Spatial genomic heterogeneity within localized, multifocal prostate cancer

Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue

(2015) Colin S Cooper et al.   NATURE GENETICS

Tumour genomic and microenvironmental heterogeneity for integrated prediction of 5-year biochemical recurrence of prostate cancer: a retrospective cohort study

(2014) Emilie Lalonde et al.   LANCET ONCOLOGY

Integrative Genomic Analyses Reveal an Androgen-Driven Somatic Alteration Landscape in Early-Onset Prostate Cancer

(2013) Joachim Weischenfeldt et al.   CANCER CELL

Punctuated Evolution of Prostate Cancer Genomes

(2013) Sylvan C. Baca et al.   CELL

Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling

(2013) Ali Bashashati et al.   JOURNAL OF PATHOLOGY

Characterisation of retinoblastomas without RB1 mutations: genomic, gene expression, and clinical studies

(2013) Diane E Rushlow et al.   LANCET ONCOLOGY

The genetic landscape of high-risk neuroblastoma

(2013) Trevor J Pugh et al.   NATURE GENETICS

Copy number alterations of c-MYC and PTEN are prognostic factors for relapse after prostate cancer radiotherapy

(2012) Gaetano Zafarana et al.   CANCER

PIK3CA Mutation H1047R Is Associated with Response to PI3K/AKT/mTOR Signaling Pathway Inhibitors in Early-Phase Clinical Trials

(2012) F. Janku et al.   CANCER RESEARCH

RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings

(2012) Shancheng Ren et al.   CELL RESEARCH

Biomarkers of Response to Akt Inhibitor MK-2206 in Breast Cancer

(2012) T. Sangai et al.   CLINICAL CANCER RESEARCH

Exome Sequencing of Prostate Cancer Supports the Hypothesis of Independent Tumour Origins

(2012) Johan Lindberg et al.   EUROPEAN UROLOGY

The Mitochondrial and Autosomal Mutation Landscapes of Prostate Cancer

(2012) Johan Lindberg et al.   EUROPEAN UROLOGY

nFuse: Discovery of complex genomic rearrangements in cancer using high-throughput sequencing

(2012) A. McPherson et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Epigenetic markers of prostate cancer in plasma circulating DNA

(2012) Rene Cortese et al.   HUMAN MOLECULAR GENETICS

Detecting false-positive signals in exome sequencing

(2012) Karin V. Fuentes Fajardo et al.   HUMAN MUTATION

Validating the Interval to Biochemical Failure for the Identification of Potentially Lethal Prostate Cancer

(2012) Mark K. Buyyounouski et al.   JOURNAL OF CLINICAL ONCOLOGY

Prognostic value of blood mRNA expression signatures in castration-resistant prostate cancer: a prospective, two-stage study

(2012) David Olmos et al.   LANCET ONCOLOGY

The mutational landscape of lethal castration-resistant prostate cancer

(2012) Catherine S. Grasso et al.   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer

(2012) Christopher E Barbieri et al.   NATURE GENETICS

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

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

Database resources of the National Center for Biotechnology Information

(2012)   NUCLEIC ACIDS RESEARCH

qpure: A Tool to Estimate Tumor Cellularity from Genome-Wide Single-Nucleotide Polymorphism Profiles

(2012) Sarah Song et al.   PLoS One

The Duplicated Genes Database: Identification and Functional Annotation of Co-Localised Duplicated Genes across Genomes

(2012) Marion Ouedraogo et al.   PLoS One

Tabix: fast retrieval of sequence features from generic TAB-delimited files

(2011) H. Li   BIOINFORMATICS

SeqWare Query Engine: storing and searching sequence data in the cloud

(2011) Brian D O’Connor et al.   BMC BIOINFORMATICS

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

(2011) Hanbo Chen et al.   BMC BIOINFORMATICS

NKX3.1 Haploinsufficiency Is Prognostic for Prostate Cancer Relapse following Surgery or Image-Guided Radiotherapy

(2011) J. A. Locke et al.   CLINICAL CANCER RESEARCH

mRNA Expression Signature of Gleason Grade Predicts Lethal Prostate Cancer

(2011) Kathryn L. Penney et al.   JOURNAL OF CLINICAL ONCOLOGY

The genomic complexity of primary human prostate cancer

(2011) Michael F. Berger et al.   NATURE

Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression

(2011) John R Prensner et al.   NATURE BIOTECHNOLOGY

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

(2011) Mark A DePristo et al.   NATURE GENETICS

CREST maps somatic structural variation in cancer genomes with base-pair resolution

(2011) Jianmin Wang et al.   NATURE METHODS

Exome sequencing identifies a spectrum of mutation frequencies in advanced and lethal prostate cancers

(2011) A. Kumar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Allelic loss of the loci containing the androgen synthesis gene, StAR, is prognostic for relapse in intermediate-risk prostate cancer

(2011) Jennifer A. Locke et al.   PROSTATE

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

(2011) Craig H Mermel et al.   GENOME BIOLOGY

A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries

(2011) Sheila Fisher et al.   GENOME BIOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Integrative Genomic Profiling of Human Prostate Cancer

(2010) Barry S. Taylor et al.   CANCER CELL

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

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

(2010) S. A. Forbes et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

High-resolution array CGH identifies novel regions of genomic alteration in intermediate-risk prostate cancer

(2009) Adrian S. Ishkanian et al.   PROSTATE