Circulating tumor DNA association with residual cancer burden after neoadjuvant chemotherapy in triple-negative breast cancer in TBCRC 030

Incorporating radiomic MRI models for presurgical response assessment in patients with early breast cancer undergoing neoadjuvant systemic therapy: Collaborative insights from breast oncologists and radiologists

The assessment of neoadjuvant treatment's response is critical for selecting the most suitable therapeutic options for patients with breast cancer to reduce the need for invasive local therapies. Breast magnetic resonance imaging (MRI) is so far one of the most accurate approaches for assessing pathological complete response, although this is limited by the qualitative and subjective nature of radiologists' assessment, often making it insufficient for deciding whether to forgo additional locoregional therapy measures. To increase the accuracy and prediction of radiomic MRI with the aid of machine learning models and deep learning methods, as part of artificial intelligence, have been used to analyse the different subtypes of breast cancer and the specific changes observed before and after therapy. This review discusses recent advancements in radiomic MRI models for presurgical response assessment for patients with early breast cancer receiving preoperative treatments, with a focus on their implications for clinical practice.

DirectHRD enables sensitive scar-based classification of homologous recombination deficiency

Homologous recombination deficiency (HRD) is a predictive biomarker for efficacy of PARP (poly ADP-ribose polymerase) inhibition and platinum chemotherapy for cancer patients but remains challenging to detect. The discovery of patients without pathogenic mutations in known HR genes but exhibiting genomic scars indicative of HRD led to the FDA approval of the first scar-based HRD test. Despite advancements in whole genome sequencing (WGS) and integration of large training datasets with machine learning models, current methods lack the sensitivity required for detecting HRD scars in low tumor purity samples, especially in liquid biopsies. Here, we describe DirectHRD, a genomic scar-based HRD classifier based on WGS. Compared to other WGS-based methods, DirectHRD exclusively utilizes a highly specific type of HRD scar-small deletions with microhomology-and its associated signatures in a probabilistic framework. We applied DirectHRD to 501 tumor and 90 cell-free DNA (cfDNA) samples from 4 cancer types: breast, ovarian, prostate, and pancreas. Among all 501 tumor biopsies, DirectHRD achieved 100% detection of HRD with high specificity (>90%). Across all 90 cfDNA samples, the method achieved an area under the curve of 0.87 and demonstrated the ability to detect HRD at tumor fractions as low as 1%, making it 10 times more sensitive than state-of-the-art methods.

Ultrasensitive Detection and Monitoring of Circulating Tumor DNA Using Structural Variants in Early-Stage Breast Cancer

PURPOSE

The detection of circulating tumor DNA (ctDNA) after curative-intent therapy in early-stage breast cancer is highly prognostic of disease recurrence. Current ctDNA assays, mainly targeting single-nucleotide variants, vary in sensitivity and specificity. Although increasing the number of single-nucleotide variants in tumor-informed assays improves sensitivity, structural variants (SV) may achieve similar or better sensitivity without compromising specificity. SVs occur across all cancers, linked to genomic instability and tumorigenesis, with unique tumor- and patient-specific breakpoints occurring throughout the genome. SVs in breast cancer are underexplored, and their potential for ctDNA detection and monitoring has not been fully evaluated.

EXPERIMENTAL DESIGN

We retrospectively analyzed a tumor-informed SV-based ctDNA assay in a cohort of patients with early-stage breast cancer (n = 100, 568 timepoints) receiving neoadjuvant systemic therapy, evaluating ctDNA dynamics and lead times to clinical recurrence in the postoperative period.

RESULTS

ctDNA was detected in 96% (91/95) of participants at baseline with a median variant allele frequency of 0.15% (range: 0.0011%-38.7%); of these, 10% (9/91) had a variant allele frequency <0.01%. ctDNA detection at cycle 2 (C2) of neoadjuvant therapy was associated with a higher likelihood of distant recurrence (log-rank P = 0.047) and enhanced residual cancer burden prognostication (log-rank P = 0.041). ctDNA was detected prior to distant recurrence in all cases (100% sensitivity) with a median lead time of 417 days (range: 4-1,931 days).

CONCLUSIONS

These results demonstrate the clinical validity of ultrasensitive ctDNA detection and monitoring using SVs. Prospective trials are required to evaluate ctDNA-guided treatment strategies.

