Cell-Free DNA Provides a Good Representation of the Tumor Genome Despite Its Biased Fragmentation Patterns

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

(2016) Matthew W. Snyder et al.   CELL

Fragment Length of Circulating Tumor DNA

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

Inhibition of ABCB1 Overcomes Cancer Stem Cell-like Properties and Acquired Resistance to MET Inhibitors in Non-Small Cell Lung Cancer

(2015) T. Sugano et al.   MOLECULAR CANCER THERAPEUTICS

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

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

Cerebrospinal fluid-derived circulating tumour DNA better represents the genomic alterations of brain tumours than plasma

(2015) Leticia De Mattos-Arruda et al.   Nature Communications

Plasma circulating tumor DNA as an alternative to metastatic biopsies for mutational analysis in breast cancer

(2014) F. Rothé et al.   ANNALS OF ONCOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Innovative personalized medicine in gastric cancer: time to move forward

(2014) J. Lee et al.   CLINICAL GENETICS

The evolution of the unstable cancer genome

(2014) Rebecca A Burrell et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage

(2014) Aaron M Newman et al.   NATURE MEDICINE

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

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

Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA

(2013) Muhammed Murtaza et al.   NATURE

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

A comprehensive survey of genomic alterations in gastric cancer reveals systematic patterns of molecular exclusivity and co-occurrence among distinct therapeutic targets

(2012) Niantao Deng et al.   GUT

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

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

High Fragmentation Characterizes Tumour-Derived Circulating DNA

(2011) Florent Mouliere et al.   PLoS One

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Relationship between nucleosome positioning and DNA methylation

(2010) Ramakrishna K. Chodavarapu et al.   NATURE

Anaplastic Lymphoma Kinase Inhibition in Non–Small-Cell Lung Cancer

(2010) Eunice L. Kwak et al.   NEW ENGLAND JOURNAL OF MEDICINE

Origin and quantification of circulating DNA in mice with human colorectal cancer xenografts

(2010) Alain R. Thierry et al.   NUCLEIC ACIDS RESEARCH

Levels of Circulating Cell-Free Nuclear and Mitochondrial DNA in Benign and Malignant Ovarian Tumors

(2010) Rebecca R. Zachariah et al.   OBSTETRICS AND GYNECOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Nucleosomes are well positioned in exons and carry characteristic histone modifications

(2009) R. Andersson et al.   GENOME RESEARCH

Dynamic Regulation of Nucleosome Positioning in the Human Genome

(2008) Dustin E. Schones et al.   CELL

Quantification of Free Circulating Tumor DNA as a Diagnostic Marker for Breast Cancer

(2008) Raquel Catarino et al.   DNA AND CELL BIOLOGY

Circulating plasma DNA as diagnostic biomarker in non-small cell lung cancer

(2008) Massimiliano Paci et al.   LUNG CANCER

Circulating mutant DNA to assess tumor dynamics

(2008) Frank Diehl et al.   NATURE MEDICINE

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