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

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

(2016) Matthew W. Snyder et al.   CELL

Integrated digital error suppression for improved detection of circulating tumor DNA

(2016) Aaron M Newman et al.   NATURE BIOTECHNOLOGY

Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors

(2016) Jaegil Kim et al.   NATURE GENETICS

Cell-free DNA levels in plasma of patients with non-small-cell lung cancer and inflammatory lung disease

(2015) A Szpechcinski et al.   BRITISH JOURNAL OF CANCER

Integrative Clinical Genomics of Advanced Prostate Cancer

(2015) Dan Robinson et al.   CELL

Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer

(2015) Giovanni Ciriello et al.   CELL

Oncotator: Cancer Variant Annotation Tool

(2015) Alex H. Ramos et al.   HUMAN MUTATION

The evolutionary history of lethal metastatic prostate cancer

(2015) Gunes Gundem et al.   NATURE

Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes

(2015) Sachet A Shukla et al.   NATURE BIOTECHNOLOGY

Paired exome analysis of Barrett's esophagus and adenocarcinoma

(2015) Matthew D Stachler et al.   NATURE GENETICS

DNA-Repair Defects and Olaparib in Metastatic Prostate Cancer

(2015) Joaquin Mateo et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer

(2015) N. A. Rizvi et al.   SCIENCE

Whole-genome sequencing reveals activation-induced cytidine deaminase signatures during indolent chronic lymphocytic leukaemia evolution

(2015) S. Kasar et al.   Nature Communications

A mutational signature in gastric cancer suggests therapeutic strategies

(2015) Ludmil B. Alexandrov et al.   Nature Communications

Multifocal clonal evolution characterized using circulating tumour DNA in a case of metastatic breast cancer

(2015) Muhammed Murtaza et al.   Nature Communications

Tumor Heterogeneity and Lesion-Specific Response to Targeted Therapy in Colorectal Cancer

(2015) M. Russo et al.   Cancer Discovery

Genomic Characterization of Brain Metastases Reveals Branched Evolution and Potential Therapeutic Targets

(2015) P. K. Brastianos et al.   Cancer Discovery

Analytical and Clinical Validation of a Digital Sequencing Panel for Quantitative, Highly Accurate Evaluation of Cell-Free Circulating Tumor DNA

(2015) Richard B. Lanman et al.   PLoS One

TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data

(2014) Gavin Ha et al.   GENOME RESEARCH

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer

(2014) Jens G Lohr et al.   NATURE BIOTECHNOLOGY

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

(2014) Aaron M Newman et al.   NATURE MEDICINE

Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine

(2014) Eliezer M Van Allen et al.   NATURE MEDICINE

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

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

Evolution and Impact of Subclonal Mutations in Chronic Lymphocytic Leukemia

(2013) Dan A. Landau et al.   CELL

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

(2013) Michael S. Lawrence et al.   NATURE

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

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

(2013) Muhammed Murtaza et al.   NATURE

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Analysis of Circulating Tumor DNA to Monitor Metastatic Breast Cancer

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

Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation

(2013) Maura Costello et al.   NUCLEIC ACIDS RESEARCH

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

Deciphering Signatures of Mutational Processes Operative in Human Cancer

(2013) Ludmil B. Alexandrov et al.   Cell Reports

Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer

(2012) G. Ha et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Automatic Relevance Determination in Nonnegative Matrix Factorization with the /spl beta/-Divergence

(2012) V. Y. F. Tan et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

The mutational landscape of lethal castration-resistant prostate cancer

(2012) Catherine S. Grasso et al.   NATURE

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

Detection of Chromosomal Alterations in the Circulation of Cancer Patients with Whole-Genome Sequencing

(2012) R. J. Leary et al.   Science Translational Medicine

ContEst: estimating cross-contamination of human samples in next-generation sequencing data

(2011) Kristian Cibulskis et al.   BIOINFORMATICS

Initial genome sequencing and analysis of multiple myeloma

(2011) Michael A. Chapman et al.   NATURE

The genomic complexity of primary human prostate cancer

(2011) Michael F. Berger et al.   NATURE

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

The landscape of somatic copy-number alteration across human cancers

(2010) Rameen Beroukhim et al.   NATURE

In This Issue

(2010)   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

NetMHCpan, a method for MHC class I binding prediction beyond humans

(2008) Ilka Hoof et al.   IMMUNOGENETICS

Circulating mutant DNA to assess tumor dynamics

(2008) Frank Diehl et al.   NATURE MEDICINE