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

Targeted methylation sequencing of plasma cell-free DNA for cancer detection and classification

(2018) L Liu et al.   ANNALS OF ONCOLOGY

GeneCT: a generalizable cancerous status and tissue origin classifier for pan-cancer biopsies

(2018) Kun Sun et al.   BIOINFORMATICS

Detection of Gastric Cancer with Novel Methylated DNA Markers: Discovery, Tissue Validation, and Pilot Testing in Plasma

(2018) Bradley W Anderson et al.   CLINICAL CANCER RESEARCH

Cell-Free DNA Modification Dynamics in Abiraterone Acetate-Treated Prostate Cancer Patients

(2018) Juozas Gordevičius et al.   CLINICAL CANCER RESEARCH

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

CancerDetector: ultrasensitive and non-invasive cancer detection at the resolution of individual reads using cell-free DNA methylation sequencing data

(2018) Wenyuan Li et al.   NUCLEIC ACIDS RESEARCH

Noninvasive reconstruction of placental methylome from maternal plasma DNA: Potential for prenatal testing and monitoring

(2018) Kun Sun et al.   PRENATAL DIAGNOSIS

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

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

Secretory microRNAs as biomarkers of cancer

(2018) Kazuharu Kai et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

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

(2018) Hai Zemmour et al.   Nature Communications

A panel of DNA methylation markers for the detection of prostate cancer from FV and DRE urine DNA

(2018) Igor Brikun et al.   Clinical Epigenetics

Automated size selection for short cell-free DNA fragments enriches for circulating tumor DNA and improves error correction during next generation sequencing

(2018) Sabine Hellwig et al.   PLoS One

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

(2018) Shu Yi Shen et al.   NATURE

Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase

(2018) Emily K Schutsky et al.   NATURE BIOTECHNOLOGY

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

Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease

(2018) Joshua Moss et al.   Nature Communications

Discovery of methylated circulating DNA biomarkers for comprehensive non-invasive monitoring of treatment response in metastatic colorectal cancer

(2017) Ludovic Barault et al.   GUT

Promoter hypermethylation in plasma-derived cell-free DNA as a prognostic marker for pancreatic adenocarcinoma staging

(2017) Stine Dam Henriksen et al.   INTERNATIONAL JOURNAL OF CANCER

Methylated free-circulatingHPP1DNA is an early response marker in patients with metastatic colorectal cancer

(2017) Andreas Herbst et al.   INTERNATIONAL JOURNAL OF CANCER

Bioinformatics Approaches for Fetal DNA Fraction Estimation in Noninvasive Prenatal Testing

(2017) Xianlu Peng et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

A Comparison of Cell-Free DNA Isolation Kits

(2017) Laure Sorber et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution

(2017) Christopher Abbosh et al.   NATURE

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

Mapping DNA methylation with high-throughput nanopore sequencing

(2017) Arthur C Rand et al.   NATURE METHODS

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

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

COFFEE: control-free noninvasive fetal chromosomal examination using maternal plasma DNA

(2017) Kun Sun et al.   PRENATAL DIAGNOSIS

Integrative single-cell and cell-free plasma RNA transcriptomics elucidates placental cellular dynamics

(2017) Jason C. H. Tsang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Methylation patterns in serum DNA for early identification of disseminated breast cancer

(2017) Martin Widschwendter et al.   Genome Medicine

Predicting cancer type from tumour DNA signatures

(2017) Kee Pang Soh et al.   Genome Medicine

The potential of circulating tumor DNA methylation analysis for the early detection and management of ovarian cancer

(2017) Martin Widschwendter et al.   Genome Medicine

Intratumoral Heterogeneity of the Epigenome

(2016) Tali Mazor et al.   CANCER CELL

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

(2016) Matthew W. Snyder et al.   CELL

Cell-free DNA in maternal plasma and serum: A comparison of quantity, quality and tissue origin using genomic and epigenomic approaches

(2016) Felix C.K. Wong et al.   CLINICAL BIOCHEMISTRY

Early Detection of Lung Cancer Using DNA Promoter Hypermethylation in Plasma and Sputum

(2016) Alicia Hulbert et al.   CLINICAL CANCER RESEARCH

Long Noncoding RNAs as Novel Biomarkers Have a Promising Future in Cancer Diagnostics

(2016) Ting Shi et al.   DISEASE MARKERS

Human blood cell levels of 5-hydroxymethylcytosine (5hmC) decline with age, partly related to acquired mutations in TET2

