Clinical relevance of blood-based ctDNA analysis: mutation detection and beyond

Hypoxia differently modulates the release of mitochondrial and nuclear DNA

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Genome-wide plasma DNA methylation features of metastatic prostate cancer

(2020) Anjui Wu et al.   JOURNAL OF CLINICAL INVESTIGATION

Low-Pass Whole-Genome Sequencing of Circulating Cell-Free DNA Demonstrates Dynamic Changes in Genomic Copy Number in a Squamous Lung Cancer Clinical Cohort

(2019) Xiaoji Chen et al.   CLINICAL CANCER RESEARCH

Intratumor heterogeneity comparison among different subtypes of non-small-cell lung cancer through multi-region tissue and matched ctDNA sequencing

(2019) Yaxiong Zhang et al.   Molecular Cancer

Assessment of circulating tumor DNA in pediatric solid tumors: The promise of liquid biopsies

(2019) Samuel D. Abbou et al.   PEDIATRIC BLOOD & CANCER

Epigenetic Biomarkers in Cell-Free DNA and Applications in Liquid Biopsy

(2019) Wanxia Gai et al.   Genes

Clinical Implications of Circulating Tumor DNA Tumor Mutational Burden (ctDNA TMB) in Non‐Small Cell Lung Cancer

(2019) Young Kwang Chae et al.   ONCOLOGIST

Liquid biopsy in central nervous system metastases: a RANO review and proposals for clinical applications

(2019) Adrienne Boire et al.   NEURO-ONCOLOGY

Liquid biopsy and minimal residual disease — latest advances and implications for cure

(2019) Klaus Pantel et al.   Nature Reviews Clinical Oncology

Molecular Analysis of Plasma From Patients With ROS1-Positive NSCLC

(2019) Ibiayi Dagogo-Jack et al.   Journal of Thoracic Oncology

Plasma Epstein-Barr virus DNA as an archetypal circulating tumour DNA marker

(2019) Wai Kei Jacky Lam et al.   JOURNAL OF PATHOLOGY

Genomic Analysis of Circulating Tumor DNA Using a Melanoma-Specific UltraSEEK Oncogene Panel

(2019) Elin S. Gray et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Orientation-aware plasma cell-free DNA fragmentation analysis in open chromatin regions informs tissue of origin

(2019) Kun Sun et al.   GENOME RESEARCH

Changes in plasma EBV-DNA and immune status in patients with nasopharyngeal carcinoma after treatment with intensity-modulated radiotherapy

(2019) Qi Chen et al.   Diagnostic Pathology

Prediction and monitoring of relapse in stage III melanoma using circulating tumor DNA

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Pre-operative ctDNA predicts survival in high-risk stage III cutaneous melanoma patients

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Life and death of circulating cell-free DNA

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Early Detection of Metastatic Relapse and Monitoring of Therapeutic Efficacy by Ultra-Deep Sequencing of Plasma Cell-Free DNA in Patients With Urothelial Bladder Carcinoma

(2019) Emil Christensen et al.   JOURNAL OF CLINICAL ONCOLOGY

Liquid biopsy of HPV DNA in cervical cancer

(2019) Tak Hong Cheung et al.   JOURNAL OF CLINICAL VIROLOGY

Genome-wide cell-free DNA fragmentation in patients with cancer

(2019) Stephen Cristiano et al.   NATURE

Utility of ctDNA to support patient selection for early phase clinical trials: the TARGET study

(2019) Dominic G. Rothwell et al.   NATURE MEDICINE

Targeting DNA Methylation and EZH2 Activity to Overcome Melanoma Resistance to Immunotherapy

(2019) Abdullah Al Emran et al.   TRENDS IN IMMUNOLOGY

Analysis of Plasma Cell-Free DNA by Ultradeep Sequencing in Patients With Stages I to III Colorectal Cancer

(2019) Thomas Reinert et al.   JAMA Oncology

Liquid biopsy in the era of immuno-oncology: is it ready for prime-time use for cancer patients?