Dynamic ctDNA tracking stratifies relapse risk for triple negative breast cancer patients receiving neoadjuvant chemotherapy

Early Triple negative breast cancer (eTNBC) is the subtype with the worst outcome. Circulating tumor DNA (ctDNA) is shown to predict the prognosis of breast cancer, but its utility in eTNBC remains unclear. 130 stage II-III female eTNBC patients receiving neoadjuvant chemotherapy (NAC) have been enrolled prospectively and subjected to ctDNA analysis. ctDNA at post-NAC (pre-surgery) and post-surgery, but not at baseline, is associated with worse prognosis. A threshold of 1.1% maximum variant allele frequency at baseline stratifies patients with different relapse risk, which is validated internally and externally. A systemic tumor burden model integrating baseline and post-surgery ctDNA is independently prognostic (p = 0.022). Combining systemic tumor burden with pathologic response identifies a highly curable subgroup and a subgroup of high-risk eTNBC patients. ctDNA surveillance during follow-up identifies patients with high relapse risk. In conclusion, systemic ctDNA analysis demonstrates the utility of a systemic tumor burden model of ctDNA in risk stratification of eTNBC patients, which may guide future treatment escalation or de-escalation trials.

Role of circulating tumor DNA in early-stage triple-negative breast cancer: a systematic review and meta-analysis

BACKGROUND

Triple-negative breast cancer (TNBC) accounts for 15% of all breast cancers and carries a worse prognosis relative to other breast cancer subtypes. This systematic review and meta-analysis evaluated the prognostic value of circulating tumor DNA (ctDNA) in early-stage TNBC.

METHODS

A literature search was conducted using Ovid Medline, Elsevier EMBASE, Cochrane Central Register of Controlled Trials, and Web of Science Databases for publications up to 11/16/2023. Results were uploaded to Covidence and assessed by two independent reviewers. Studies assessing the use of ctDNA to predict recurrence free survival and related outcomes as well as overall survival were included. All recurrence outcomes were combined during analysis. Statistical analysis was performed using Revman Web. Log-hazard ratios (HR) were pooled for studies reporting recurrence and death as a time-to-event outcomes. Odds ratios (OR) were calculated and pooled for studies reporting patient-level data on recurrence, death, and pathological complete response (pCR). Prospero ID: CRD42023492529.

RESULTS

A total of 3,526 publications were identified through our literature search, and 20 publications (n = 1202 patients) were included in the meta-analysis. In studies that reported recurrence as a time-to-event outcome, post-neoadjuvant (before or after surgery) ctDNA + status was associated with a higher likelihood of disease recurrence (HR 4.12, 95% confidence interval [CI] 2.81-6.04). For studies that reported patient-level data, post-neoadjuvant ctDNA + status was associated with higher odds of disease recurrence (OR 6.72, 95% CI 3.61-12.54). Pooled log-HR also revealed that ctDNA + status in the post-neoadjuvant setting (before or after surgery) was associated with worse overall survival (HR 3.26, 95% CI 1.88-5.63).

CONCLUSIONS

Our findings suggest that ctDNA could be used as a prognostic biomarker to anticipate the risk of relapse. However, it remains unclear if therapeutic intervention for patients who are ctDNA + can improve outcomes. While more studies are needed before incorporating ctDNA into clinical practice, the findings of this meta-analysis are reassuring and show the promise of ctDNA as a biomarker.

Immediate postoperative minimal residual disease detection with MAESTRO predicts recurrence and survival in head and neck cancer patients treated with surgery

Purpose

While circulating tumor DNA (ctDNA) is a promising biomarker for minimal residual disease (MRD) detection in head and neck squamous cell carcinoma (HNSCC), more sensitive assays are needed for accurate MRD detection at clinically-relevant timepoints. Ultrasensitive MRD detection immediately after surgery could guide adjuvant therapy decisions, but early ctDNA dynamics are poorly understood.

Experimental Design

We applied MAESTRO, a whole-genome, tumor-informed, mutation-enrichment sequencing assay, in a pooled testing format called MAESTRO-Pool, to plasma samples from HNSCC patients collected immediately after surgery and during surveillance. We evaluated whether early MRD detection could predict outcomes.

