demonstrated a numerical improvement vs the PCET arm, with a hazard ratio of 0.81 (95% confidence interval: 0.60, 1.10), and encouraging results for key secondary efficacy endpoints (clinical benefit rate [CBR]: 32% vs 21%, respectively; objective response rate [ORR]: 13% vs 7%, respectively). We report exploratory subgroup analyses of these efficacy endpoints by prior treatments and by baseline circulating tumor (ct)DNA biomarkers. METHODS Patients were post- and pre- or peri-menopausal women, or men, with ER+, HER2– aBC who had progressed after 1–2 lines of systemic therapy in the advanced setting (≤1 targeted agent; ≤1 chemotherapy regimen; prior fulvestrant allowed). Randomization was 1:1 to giredestrant (30 mg oral daily) or PCET between fulvestrant or an aromatase inhibitor (AI), stratified by disease site (visceral vs non-visceral), prior CDK4/6 inhibitor, and prior fulvestrant. Biomarkers were assessed in baseline ctDNA isolated from plasma using the FoundationOne Liquid CDx or PredicineCARE assays. ESR1 mutations were defined as short variants with known or likely impact on ER protein function. RESULTS Among the 303 patients enrolled, prior aBC therapies included CDK4/6 inhibitors (42%), fulvestrant (19%), and chemotherapy (32%). Overall, most baseline characteristics were balanced across arms in subgroups. Efficacy in key subgroups by prior treatment and in ESR1-mutated tumors is shown in the table. Efficacy by PCET (75% received fulvestrant; 25%, an AI) and by type of ESR1 mutation will be presented. Clinical benefit (INV-PFS, CBR, ORR) was most prominently observed with giredestrant in patients with ESR1-mutated tumors. In the baseline ctDNA-evaluable population (232/303 patients; 77%), ESR1 and PIK3CA were the most prevalent mutations overall (39% and 36%, respectively). The most common ESR1 mutations were D538G, Y537S, Y537N, and E380Q; 54% of baseline ctDNA samples classified as ESR1-mutated had multiple ESR1 mutations detected (range of 2–7 mutations), demonstrating clonal heterogeneity. Clinical benefit was also observed with giredestrant in patients expressing different ESR1 mutations. Updated data will be presented. CONCLUSIONS Exploratory subgroup analyses showed favorable outcomes with giredestrant in terms of INV-PFS, CBR, and ORR across most key subgroups. The benefit was more pronounced in a) patients with ESR1-mutated tumors and b) patients who received prior fulvestrant (the majority of AI-treated patients in the PCET arm). Overall, these data support continued investigation of giredestrant to advance and improve treatment outcomes in hormone receptor+ BC. Table 1: Exploratory subgroup analyses Citation Format: Elgene Lim, Marianna Chavez, Aditya Bardia, Joo Hyuk Sohn, Heather M. Moore, Mahesh Shivhare, Jorge Martinalbo, Laura Roncoroni, Pablo D. Perez-Moreno, Miguel Martín. PD13-04 Exploratory subgroup and biomarker analyses of acelERA Breast Cancer: Phase II study of giredestrant (GDC-9545) vs physician’s choice of endocrine therapy for previously treated, estrogen receptor+, HER2– advanced breast cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD13-04.

OA01.08 Clinical Response to Tepotinib According to Circulating Tumor (ct)DNA Biomarkers in Patients with Advanced/Metastatic NSCLC with High-level MET Amplification (METamp) Detected by Liquid Biopsy (LBx)

OA01.08 Clinical Response to Tepotinib According to Circulating Tumor (ct)DNA Biomarkers in Patients with Advanced/Metastatic NSCLC with High-level MET Amplification (METamp) Detected by Liquid Biopsy (LBx)

