Epigenetics, fragmentomics, and topology of cell-free DNA in liquid biopsies

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

Blood contains circulating cell‐free respiratory competent mitochondria

(2020) Zahra Al Amir Dache et al.   FASEB JOURNAL

Differential DNA Methylation in Placenta Associated With Maternal Blood Pressure During Pregnancy

(2020) Tsegaselassie Workalemahu et al.   HYPERTENSION

A novel NGS library preparation method to characterize native termini of fragmented DNA

(2020) Kelly M Harkins et al.   NUCLEIC ACIDS RESEARCH

Identification and characterization of extrachromosomal circular DNA in maternal plasma

(2020) Sarah T. K. Sin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plasma DNA end motif profiling as a fragmentomic marker in cancer, pregnancy and transplantation

(2020) Peiyong Jiang et al.   Cancer Discovery

Fragment Size Analysis May Distinguish Clonal Hematopoiesis from Tumor-Derived Mutations in Cell-Free DNA

(2020) Francesco Marass et al.   CLINICAL CHEMISTRY

Integrating genomic features for non-invasive early lung cancer detection

(2020) Jacob J. Chabon et al.   NATURE

Microbiome analyses of blood and tissues suggest cancer diagnostic approach

(2020) Gregory D. Poore et al.   NATURE

Sensitive and specific multi-cancer detection and localization using methylation signatures in cell-free DNA

(2020) M.C. Liu et al.   ANNALS OF ONCOLOGY

Detection of renal cell carcinoma using plasma and urine cell-free DNA methylomes

(2020) Pier Vitale Nuzzo et al.   NATURE MEDICINE

Detection and discrimination of intracranial tumors using plasma cell-free DNA methylomes

(2020) Farshad Nassiri et al.   NATURE MEDICINE

Senescence, Necrosis, and Apoptosis Govern Circulating Cell-free DNA Release Kinetics

(2020) Ariana Rostami et al.   Cell Reports

Plasma DNA Profile Associated with DNASE1L3 Gene Mutations: Clinical Observations, Relationships to Nuclease Substrate Preference, and In Vivo Correction

(2020) Rebecca W.Y. Chan et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Cell-free DNA Methylation and Transcriptomic Signature Prediction of Pregnancies with Adverse Outcomes

(2020) Giorgia Del Vecchio et al.   Epigenetics

Detection and characterization of jagged ends of double-stranded DNA in plasma

(2020) Peiyong Jiang et al.   GENOME RESEARCH

Screening for Fetal Chromosomal Abnormalities

(2020) et al.   OBSTETRICS AND GYNECOLOGY

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

(2019) Kun Sun et al.   GENOME RESEARCH

Bayesian-based noninvasive prenatal diagnosis of single-gene disorders

(2019) Tom Rabinowitz et al.   GENOME RESEARCH

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

(2019) Stephen Cristiano et al.   NATURE

Topologic Analysis of Plasma Mitochondrial DNA Reveals the Coexistence of Both Linear and Circular Molecules

(2019) Mary-Jane L. Ma et al.   CLINICAL CHEMISTRY

Methylation analysis of plasma DNA informs etiologies of Epstein-Barr virus-associated diseases

(2019) W. K. Jacky Lam et al.   Nature Communications

Cell-free DNA in blood circulation is generated by DNase1L3 and caspase-activated DNase

(2019) Taiki Watanabe et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

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

(2019) Peter Ulz et al.   Nature Communications

TRIDENT-2: National Implementation of Genome-wide Non-invasive Prenatal Testing as a First-Tier Screening Test in the Netherlands

(2019) Karuna R.M. van der Meij et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Analysis of microbial sequences in plasma cell-free DNA for early-onset breast cancer patients and healthy females

(2018) Yu-Feng Huang et al.   BMC Medical Genomics

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

Size-tagged preferred ends in maternal plasma DNA shed light on the production mechanism and show utility in noninvasive prenatal testing

(2018) Kun Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2018) Hai Zemmour et al.   Nature Communications

Enrichment of fetal and maternal long cell-free DNA fragments from maternal plasma following DNA repair

(2018) Joaquim S.L. Vong et al.   PRENATAL DIAGNOSIS

Dnase1l3 deletion causes aberrations in length and end-motif frequencies in plasma DNA

(2018) Lee Serpas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Preferred end coordinates and somatic variants as signatures of circulating tumor DNA associated with hepatocellular carcinoma

(2018) Peiyong Jiang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enhanced detection of circulating tumor DNA by fragment size analysis

(2018) Florent Mouliere et al.   Science Translational Medicine

Normal and Cancerous Tissues Release Extrachromosomal Circular DNA (eccDNA) into the Circulation

(2017) Pankaj Kumar et al.   MOLECULAR CANCER RESEARCH

Identification of methylation haplotype blocks aids in deconvolution of heterogeneous tissue samples and tumor tissue-of-origin mapping from plasma DNA