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Prospective Observation: Clinical Utility of Plasma Epstein‐Barr‐Virus DNA Load in EBV‐associated Gastric Carcinoma Patients

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Head and neck cancer: searching for genomic and epigenetic biomarkers in body fluids – the state of art

(2019) Ilda Patrícia Ribeiro et al.   Molecular Cytogenetics

Tumor mutation burden and circulating tumor DNA in combined CTLA-4 and PD-1 antibody therapy in metastatic melanoma – results of a prospective biomarker study

(2019) Andrea Forschner et al.   Journal for ImmunoTherapy of Cancer

Non-blood sources of cell-free DNA for cancer molecular profiling in clinical pathology and oncology

(2019) Giovanni Ponti et al.   CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY

Liquid versus tissue biopsy for detecting acquired resistance and tumor heterogeneity in gastrointestinal cancers

(2019) Aparna R. Parikh et al.   NATURE MEDICINE

Salivary HPV DNA informs locoregional disease status in advanced HPV-associated oropharyngeal cancer

(2019) Glenn J. Hanna et al.   ORAL ONCOLOGY

DNA analysis of low- and high-density fractions defines heterogeneous subpopulations of small extracellular vesicles based on their DNA cargo and topology

(2019) Elisa Lázaro-Ibáñez et al.   Journal of Extracellular Vesicles

Toward the Early Detection of Cancer by Decoding the Epigenetic and Environmental Fingerprints of Cell-Free DNA

(2019) Ymke van der Pol et al.   CANCER CELL

Multicenter Evaluation of Circulating Cell-Free DNA Extraction and Downstream Analyses for the Development of Standardized (Pre)analytical Work Flows

(2019) Rita Lampignano et al.   CLINICAL CHEMISTRY

High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants

(2019) Pedram Razavi et al.   NATURE MEDICINE

Inference of transcription factor binding from cell-free DNA enables tumor subtype prediction and early detection

(2019) Peter Ulz et al.   Nature Communications

Liquid biopsy tracking during sequential chemo-radiotherapy identifies distinct prognostic phenotypes in nasopharyngeal carcinoma

(2019) Jiawei Lv et al.   Nature Communications

Salivary Biomarkers for Oral Squamous Cell Carcinoma Diagnosis and Follow-Up: Current Status and Perspectives

(2019) Marta Cristaldi et al.   Frontiers in Physiology

Validation of a Plasma-Based Comprehensive Cancer Genotyping Assay Utilizing Orthogonal Tissue- and Plasma-Based Methodologies

(2018) Justin I. Odegaard et al.   CLINICAL CANCER RESEARCH

Liquid Profiling of Circulating Tumor DNA in Plasma of Melanoma Patients for Companion Diagnostics and Monitoring of BRAF Inhibitor Therapy

(2018) Verena Haselmann et al.   CLINICAL CHEMISTRY

Liver- and Colon-Specific DNA Methylation Markers in Plasma for Investigation of Colorectal Cancers With or Without Liver Metastases

(2018) Wanxia Gai et al.   CLINICAL CHEMISTRY

Circulating human papillomavirus DNA as a surveillance tool in head and neck squamous cell carcinoma: A systematic review and meta-analysis

(2018) K.K. Jensen et al.   CLINICAL OTOLARYNGOLOGY

Genomic alterations in plasma DNA from patients with metastasized prostate cancer receiving abiraterone or enzalutamide

(2018) Jelena Belic et al.   INTERNATIONAL JOURNAL OF CANCER

Circulating Tumor DNA Analysis in Patients With Cancer: American Society of Clinical Oncology and College of American Pathologists Joint Review

(2018) Jason D. Merker et al.   JOURNAL OF CLINICAL ONCOLOGY

Early stage NSCLC — challenges to implementing ctDNA-based screening and MRD detection

(2018) Christopher Abbosh et al.   Nature Reviews Clinical Oncology

Clinical utility of circulating non-coding RNAs — an update

(2018) Simone Anfossi et al.   Nature Reviews Clinical Oncology

A pilot study of ultra-deep targeted sequencing of plasma DNA identifies driver mutations in hepatocellular carcinoma

