Low Input Whole-Exome Sequencing to Determine the Representation of the Tumor Exome in Circulating DNA of Non-Small Cell Lung Cancer Patients

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

(2016) Matthew W. Snyder et al.   CELL

Serial Next-Generation Sequencing of Circulating Cell-Free DNA Evaluating Tumor Clone Response To Molecularly Targeted Drug Administration

(2015) J. S. Frenel et al.   CLINICAL CANCER RESEARCH

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Exome Sequencing of Cell-Free DNA from Metastatic Cancer Patients Identifies Clinically Actionable Mutations Distinct from Primary Disease

(2015) Timothy M. Butler et al.   PLoS One

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

Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants

(2015) Aziz Belkadi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Mutational signatures: the patterns of somatic mutations hidden in cancer genomes

(2014) Ludmil B Alexandrov et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Somatic mutations found in the healthy blood compartment of a 115-yr-old woman demonstrate oligoclonal hematopoiesis

(2014) H. Holstege et al.   GENOME RESEARCH

Cancer incidence and mortality worldwide: Sources, methods and major patterns in GLOBOCAN 2012

(2014) Jacques Ferlay et al.   INTERNATIONAL JOURNAL OF CANCER

Liquid Biopsies: Genotyping Circulating Tumor DNA

(2014) Luis A. Diaz et al.   JOURNAL OF CLINICAL ONCOLOGY

Comprehensive molecular profiling of lung adenocarcinoma

(2014) Eric A. Collisson et al.   NATURE

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

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

(2014) Aaron M Newman et al.   NATURE MEDICINE

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

(2014) Alain R Thierry et al.   NATURE MEDICINE

Evaluation of Exome Sequencing to Estimate Tumor Burden in Plasma

(2014) Daniel Klevebring et al.   PLoS One

Similarities and Differences between Exome Sequences Found in a Variety of Tissues from the Same Individual

(2014) Alberto Gómez-Ramos et al.   PLoS One

Exome Sequencing from Nanogram Amounts of Starting DNA: Comparing Three Approaches

(2014) Vera N. Rykalina et al.   PLoS One

Quantification and Dynamic Monitoring of EGFR T790M in Plasma Cell-Free DNA by Digital PCR for Prognosis of EGFR-TKI Treatment in Advanced NSCLC

(2014) Zhijie Wang et al.   PLoS One

Spatial and temporal diversity in genomic instability processes defines lung cancer evolution

(2014) E. C. de Bruin et al.   SCIENCE

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

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

Changes in Colorectal Carcinoma Genomes under Anti-EGFR Therapy Identified by Whole-Genome Plasma DNA Sequencing

(2014) Sumitra Mohan et al.   PLoS Genetics

Establishment of tumor-specific copy number alterations from plasma DNA of patients with cancer

(2013) Ellen Heitzer et al.   INTERNATIONAL JOURNAL OF CANCER

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

(2013) Muhammed Murtaza et al.   NATURE

Analysis of Circulating Tumor DNA to Monitor Metastatic Breast Cancer

(2013) Sarah-Jane Dawson et al.   NEW ENGLAND JOURNAL OF MEDICINE

Genome Mosaicism--One Human, Multiple Genomes

(2013) J. R. Lupski   SCIENCE

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Comprehensive genomic characterization of squamous cell lung cancers

(2012)   NATURE

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

(2012) Marco Gerlinger et al.   NEW ENGLAND JOURNAL OF MEDICINE

Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes

(2012) J. A. Tennessen et al.   SCIENCE

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

TEQC: an R package for quality control in target capture experiments

(2011) M. Hummel et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

Use of cancer-specific genomic rearrangements to quantify disease burden in plasma from patients with solid tumors

(2010) David J. McBride et al.   GENES CHROMOSOMES & CANCER

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

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

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

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

Targeted capture and massively parallel sequencing of 12 human exomes

(2009) Sarah B. Ng et al.   NATURE

Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes

(2009) Iwanka Kozarewa et al.   NATURE METHODS

Circulating mutant DNA to assess tumor dynamics

(2008) Frank Diehl et al.   NATURE MEDICINE

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