Septin9 DNA methylation as a promising biomarker for cervical cancer

Aberrant Septin9 methylation in cervical cancer has been rarely studied. We aimed to identify its diagnostic value in cervical cancer using cervical scrapings, and its predictive potential in plasma for pelvic nodal metastasis of cervical cancer. The statuses of methylated Septin9 in fresh cervical lesions and cervical scrapings were first evaluated by using quantitative methylation-specific PCR. Subsequently, the relationship between Septin9 methylation in 113 plasma samples and pelvic nodal metastasis of cervical cancer was evaluated. Methylated Septin9 was detected in all cancerous tissues, but not in cervicitis. The degrees of Septin9 methylation increased with growing severity of cervical lesions in cervical scrapings. The sensitivity of methylated Septin9 was lower than that of cytology, while it yielded a high specificity and area under the curve in detecting high-grade squamous intraepithelial lesion or cervical cancer; and when Septin9 methylation combined with HPV16/18 genotyping, the sensitivity would increase from 70.42% to 82.39%. Plasma-based Septin9 methylation had a high discriminatory power in predicting pelvic nodal metastasis of cervical cancer, with an optimal specificity of 81.48%. In conclusion, we demonstrated methylated Septin9 to be an innovative diagnostic biomarker for cervical cancer and its non-invasive predictive potential in plasma for pelvic nodal metastasis of cervical cancer. Impact statement What is already known on this subject? The occurrence of cervical cancer is related to Septin9 methylation. In fresh specimens and cervical scrapings, we found the degrees of methylated Septin9 increased with growing severity of cervical lesions. Compared with HPV16/18 genotyping and cytological detection, Septin9 methylation had a better specificity and AUC in detecting ≥ HSIL. Furthermore, plasma-based Septin9 methylation also had a high specificity for pelvic lymphatic metastasis prediction. What the results of this study add? Methylation analysis of Septin9 indicated a similar sensitivity, specificity and AUC in detecting ≥ HSIL, relative to HPV16/18 genotyping. Compared with cytological method, Septin9 methylation also yielded a higher specificity and AUC in detecting ≥ HSIL. And we also found plasma-based Septin9 methylation had a high discriminatory power in predicting pelvic nodal metastasis of cervical cancer, with an optimal specificity of 81.48%; additionally an increasing sensitivity from 50% to nearly 80% was found when combined with SCCAg. What the implications are of these findings for clinical practice and/or further research? This study aimed to evaluate the relationship between Septin9 methylation and cervical cancer, and to explore the value of methylated Septin9 in the detection of cervical (pre)cancerous lesions. Moreover, we would explore plasma-based ctDNA biomarkers for pelvic lymphatic metastasis prediction of cervical cancer, to improve non-invasive predictive accuracy of pelvic nodal metastasis and reduce the complications caused by pelvic lymphadenectomy.

Circulating Tumor DNA as a Biomarker for Monitoring Patients with Solid Cancers: Comparison with Standard Protein Biomarkers.

Protein-based biomarkers are widely used in monitoring patients with diagnosed cancer. These biomarkers however, lack specificity for cancer and have poor sensitivity in detecting early recurrences and monitoring therapy effectiveness. Emerging data suggest that the use of circulating tumor DNA (ctDNA) has several advantages over standard biomarkers. Following curative-intent surgery for cancer, the presence of ctDNA is highly predictive of early disease recurrence, while in metastatic cancer an early decline in ctDNA following the initiation of treatment is predictive of good outcome. Compared with protein biomarkers, ctDNA provides greater cancer specificity and sensitivity for detecting early recurrent/metastatic disease. Thus, in patients with surgically resected colorectal cancer, multiple studies have shown that ctDNA is superior to carcinoembryonic antigen (CEA) in detecting residual disease and early recurrence. Similarly, in breast cancer, ctDNA was shown to be more accurate than carbohydrate antigen 15-3 (CA 15-3) in detecting early recurrences. Other advantages of ctDNA over protein biomarkers in monitoring cancer patients include a shorter half-life in plasma and an ability to predict likely response to specific therapies and identify mechanisms of therapy resistance. However, in contrast to proteins, ctDNA biomarkers are more expensive to measure, less widely available, and have longer turnaround times for reporting. Furthermore, ctDNA assays are less well standardized. Because of their advantages, it is likely that ctDNA measurements will enter clinical use in the future, where they will complement existing biomarkers and imaging in managing patients with cancer. Hopefully, these combined approaches will lead to a better outcome for patients.

Detection of methylated BCAT1 and IKZF1 after curative-intent treatment as a prognostic indicator for colorectal cancer recurrence.

The risk of recurrence after completion of curative-intent treatment of colorectal cancer (CRC) is hard to predict. Post-treatment assaying for circulating tumor DNA (ctDNA) is an encouraging approach for stratifying patients for therapy, but the prognostic value of this approach is less explored. This study aimed to determine if detection of methylated BCAT1 and IKZF1 following completion of initial treatment identified patients with a poorer recurrence-free survival (RFS). 142 CRC stage I-III cases with at least 2 years of follow up (unless recurrence was evident sooner) and a methylated BCAT1/IKZF1 test result between 2 weeks and 12 months after completion of initial treatment were eligible for study inclusion. The association between BCAT1/IKZF1 and RFS was assessed by the log-rank (Mantel-Cox) method. Cox proportional hazard regression analysis was used for multivariable survival analysis. Thirty-three (23.2%) had recurrence at a median 1.6y (interquartile range: 0.8-2.4). Methylated BCAT1/IKZF1 was detected in 19 of the 142 patients (13.4%) and was associated with a significant risk of recurrence (hazard ratio [HR] 5.7, 95%CI: 1.9-17.3, p=0.002). Three-year RFS for patients with or without detectable methylated BCAT1/IKZF1 was 56.5% and 83.3%, respectively. Multivariable analysis showed that detection of methylated BCAT1/IKZF1 (HR=2.6, p=0.049) and site of the primary tumor (HR=4.2, p=0.002) were the only significant prognostic indicators of poor RFS. BCAT1/IKZF1 methylation testing after curative-intent treatment is an independent prognostic indicator for RFS and identifies a subgroup at high risk. Personalized surveillance is warranted for patients with these ctDNA biomarkers detectable after curative-intent treatment.