Results

Among 24 predominantly HPV-independent (95.8%) HNSCC patients, rapid ctDNA clearance occurred by the first postoperative sample (1-3 days postoperatively) in 9 patients without an event (recurrence or death). 13/15 patients with an event were MRD+ (PPV = 92.9%; NPV = 80%) with a median tumor fraction (TFx) of 54 ppm (range 6-1,177 ppm). In the first and last sample of the immediate postoperative window, 8/13 and 10/13 patients had TFx below 100 ppm, respectively, the detection limit of leading commercial assays. Early MRD detection correlated with worse overall survival (HR = 8.3; 95% CI: 1.1-66.1; P = 0.02) and event-free survival (HR = 27.4; 95% CI: 3.5-214.5; P < 0.0001) independent of high-risk pathology.

Conclusions

Immediate postoperative MRD detection by MAESTRO was predictive of recurrence and death. Given the ultralow TFxs observed, ultrasensitive assays will be essential for reliable MRD detection during early postoperative timepoints to enable personalized adjuvant therapy decision-making in HNSCC.

Multiple time points for detecting circulating tumor DNA to monitor the response to neoadjuvant therapy in breast cancer: a meta-analysis

BACKGROUND

Not all breast cancer (BC) patients can benefit from neoadjuvant therapy (NAT). A poor response may result in patients missing the best opportunity for treatment, ultimately leading to a poor prognosis. Thus, to identify an effective predictor that can assess and predict patient response at early time points, we focused on circulating tumor DNA (ctDNA), which is a vital noninvasive liquid biopsy biomarker. We performed a meta-analysis to explore the predictive value of response by monitoring ctDNA at four time points of NAT using pathologic complete response (pCR) and residual cancer burden (RCB).

METHODS

By searching Embase, PubMed, the Cochrane Library, and the Web of Science until December 24, 2023, we selected studies concerning the relationship between ctDNA and response or prognosis. We analysed the results at the following various time points: baseline (T0), first cycle of NAT (T1), mid-treatment (MT), and end of NAT (EOT). pCR and RCB were used to evaluate the response as the primary endpoint. The secondary endpoint was to investigate the relationship between ctDNA and prognosis. Odds ratios (ORs) and hazard ratios (HRs) were used as effect indicators.

RESULTS

Thirteen reports from twelve studies were eligible for inclusion in this meta-analysis. The results demonstrated that ctDNA negativity was associated with pCR at T1 (OR = 0.34; 95% CI: 0.21-0.57), MT (OR = 0.35; 95% CI: 0.20-0.60), and EOT (OR = 0.38; 95% CI: 0.22-0.66). When RCB was used to evaluate responses, ctDNA negativity was associated with RCB-0/I at the MT (OR = 0.34; 95% CI: 0.21-0.55) and EOT (OR = 0.26; 95% CI: 0.15-0.46). Furthermore, ctDNA positivity at T1 predicted a worse prognosis for patients (HR = 2.73; 95% CI: 1.29-5.75). We also performed a subgroup analysis to more accurately assess the predictive value of ctDNA for triple-negative breast cancer.

CONCLUSIONS

Our meta-analysis suggested that the ctDNA status at the early stage of NAT can predict patient response, which provides evidence for adjusting personalized treatment strategies and improving patient survival.

PROSPERO REGISTRATION NUMBER

CRD42024496465.

Impact of Higher Cell-Free DNA Yields on Liquid Biopsy Testing in Glioblastoma Patients

BACKGROUND

Minimally invasive molecular profiling using cell-free DNA (cfDNA) is increasingly important to the management of cancer patients; however, low sensitivity remains a major limitation, particularly for brain tumor patients. Transiently attenuating cfDNA clearance from the body-thereby, allowing more cfDNA to be sampled-has been proposed to improve the performance of liquid biopsy diagnostics. However, there is a paucity of clinical data on the effect of higher cfDNA recovery. Here, we investigated the impact of collecting greater quantities of cfDNA on circulating tumor DNA (ctDNA) sensitivity in the "low-shedding" cancer type glioblastoma by analyzing up to approximately 15-fold more plasma than routinely obtained clinically.