(2017) Shicheng Guo et al.   NATURE GENETICS

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

Host DNases prevent vascular occlusion by neutrophil extracellular traps

(2017) Miguel Jiménez-Alcázar et al.   SCIENCE

Performance of the neoBona test: a new paired-end massively parallel shotgun sequencing approach for cell-free DNA-based aneuploidy screening

(2017) V. Cirigliano et al.   ULTRASOUND IN OBSTETRICS & GYNECOLOGY

Graft-derived cell-free DNA, a noninvasive early rejection and graft damage marker in liver transplantation: A prospective, observational, multicenter cohort study

(2017) Ekkehard Schütz et al.   PLOS MEDICINE

Circulating Nucleosomes and Nucleosome Modifications as Biomarkers in Cancer

(2017) Peter McAnena et al.   Cancers

Molecular characterization of cell-free eccDNAs in human plasma

(2017) Jing Zhu et al.   Scientific Reports

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

(2016) Matthew W. Snyder et al.   CELL

Gestational Age Assessment by Methylation and Size Profiling of Maternal Plasma DNA: A Feasibility Study

(2016) Peiyong Jiang et al.   CLINICAL CHEMISTRY

Inferring expressed genes by whole-genome sequencing of plasma DNA

(2016) Peter Ulz et al.   NATURE GENETICS

Calculating the fetal fraction for noninvasive prenatal testing based on genome-wide nucleosome profiles

(2016) Roy Straver et al.   PRENATAL DIAGNOSIS

Second generation noninvasive fetal genome analysis reveals de novo mutations, single-base parental inheritance, and preferred DNA ends

(2016) K. C. Allen Chan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fragment Length of Circulating Tumor DNA

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

Single-stranded DNA library preparation uncovers the origin and diversity of ultrashort cell-free DNA in plasma

(2016) Philip Burnham et al.   Scientific Reports

Better prediction of functional effects for sequence variants

(2015) Maximilian Hecht et al.   BMC GENOMICS

High-resolution characterization of sequence signatures due to non-random cleavage of cell-free DNA

(2015) Dineika Chandrananda et al.   BMC Medical Genomics

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

Circulating nucleosomes as epigenetic biomarkers in pancreatic cancer

(2015) Monika Bauden et al.   Clinical Epigenetics

Whole genome bisulfite sequencing of cell-free DNA and its cellular contributors uncovers placenta hypomethylated domains

(2015) Taylor J Jensen et al.   GENOME BIOLOGY

Microarray-Based Analysis of Methylation Status of CpGs in Placental DNA and Maternal Blood DNA – Potential New Epigenetic Biomarkers for Cell Free Fetal DNA-Based Diagnosis

(2015) Lotte Hatt et al.   PLoS One

Size-based molecular diagnostics using plasma DNA for noninvasive prenatal testing

(2014) S. C. Y. Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Circulating Cell-Free DNA Enables Noninvasive Diagnosis of Heart Transplant Rejection

(2014) I. De Vlaminck et al.   Science Translational Medicine

Fetal Aneuploidy Detection by Cell-Free DNA Sequencing for Multiple Pregnancies and Quality Issues with Vanishing Twins

(2014) Sebastian Grömminger et al.   Journal of Clinical Medicine

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

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

Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing

(2013) K. C. A. Chan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues

(2012) Gilad Landan et al.   NATURE GENETICS

Extrachromosomal MicroDNAs and Chromosomal Microdeletions in Normal Tissues

(2012) Y. Shibata et al.   SCIENCE

Nonhematopoietically Derived DNA Is Shorter than Hematopoietically Derived DNA in Plasma: A Transplantation Model

(2011) Y. W. L. Zheng et al.   CLINICAL CHEMISTRY

Loss-of-function variant in DNASE1L3 causes a familial form of systemic lupus erythematosus

(2011) Sulaiman M Al-Mayouf et al.   NATURE GENETICS

High Fragmentation Characterizes Tumour-Derived Circulating DNA

(2011) Florent Mouliere et al.   PLoS One

Quantification of Fetal DNA by Use of Methylation-Based DNA Discrimination

(2010) A. O. H. Nygren et al.   CLINICAL CHEMISTRY

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

Persistent Aberrations in Circulating DNA Integrity after Radiotherapy Are Associated with Poor Prognosis in Nasopharyngeal Carcinoma Patients

(2008) K.C. A. Chan et al.   CLINICAL CANCER RESEARCH

Noninvasive prenatal diagnosis of monogenic diseases by digital size selection and relative mutation dosage on DNA in maternal plasma

(2008) F. M. F. Lun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma

(2008) R. W. K. Chiu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood

(2008) H. C. Fan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characterization of circulating DNA in healthy human plasma

(2007) Nobuyasu Suzuki et al.   CLINICA CHIMICA ACTA