(2018) Ismail Labgaa et al.   ONCOGENE

Detection of aneuploidy in patients with cancer through amplification of long interspersed nucleotide elements (LINEs)

(2018) Christopher Douville et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequencing-based counting and size profiling of plasma Epstein–Barr virus DNA enhance population screening of nasopharyngeal carcinoma

(2018) W. K. Jacky Lam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection and localization of surgically resectable cancers with a multi-analyte blood test

(2018) Joshua D. Cohen et al.   SCIENCE

Urinary cell-free DNA is a versatile analyte for monitoring infections of the urinary tract

(2018) Philip Burnham et al.   Nature Communications

Non-invasive detection of human cardiomyocyte death using methylation patterns of circulating DNA

(2018) Hai Zemmour et al.   Nature Communications

Evaluation of pre-analytical factors affecting plasma DNA analysis

(2018) Havell Markus et al.   Scientific Reports

Combination of Tumor Volume and Epstein-Barr Virus DNA Improved Prognostic Stratification of Stage II Nasopharyngeal Carcinoma in the Intensity Modulated Radiotherapy Era: A Large-Scale Cohort Study

(2018) Qiu-Yan Chen et al.   Cancer Research and Treatment

Dynamic changes in plasma Epstein-Barr virus DNA load during treatment have prognostic value in nasopharyngeal carcinoma: a retrospective study

(2018) Sha-Sha He et al.   Cancer Medicine

Epstein–Barr Virus and Cancer

(2018) Paul J. Farrell   Annual Review of Pathology-Mechanisms of Disease

Ultra-Sensitive Mutation Detection and Genome-Wide DNA Copy Number Reconstruction by Error-Corrected Circulating Tumor DNA Sequencing

(2018) Sonia Mansukhani et al.   CLINICAL CHEMISTRY

Clinical potential of circulating tumour DNA in patients receiving anticancer immunotherapy

(2018) Luc Cabel et al.   Nature Reviews Clinical Oncology

Longitudinal Liquid Biopsy and Mathematical Modeling of Clonal Evolution Forecast Time to Treatment Failure in the PROSPECT-C Phase II Colorectal Cancer Clinical Trial

(2018) Khurum H. Khan et al.   Cancer Discovery

Measurement of Plasma Cell-Free Mitochondrial Tumor DNA Improves Detection of Glioblastoma in Patient-Derived Orthotopic Xenograft Models

(2018) Richard Mair et al.   CANCER RESEARCH

Clinical validity of HPV circulating tumor DNA in advanced anal carcinoma: an ancillary study to the Epitopes-HPV02 trial

(2018) Alice Bernard-Tessier et al.   CLINICAL CANCER RESEARCH

Detection of cell‐free DNA fragmentation and copy number alterations in cerebrospinal fluid from glioma patients

(2018) Florent Mouliere et al.   EMBO Molecular Medicine

Does Size Matter? Comparison of Extraction Yields for Different-Sized DNA Fragments by Seven Different Routine and Four New Circulating Cell-Free Extraction Methods

(2018) Linda Cook et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Sensitive tumour detection and classification using plasma cell-free DNA methylomes

(2018) Shu Yi Shen et al.   NATURE

Current and future perspectives of liquid biopsies in genomics-driven oncology

(2018) Ellen Heitzer et al.   NATURE REVIEWS GENETICS

Enhanced detection of circulating tumor DNA by fragment size analysis

(2018) Florent Mouliere et al.   Science Translational Medicine

Donor-specific Cell-Free DNA as a Biomarker in Solid Organ Transplantation. A Systematic Review

(2018) Simon R. Knight et al.   TRANSPLANTATION

New insights into structural features and optimal detection of circulating tumor DNA determined by single-strand DNA analysis

(2018) Cynthia Sanchez et al.   npj Genomic Medicine

Viral-Cellular DNA Junctions as Molecular Markers for Assessing Intra-Tumor Heterogeneity in Cervical Cancer and for the Detection of Circulating Tumor DNA