METHODS

We tested 70 plasma samples (median 17.0 mL, range 2.5-66.5) from 8 IDH-wild-type glioblastoma patients using an optimized version of the MAESTRO-Pool ctDNA assay. Results were compared with simulated single-blood-tube equivalents of cfDNA. ctDNA results were then compared with magnetic resonance imaging (MRI) and pathology assessments of true progression vs pseudoprogression in glioblastoma patients.

RESULTS

Larger cfDNA yields exhibited a doubling in ctDNA-positivity while achieving a median specificity of 99% and more precise ctDNA quantification. In 8 glioblastoma patients, ctDNA was detected in 88%, including at multiple timepoints in 6/7. In the setting of indeterminate progression by MRI, our data suggested that MAESTRO-Pool with large plasma volumes can help distinguish true glioblastoma progression from pseudoprogression.

CONCLUSIONS

Our findings provide a proof-of-principle that most glioblastomas shed ctDNA into plasma and that greater ctDNA yields could help improve liquid biopsies for "low-shedding" cancer types such as glioblastoma.

Minimal residual disease as a target for liquid biopsy in patients with solid tumours

Metastasis is the leading cause of cancer-related death in patients with solid tumours. Current imaging technologies are not sufficiently sensitive to detect minimal residual disease (MRD; also known as measurable or molecular residual disease) after initial surgery or chemotherapy, pointing to the need for more sensitive tests to detect remaining traces of cancer in the body. Liquid biopsy, or the analysis of tumour-derived or tumour-induced cells or cellular products in the blood or other body fluids, has opened a new diagnostic avenue to detect and monitor MRD. Liquid biopsy is already used in clinical decision making for patients with haematological malignancies. Here, we review current knowledge on the use of circulating tumour DNA (ctDNA) to detect and monitor MRD in patients with solid tumours. We also discuss how ctDNA-guided MRD detection and characterization could herald a new era of novel 'post-adjuvant therapies' with the potential to eliminate MRD and cure patients before terminal metastatic disease is evident on imaging.

Immunohistochemical Expression of Vitamin D Receptors (VDRs) and Estrogen Receptor Beta 1 (ERβ1) in Molecular Subtypes of Triple-Negative Breast Cancer Tumors: A Cross-Sectional Study

Introduction Breast cancer (BC) is still the most common malignancy among women globally, and triple-negative breast cancer (TNBC) presents major therapeutic and management issues due to its aggressive nature. Recent studies suggest that the vitamin D receptor (VDR) and estrogen receptor beta 1 (ERβ1) play crucial roles in regulating TNBC progression. Increased expression of VDR and ERβ1 has been linked to tumor suppression, highlighting their potential to impact cancer progression via various signaling pathways. This study analyzes VDR and ERβ1 expressions in TNBC subtypes to discover potential therapeutic targets and improve treatment outcomes for this challenging BC subtype. Method This cross-sectional study analyzed 30 invasive ductal carcinoma (IDC) cases of TNBC subtypes using formalin-fixed paraffin embedding (FFPE) tissues. Immunohistochemistry assessed cytoplasmic and nuclear VDR and ERβ1 expression, scoring staining intensity and extent, categorized as negative/low, moderate, or high expression. Results High VDR and ERβ1 expressions were analyzed across molecular subtypes of TNBC to explore their therapeutic potential, particularly in TNBC. In TNBC, a high VDR expression was observed in the cytoplasm (n = 10, 33.3%) and the nucleus (n = 2, 6.6%), with statistical significance (p < 0.042). Luminal A cases demonstrated high VDR expression in the cytoplasm (n = 6, 20%) and the nucleus (n = 2, 6.6%) (p < 0.042), while luminal B exhibited high VDR expression exclusively in the cytoplasm (n = 4, 13.3%) (p < 0.042). In HER2-enriched, high VDR expression was confined to the nucleus (n = 3, 10%) (p < 0.042). ERβ1 expression patterns in TNBC showed moderate cytoplasmic expression (n = 9, 50%) and high cytoplasmic expression (n = 1, 5.5%), with statistical significance (p < 0.025). By contrast, luminal A displayed moderate cytoplasmic expression (n = 3, 16.6%) and high cytoplasmic expression (n = 5, 27.7%) (p < 0.025). These findings suggest that VDR and ERβ1 exhibit subtype-specific expression patterns, with significant expression in TNBC, indicating their potential as therapeutic targets. Conclusion VDR and ERβ1 expressions differ between TNBC subtypes, indicating their potential as targeted therapies, particularly in TNBC.