(2016) Manuel Buscarlet et al.   EXPERIMENTAL HEMATOLOGY

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

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

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

Blood-based DNA methylation as biomarker for breast cancer: a systematic review

(2016) Qiuqiong Tang et al.   Clinical Epigenetics

Cell-Free DNA: An Upcoming Biomarker in Transplantation

(2015) E. M. Gielis et al.   AMERICAN JOURNAL OF TRANSPLANTATION

Digital PCR quantification ofMGMTmethylation refines prediction of clinical benefit from alkylating agents in glioblastoma and metastatic colorectal cancer

(2015) L. Barault et al.   ANNALS OF ONCOLOGY

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

(2015) Maxim Ivanov et al.   BMC GENOMICS

Genome-scale detection of hypermethylated CpG islands in circulating cell-free DNA of hepatocellular carcinoma patients

(2015) Lu Wen et al.   CELL RESEARCH

Noninvasive Prenatal Testing by Nanopore Sequencing of Maternal Plasma DNA: Feasibility Assessment

(2015) S. H. Cheng et al.   CLINICAL CHEMISTRY

The impact of digital DNA counting technologies on noninvasive prenatal testing

(2015) Kun Sun et al.   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

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

Noninvasive fetal genomic, methylomic, and transcriptomic analyses using maternal plasma and clinical implications

(2015) Ada I.C. Wong et al.   TRENDS IN MOLECULAR MEDICINE

DNA methylation and microRNA biomarkers for noninvasive detection of gastric and colorectal cancer

(2014) Yuji Toiyama et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Novel Methylated Biomarkers and a Robust Assay to Detect Circulating Tumor DNA in Metastatic Breast Cancer

(2014) Mary Jo Fackler et al.   CANCER RESEARCH

A Novel Wnt Regulatory Axis in Endometrioid Endometrial Cancer

(2014) Y. Zhao et al.   CANCER RESEARCH

The role of 5-hydroxymethylcytosine in human cancer

(2014) Gerd P. Pfeifer et al.   CELL AND TISSUE RESEARCH

Validation of a Real-Time PCR-Based Qualitative Assay for the Detection of Methylated SEPT9 DNA in Human Plasma

(2014) N. T. Potter et al.   CLINICAL CHEMISTRY

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

Noninvasive in vivo monitoring of tissue-specific global gene expression in humans

(2014) W. Koh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Commonality and differences of methylation signatures in the plasma of patients with pancreatic cancer and colorectal cancer

(2013) Joshua Melson et al.   INTERNATIONAL JOURNAL OF CANCER

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

Liquid biopsy: monitoring cancer-genetics in the blood

(2013) Emily Crowley et al.   Nature Reviews Clinical Oncology

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

Mutation-based detection and monitoring of cell-free tumor DNA in peripheral blood of cancer patients

(2012) L. Benesova et al.   ANALYTICAL BIOCHEMISTRY

SOX17 Promoter Methylation in Circulating Tumor Cells and Matched Cell-Free DNA Isolated from Plasma of Patients with Breast Cancer

(2012) M. Chimonidou et al.   CLINICAL CHEMISTRY

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

Circulating Tumor Cells: Personalized Medicine in Interventional Oncology?

(2012) Rahul A. Sheth et al.   JOURNAL OF VASCULAR AND INTERVENTIONAL RADIOLOGY

Fetal tests spur legal battle

(2012) Erika Check Hayden   NATURE

Racial differences in gene-specific DNA methylation levels are present at birth

(2011) Ronald M. Adkins et al.   BIRTH DEFECTS RESEARCH PART A-CLINICAL AND MOLECULAR TERATOLOGY

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

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

Significant differences in global genomic DNA methylation by gender and race/ethnicity in peripheral blood

(2011) Fang Fang Zhang et al.   Epigenetics

Genetic Control of Individual Differences in Gene-Specific Methylation in Human Brain

(2010) Dandan Zhang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

Hypomethylation of repeated DNA sequences in cancer

(2010) Jason P Ross et al.   Epigenomics

Noninvasive Prenatal Detection of Trisomy 21 by an Epigenetic-Genetic Chromosome-Dosage Approach

(2009) Y. K. Tong et al.   CLINICAL CHEMISTRY

Nucleosome positioning: How is it established, and why does it matter?

(2009) Marta Radman-Livaja et al.   DEVELOPMENTAL BIOLOGY

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Quantitative Analysis of Circulating Methylated DNA as a Biomarker for Hepatocellular Carcinoma

(2008) K. C. A. Chan et al.   CLINICAL CHEMISTRY

Intra-individual Change Over Time in DNA Methylation With Familial Clustering

(2008) Hans T. Bjornsson   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

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