(2017) Katrin Carow et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution

(2017) Christopher Abbosh et al.   NATURE

Circulating tumour DNA methylation markers for diagnosis and prognosis of hepatocellular carcinoma

(2017) Rui-hua Xu et al.   NATURE MATERIALS

Analysis of Plasma Epstein–Barr Virus DNA to Screen for Nasopharyngeal Cancer

(2017) K.C. Allen Chan et al.   NEW ENGLAND JOURNAL OF MEDICINE

Human papillomavirus DNA detection in plasma and cervical samples of women with a recent history of low grade or precancerous cervical dysplasia

(2017) Clementina Elvezia Cocuzza et al.   PLoS One

Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors

(2017) Viktor A. Adalsteinsson et al.   Nature Communications

Genomic Landscape of Cell-Free DNA in Patients with Colorectal Cancer

(2017) John H. Strickler et al.   Cancer Discovery

Detection of ubiquitous and heterogeneous mutations in cell-free DNA from patients with early-stage non-small-cell lung cancer

(2016) M. Jamal-Hanjani et al.   ANNALS OF ONCOLOGY

Distinct subclonal tumour responses to therapy revealed by circulating cell-free DNA

(2016) G. Gremel et al.   ANNALS OF ONCOLOGY

Characterization of the cell-free DNA released by cultured cancer cells

(2016) Abel Jacobus Bronkhorst et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Nanopore sequencing detects structural variants in cancer

(2016) Alexis L. Norris et al.   CANCER BIOLOGY & THERAPY

Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin

(2016) Matthew W. Snyder et al.   CELL

Methylated circulating tumor DNA in blood: power in cancer prognosis and response

(2016) Kristina Warton et al.   ENDOCRINE-RELATED CANCER

Nucleosome mapping in plasma DNA predicts cancer gene expression

(2016) Muhammed Murtaza et al.   NATURE GENETICS

Inferring expressed genes by whole-genome sequencing of plasma DNA

(2016) Peter Ulz et al.   NATURE GENETICS

Epigenetic modulators, modifiers and mediators in cancer aetiology and progression

(2016) Andrew P. Feinberg et al.   NATURE REVIEWS GENETICS

Assessment of the total cfDNA and HPV16/18 detection in plasma samples of head and neck squamous cell carcinoma patients

(2016) Agnieszka M. Mazurek et al.   ORAL ONCOLOGY

Identification of tissue-specific cell death using methylation patterns of circulating DNA

(2016) Roni Lehmann-Werman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Profiling genome-wide DNA methylation

(2016) Wai-Shin Yong et al.   Epigenetics & Chromatin

Fragment Length of Circulating Tumor DNA

(2016) Hunter R. Underhill et al.   PLoS Genetics

Exploratory Analysis of TP53 Mutations in Circulating Tumour DNA as Biomarkers of Treatment Response for Patients with Relapsed High-Grade Serous Ovarian Carcinoma: A Retrospective Study

(2016) Christine A. Parkinson et al.   PLOS MEDICINE

High level of chromosomal instability in circulating tumor cells of ROS1-rearranged non-small-cell lung cancer

(2015) E. Pailler et al.   ANNALS OF ONCOLOGY

Non-random fragmentation patterns in circulating cell-free DNA reflect epigenetic regulation

(2015) Maxim Ivanov et al.   BMC GENOMICS

PIK3CA mutations in serum DNA are predictive of recurrence in primary breast cancer patients

(2015) Chiya Oshiro et al.   BREAST CANCER RESEARCH AND TREATMENT

Circulating human papillomavirus DNA as a marker for disease extent and recurrence among patients with oropharyngeal cancer

(2015) Kristina R. Dahlstrom et al.   CANCER

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Plasma DNA tissue mapping by genome-wide methylation sequencing for noninvasive prenatal, cancer, and transplantation assessments

(2015) Kun Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lengthening and shortening of plasma DNA in hepatocellular carcinoma patients

(2015) Peiyong Jiang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection of somatic mutations and HPV in the saliva and plasma of patients with head and neck squamous cell carcinomas