Modulating cell-free DNA biology as the next frontier in liquid biopsies

Technical advances over the past two decades have enabled robust detection of cell-free DNA (cfDNA) in biological samples. Yet, higher clinical sensitivity is required to realize the full potential of liquid biopsies. This opinion article argues that to overcome current limitations, the abundance of informative cfDNA molecules - such as circulating tumor DNA (ctDNA) - collected in a sample needs to increase. To accomplish this, new methods to modulate the biological processes that govern cfDNA production, trafficking, and clearance in the body are needed, informed by a deeper understanding of cfDNA biology. Successful development of such methods could enable a major leap in the performance of liquid biopsies and vastly expand their utility across the spectrum of clinical care.

Factors Associated With Additional Axillary Disease in Patients With Positive Sentinel Lymph Nodes After Neoadjuvant Chemotherapy for Breast Cancer

Background: In previous studies, breast cancer patients with positive sentinel lymph node(s) (SLN) after neoadjuvant chemotherapy (NAC) frequently had additional nonSLN involvement. Per guidelines, residual SLN disease warrants completion axillary lymph node dissection (cALND), which has increased morbidity. Given recent improvements in NAC, we hypothesized that nonSLN positivity may be lower than previously reported for certain subgroups.Methods: We retrospectively reviewed breast cancer patients who received NAC and had positive lymph nodes on SLN biopsy or targeted axillary dissection and underwent cALND at one institution in 1/2018-8/2023. Associations between nonSLN positivity and clinicopathologic factors were assessed with Fisher's exact test and multivariable logistic regression.Results: There were 122 female patients. Median age was 48 years. Initially, 15 patients (12.3%) were cN0 and 107 patients (87.7%) were cN1. Largest SLN deposit was macrometastasis in 96 patients (78.7%), micrometastasis in 23 patients (18.9%), and isolated tumor cells in 3 patients (2.5%). Overall, 53 patients (43.4%) had nonSLN involvement. NonSLN positivity was higher in patients with cN1, ER+ HER2-, ypT2-3, SLN macrometastasis, and multiple positive SLN. On multivariable analysis, cN1 and ER+ HER2- remained associated with nonSLN positivity.Discussion: Among patients with positive SLN after NAC, clinically node positive and ER+ HER2- patients were more likely to have nonSLN involvement. Our findings support guidelines to consider omitting cALND in clinically node negative patients. With improving NAC, optimal axillary sampling, and radiation, omitting cALND may be safe in some clinically node positive triple negative or HER2+ patients with low volume residual disease, but further research is needed.

Pyrimidine-Dependent UV-Mediated Cross-Linking Magnifies Minor Genetic or Epigenetic Changes in Clinical Samples

BACKGROUND

Detection of minor DNA allele alterations is becoming increasingly important for early detection and monitoring of cancer. We describe a new method that uses ultraviolet light to eliminate wild-type DNA alleles and enables improved detection of minor genetic or epigenetic changes.

METHODS

Pyrimidine-dependent UV-based minor-allele enrichment (PD-UVME) employed oligonucleotide probes that incorporated a UVA-sensitive 3-cyanovinylcarbazole (CNVK), placed directly opposite interrogated pyrimidines, such as thymine (T) or cytosine (C) in wild-type (WT) DNA. Upon UVA-illumination, CNVK cross-linked with T/C, preventing subsequent amplification. Mutations that removed the T/C escaped cross-linking and were amplified and detected. Similarly, CNVK discriminated between methylated and unmethylated cytosine in CpG dinucleotides, enabling direct enrichment of unmethylated DNA targets. PD-UVME was combined with digital droplet PCR (ddPCR) to detect serine/threonine-protein kinase B-Raf (BRAF) V600E mutations in model systems, thyroid patient cancer tissue samples, and circulating DNA of tumor origin (ctDNA) from melanoma patients.

