ArticleEMBO molecular medicine2023
Comparison of tumor-informed and tumor-naïve sequencing assays for ctDNA detection in breast cancer.
Article in EMBO molecular medicine, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers, 2 of them syntheses that pooled it.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
46 citing papers in PubMed, 2 syntheses or guidelines pooled it, 56 citations in OpenAlex.
- Circulating Tumor DNA as a Real-Time Biomarker for Minimal Residual Disease and Recurrence Prediction in Stage II Colorectal Cancer: A Systematic Review and Meta-Analysis.International journal of molecular sciences · 2025Pooled it
- Circulating tumor DNA predicts prognosis at different time points in patients with esophageal cancer: a systematic review and meta-analysis.Frontiers in oncology · 2025Pooled it
- CfDNA-based copy-number dynamics during anti-PD1 treatment in metastatic triple negative breast cancer.Cell reports. Medicine · 2025Trial
- Tumor-Informed ctDNA in Guiding First-Line Immunochemotherapy in Advanced Non-Small Cell Lung Cancers.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Trial
- Early versus deferred use of CDK4/6 inhibitors in advanced breast cancer: circulating tumor DNA analysis of a randomized phase 3 trial.Nature medicine · 2025Trial
- Minimal residual disease combined with radiological tumor volume as a tool for identification of resected NSCLC patients at high risk of recurrence.The journal of liquid biopsy · 2026Article
- Concordance of tumor-informed and tumor-agnostic ctDNA assays for treatment response monitoring in advanced solid tumors.The journal of liquid biopsy · 2026Article
- Towards liquid biopsy-based analysis of antitumour immunity.Nature reviews. Clinical oncology · 2026Review
- The role of serologic biomarkers "liquid biopsy" in the fight against breast cancer: From biological foundations to clinical impact.iScience · 2026Review
- Combined circulating tumor antigen model demonstrates additional prognostic value in first-line treatment of non-small cell lung cancer.Journal for immunotherapy of cancer · 2026Article
- A scalable deep-learning framework for cancer detection using cell-free DNA shallow whole-genome sequencing.Science advances · 2026Article
- Review
- Cell-free DNA size deconvolution resolves nucleosomal origins and reveals tumor-associated fragmentomic alterations.Nature communications · 2026Article
- Pan-Cancer Pre-Treatment ctDNA Detection Using a Highly Sensitive Tumor-Informed Assay.International journal of molecular sciences · 2026Article
- ctDNA monitoring using tumor-informed copy number analysis.EMBO molecular medicine · 2026Article
- Tracking response to neoadjuvant systemic therapy through circulating tumor DNA analysis in breast cancer.NPJ breast cancer · 2026Article
- Targeting rare oncogenic mutations in resectable non-small cell lung cancer: emerging perioperative strategies.Journal of thoracic disease · 2026Review
- Noninvasive biomarkers in thymic epithelial tumors: a systematic review of cfDNA/ctDNA detection, molecular profiling, and organoid-based monitoring.Journal of thoracic disease · 2026Review
- Tumor-informed circulating tumor DNA stratifies recurrence risk and survival in anal squamous cell carcinoma.Nature communications · 2026Article
- Molecular residual disease assessment in colorectal and bladder cancer by somatic structural variant analysis of cell-free DNA whole-genome sequencing data.Journal of translational medicine · 2026Article
Corrections and comments
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Authors and funding
23 authors at 1 institution in 1 country.
Funding
Abstract
Analysis of circulating tumor DNA (ctDNA) to monitor cancer dynamics and detect minimal residual disease has been an area of increasing interest. Multiple methods have been proposed but few studies have compared the performance of different approaches. Here, we compare detection of ctDNA in serial plasma samples from patients with breast cancer using different tumor-informed and tumor-naïve assays designed to detect structural variants (SVs), single nucleotide variants (SNVs), and/or somatic copy-number aberrations, by multiplex PCR, hybrid capture, and different depths of whole-genome sequencing. Our results demonstrate that the ctDNA dynamics and allele fractions (AFs) were highly concordant when analyzing the same patient samples using different assays. Tumor-informed assays showed the highest sensitivity for detection of ctDNA at low concentrations. Hybrid capture sequencing targeting between 1,347 and 7,491 tumor-identified mutations at high depth was the most sensitive assay, detecting ctDNA down to an AF of 0.00024% (2.4 parts per million, ppm). Multiplex PCR targeting 21-47 tumor-identified SVs per patient detected ctDNA down to 0.00047% AF (4.7 ppm) and has potential as a clinical assay.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.