Somatic copy number alteration and fragmentation analysis in circulating tumor DNA for cancer screening and treatment monitoring in colorectal cancer patients

Clinical Validity of Circulating Tumor DNA as Prognostic and Predictive Marker for Personalized Colorectal Cancer Patient Management

(2022) Ariane Hallermayr et al.   Cancers

Updates on liquid biopsy: current trends and future perspectives for clinical application in solid tumors

(2021) Pamela Pinzani et al.   CLINICAL CHEMISTRY AND LABORATORY MEDICINE

Epigenomic landscape of human colorectal cancer unveils an aberrant core of pan-cancer enhancers orchestrated by YAP/TAZ

(2021) Giulia Della Chiara et al.   Nature Communications

Liquid Biopsy Hotspot Variant Assays: Analytical Validation for Application in Residual Disease Detection and Treatment Monitoring

(2021) Ariane Hallermayr et al.   CLINICAL CHEMISTRY

Multimodal analysis of cell-free DNA whole-genome sequencing for pediatric cancers with low mutational burden

(2021) Peter Peneder et al.   Nature Communications

Detection and characterization of lung cancer using cell-free DNA fragmentomes

(2021) Dimitrios Mathios et al.   Nature Communications

An Exploratory Pilot Study of Changes in Global DNA Methylation in Patients Undergoing Major Breast Surgery Under Opioid-Based General Anesthesia

(2021) Francesca Felicia Caputi et al.   Frontiers in Pharmacology

The Biology of Cell-free DNA Fragmentation and the Roles of DNASE1, DNASE1L3, and DFFB

(2020) Diana S.C. Han et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The effect of surgical trauma on circulating free DNA levels in cancer patients – implications for studies of circulating tumor DNA

(2020) Tenna V. Henriksen et al.   Molecular Oncology

Nonreportable rates and cell‐free DNA profiles in noninvasive prenatal testing among women with heparin treatment

(2020) Noriyuki Nakamura et al.   PRENATAL DIAGNOSIS

Major surgery induces acute changes in measured DNA methylation associated with immune response pathways

(2020) Ryoichi Sadahiro et al.   Scientific Reports

Non-invasive early detection of cancer four years before conventional diagnosis using a blood test

(2020) Xingdong Chen et al.   Nature Communications

Generic Protocols for the Analytical Validation of Next-Generation Sequencing-Based ctDNA Assays: A Joint Consensus Recommendation of the BloodPAC’s Analytical Variables Working Group

(2020) James H Godsey et al.   CLINICAL CHEMISTRY

International liquid biopsy standardization alliance white paper

(2020) Dana Connors et al.   CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY

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

(2019) Kun Sun et al.   GENOME RESEARCH

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

(2019) Stephen Cristiano et al.   NATURE

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

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

(2019) Peter Ulz et al.   Nature Communications

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

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

Advantage of Next-Generation Sequencing in Dynamic Monitoring of Circulating Tumor DNA over Droplet Digital PCR in Cetuximab Treated Colorectal Cancer Patients

(2018) Hangyu Zhang et al.   Translational Oncology

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

The evidence framework for precision cancer medicine

(2017) Jeffrey A. Moscow et al.   Nature Reviews Clinical Oncology

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

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

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

(2016) Matthew W. Snyder et al.   CELL

Screening for Colorectal Cancer

(2016) Jennifer S. Lin et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Whole-genome plasma sequencing reveals focal amplifications as a driving force in metastatic prostate cancer

(2016) Peter Ulz et al.   Nature Communications

Molecular profiling of advanced solid tumors and patient outcomes with genotype-matched clinical trials: the Princess Margaret IMPACT/COMPACT trial

(2016) Tracy L. Stockley et al.   Genome Medicine

DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly

(2014) Ilari Scheinin et al.   GENOME RESEARCH

Comparative genomic hybridisation array and DNA sequencing to direct treatment of metastatic breast cancer: a multicentre, prospective trial (SAFIR01/UNICANCER)

(2014) Fabrice André et al.   LANCET ONCOLOGY

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

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

Multiplex Picodroplet Digital PCR to Detect KRAS Mutations in Circulating DNA from the Plasma of Colorectal Cancer Patients

(2013) V. Taly 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

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

(2010) Nynke L. van Berkum et al.   Jove-Journal of Visualized Experiments

Circulating mutant DNA to assess tumor dynamics

(2008) Frank Diehl et al.   NATURE MEDICINE