RESULTS

One thyroid cancer sample out of 9, and 6 circulating-DNA samples out of 7 were found to be BRAF V600E-positive via PD-UVME while classified as negative by conventional ddPCR. Positive samples via conventional ddPCR were also found positive via PD-UVME. All 10 circulating cell-free DNA (cfDNA) samples obtained from normal volunteers were negative via both approaches. Furthermore, preferential enrichment of unmethylated alleles in MAGEA1 promoters using PD-UVME was demonstrated.

CONCLUSIONS

PD-UVME mutation/methylation enrichment performed prior to ddPCR magnifies low-level mutations or epigenetic changes and increases sensitivity and confidence in the results. It can assist with clinical decisions that hinge on the presence of trace alterations like BRAF V600E.

Longitudinal dynamics of circulating tumor DNA for treatment monitoring in patients with breast cancer recurrence

The prevalence and dynamics of circulating tumor DNA (ctDNA) in patients with breast cancer recurrence or de novo metastatic cancer were examined in a retrospective analysis of a prospective observational cohort. Twenty-three recurrent/metastatic breast cancer cases (8 locoregional, 15 distant metastasis) were enrolled, and sequential plasma samples were obtained. Anchor mutations were selected from the target sequencing of each patient's primary and/or metastatic tumor. An in-house developed assay (UHS assay) was employed for a tumor-informed ctDNA assay during treatment and follow-up. A median of three (range 1-5) anchor mutations per case were applied for ctDNA detection. ctDNA was detected in 14 (63.6%, 14/22) cases at the time of enrollment and 18 (78.5%, 18/23) cases during follow-up. More anchor mutations and higher tumor burden were significantly related to higher ctDNA positive rates (p-value 0.036, 0.043, respectively). The mean enriched variant allele frequency (eVAF) at each time point was significantly higher for stable or progressive disease responses (ANOVA test p-value < 0.001). Eight patients showed an increase in their ctDNA eVAF prior to clinical progression with a mean lead time of 6.2 months (range 1.5-11 months). ctDNA dynamics measured using personalized assay reflected the clinical course of breast cancer recurrence.

Decoding the Dynamics of Circulating Tumor DNA in Liquid Biopsies

Circulating tumor DNA (ctDNA), a fragment of tumor DNA found in the bloodstream, has emerged as a revolutionary tool in cancer management. This review delves into the biology of ctDNA, examining release mechanisms, including necrosis, apoptosis, and active secretion, all of which offer information about the state and nature of the tumor. Comprehensive DNA profiling has been enabled by methods such as whole genome sequencing and methylation analysis. The low abundance of the ctDNA fraction makes alternative techniques, such as digital PCR and targeted next-generation exome sequencing, more valuable and accurate for mutation profiling and detection. There are numerous clinical applications for ctDNA analysis, including non-invasive liquid biopsies for minimal residual disease monitoring to detect cancer recurrence, personalized medicine by mutation profiling for targeted therapy identification, early cancer detection, and real-time evaluation of therapeutic response. Integrating ctDNA analysis into routine clinical practice creates promising avenues for successful and personalized cancer care, from diagnosis to treatment and follow-up.

Use of ctDNA in early breast cancer: analytical validity and clinical potential

Circulating free tumor DNA (ctDNA) analysis is gaining popularity in precision oncology, particularly in metastatic breast cancer, as it provides non-invasive, real-time tumor information to complement tissue biopsies, allowing for tailored treatment strategies and improved patient selection in clinical trials. Its use in early breast cancer has been limited so far, due to the relatively low sensitivity of available techniques in a setting characterized by lower levels of ctDNA shedding. However, advances in sequencing and bioinformatics, as well as the use of methylome profiles, have led to an increasing interest in the application of ctDNA analysis in early breast cancer, from screening to curative treatment evaluation and minimal residual disease (MRD) detection. With multiple prospective clinical trials in this setting, ctDNA evaluation may become useful in clinical practice. This article reviews the data regarding the analytical validity of the currently available tests for ctDNA detection and the clinical potential of ctDNA analysis in early breast cancer.

