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

Detection and localization of surgically resectable cancers with a multi-analyte blood test

(2018) Joshua D. Cohen et al.   SCIENCE

Monitoring of Serum DNA Methylation as an Early Independent Marker of Response and Survival in Metastatic Breast Cancer: TBCRC 005 Prospective Biomarker Study

(2017) Kala Visvanathan et al.   JOURNAL OF CLINICAL ONCOLOGY

Direct detection of early-stage cancers using circulating tumor DNA

(2017) Jillian Phallen et al.   Science Translational Medicine

A Landscape of Pharmacogenomic Interactions in Cancer

(2016) Francesco Iorio et al.   CELL

Integrated digital error suppression for improved detection of circulating tumor DNA

(2016) Aaron M Newman et al.   NATURE BIOTECHNOLOGY

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

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

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays

(2014) Martin J. Aryee et al.   BIOINFORMATICS

Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin

(2014) Katherine A. Hoadley et al.   CELL

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

Liquid Biopsies: Genotyping Circulating Tumor DNA

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

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

(2014) Aaron M Newman et al.   NATURE MEDICINE

Detecting ultralow-frequency mutations by Duplex Sequencing

(2014) Scott R Kennedy et al.   Nature Protocols

MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments

(2013) Matthias Lienhard et al.   BIOINFORMATICS

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

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

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Methylome analysis using MeDIP-seq with low DNA concentrations

(2012) Oluwatosin Taiwo et al.   Nature Protocols

Detection of ultra-rare mutations by next-generation sequencing

(2012) M. W. Schmitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling

(2011) Hongcang Gu et al.   Nature Protocols

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

Epigenetics in cancer

(2009) S. Sharma et al.   CARCINOGENESIS

An Epigenetic Signature in Peripheral Blood Predicts Active Ovarian Cancer

(2009) Andrew E. Teschendorff et al.   PLoS One