(2015) Yuxuan Wang et al.   Science Translational Medicine

Detection of Clonal and Subclonal Copy-Number Variants in Cell-Free DNA from Patients with Breast Cancer Using a Massively Multiplexed PCR Methodology

(2015) Eser Kirkizlar et al.   Translational Oncology

Multifocal clonal evolution characterized using circulating tumour DNA in a case of metastatic breast cancer

(2015) Muhammed Murtaza et al.   Nature Communications

Plasma Epstein–Barr viral DNA load at midpoint of radiotherapy course predicts outcome in advanced-stage nasopharyngeal carcinoma

(2014) S. F. Leung et al.   ANNALS OF ONCOLOGY

Capturing intra-tumor genetic heterogeneity by de novo mutation profiling of circulating cell-free tumor DNA: a proof-of-principle

(2014) L. De Mattos-Arruda et al.   ANNALS OF ONCOLOGY

Comparison of KRAS mutation analysis of primary tumors and matched circulating cell-free DNA in plasmas of patients with colorectal cancer

(2014) Yung-Bin Kuo et al.   CLINICA CHIMICA ACTA

Clinical validation of the detection of KRAS and BRAF mutations from circulating tumor DNA

(2014) Alain R Thierry et al.   NATURE MEDICINE

Detection of Circulating Tumor DNA in Early- and Late-Stage Human Malignancies

(2014) C. Bettegowda et al.   Science Translational Medicine

Saliva and Plasma Quantitative Polymerase Chain Reaction–Based Detection and Surveillance of Human Papillomavirus–Related Head and Neck Cancer

(2014) Sun M. Ahn et al.   JAMA Otolaryngology-Head & Neck Surgery

Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives

(2013) Min Zhao et al.   BMC BIOINFORMATICS

Noninvasive Prenatal Methylomic Analysis by Genomewide Bisulfite Sequencing of Maternal Plasma DNA

(2013) F. M. F. Lun et al.   CLINICAL CHEMISTRY

Tumor-associated copy number changes in the circulation of patients with prostate cancer identified through whole-genome sequencing

(2013) Ellen Heitzer et al.   Genome Medicine

Cancer Genome Scanning in Plasma: Detection of Tumor-Associated Copy Number Aberrations, Single-Nucleotide Variants, and Tumoral Heterogeneity by Massively Parallel Sequencing

(2012) K. C. A. Chan et al.   CLINICAL CHEMISTRY

Genome-wide nucleosome positioning during embryonic stem cell development

(2012) Vladimir B Teif et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Human Papillomavirus Mutational Insertion: Specific Marker of Circulating Tumor DNA in Cervical Cancer Patients

(2012) Maura Campitelli et al.   PLoS One

Noninvasive Identification and Monitoring of Cancer Mutations by Targeted Deep Sequencing of Plasma DNA

(2012) T. Forshew et al.   Science Translational Medicine

Detection of Chromosomal Alterations in the Circulation of Cancer Patients with Whole-Genome Sequencing

(2012) R. J. Leary et al.   Science Translational Medicine

Quantitation of Human Papillomavirus DNA in Plasma of Oropharyngeal Carcinoma Patients

(2011) Hongbin Cao et al.   INTERNATIONAL JOURNAL OF RADIATION ONCOLOGY BIOLOGY PHYSICS

Determinants of nucleosome organization in primary human cells

(2011) Anton Valouev et al.   NATURE

High Fragmentation Characterizes Tumour-Derived Circulating DNA

(2011) Florent Mouliere et al.   PLoS One

Maternal Plasma DNA Sequencing Reveals the Genome-Wide Genetic and Mutational Profile of the Fetus

(2010) Y. M. D. Lo et al.   Science Translational Medicine

Circulating tumour cells in cancer patients: challenges and perspectives

(2010) Klaus Pantel et al.   TRENDS IN MOLECULAR MEDICINE

Nucleosome destabilization in the epigenetic regulation of gene expression

(2007) Steven Henikoff   NATURE REVIEWS GENETICS