Bridging horizons beyond CIRCULATE-Japan: a new paradigm in molecular residual disease detection via whole genome sequencing-based circulating tumor DNA assay

Circulating tumor DNA (ctDNA) is the fraction of cell-free DNA in patient blood that originates from a tumor. Advances in DNA sequencing technologies and our understanding of the molecular biology of tumors have increased interest in exploiting ctDNA to facilitate detection of molecular residual disease (MRD). Analysis of ctDNA as a promising MRD biomarker of solid malignancies has a central role in precision medicine initiatives exemplified by our CIRCULATE-Japan project involving patients with resectable colorectal cancer. Notably, the project underscores the prognostic significance of the ctDNA status at 4 weeks post-surgery and its correlation to adjuvant therapy efficacy at interim analysis. This substantiates the hypothesis that MRD is a critical prognostic indicator of relapse in patients with colorectal cancer. Despite remarkable advancements, challenges endure, primarily attributable to the exceedingly low ctDNA concentration in peripheral blood, particularly in scenarios involving low tumor shedding and the intrinsic error rates of current sequencing technologies. These complications necessitate more sensitive and sophisticated assays to verify the clinical utility of MRD across all solid tumors. Whole genome sequencing (WGS)-based tumor-informed MRD assays have recently demonstrated the ability to detect ctDNA in the parts-per-million range. This review delineates the current landscape of MRD assays, highlighting WGS-based approaches as the forefront technique in ctDNA analysis. Additionally, it introduces our upcoming endeavor, WGS-based pan-cancer MRD detection via ctDNA, in our forthcoming project, SCRUM-Japan MONSTAR-SCREEN-3.

Priming agents transiently reduce the clearance of cell-free DNA to improve liquid biopsies

Liquid biopsies enable early detection and monitoring of diseases such as cancer, but their sensitivity remains limited by the scarcity of analytes such as cell-free DNA (cfDNA) in blood. Improvements to sensitivity have primarily relied on enhancing sequencing technology ex vivo. We sought to transiently augment the level of circulating tumor DNA (ctDNA) in a blood draw by attenuating its clearance in vivo. We report two intravenous priming agents given 1 to 2 hours before a blood draw to recover more ctDNA. Our priming agents consist of nanoparticles that act on the cells responsible for cfDNA clearance and DNA-binding antibodies that protect cfDNA. In tumor-bearing mice, they greatly increase the recovery of ctDNA and improve the sensitivity for detecting small tumors.

Circulating tumour mutation detection in triple-negative breast cancer as an adjunct to tissue response assessment

Circulating tumour DNA (ctDNA) detection via liquid biopsy is an emerging alternative to tissue biopsy, but its potential in treatment response monitoring and prognosis in triple negative breast cancer (TNBC) is not yet well understood. Here we determined the prevalence of actionable mutations detectable in ctDNA using a clinically validated cancer gene panel assay in patients with TNBC, without recurrence at the time of study entry. Sequencing of plasma DNA and validation of variants from 130 TNBC patients collected within 7 months of primary treatment completion revealed that 7.7% had detectable residual disease with a hotspot panel. Among neoadjuvant treated patients, we observed a trend where patients with incomplete pathologic response and positive ctDNA within 7 months of treatment completion were at much higher risk of reduced progression free survival. We propose that a high risk subset of early TNBC patients treated in neoadjuvant therapy protocols may be identifiable by combining tissue response and sensitive ctDNA detection.

Emerging ctDNA detection strategies in clinical cancer theranostics

Circulating tumor DNA (ctDNA) is naked DNA molecules shed from the tumor cells into the peripheral blood circulation. They contain tumor-specific gene mutations and other valuable information. ctDNA is considered to be one of the most significant analytes in liquid biopsies. Over the past decades, numerous researchers have developed various detection strategies to perform quantitative or qualitative ctDNA analysis, including PCR-based detection and sequencing-based detection. More and more studies have illustrated the great value of ctDNA as a biomarker in the diagnosis, prognosis and heterogeneity of tumor. In this review, we first outlined the development of digital PCR (dPCR)-based and next generation sequencing (NGS)-based ctDNA detection systems. Besides, we presented the introduction of the emerging ctDNA analysis strategies based on various biosensors, such as electrochemical biosensors, fluorescent biosensors, surface plasmon resonance and Raman spectroscopy, as well as their applications in the field of biomedicine. Finally, we summarized the essentials of the preceding discussions, and the existing challenges and prospects for the future are also involved.