Copy number signatures and mutational processes in ovarian carcinoma

Chromosomal instability drives metastasis through a cytosolic DNA response

(2018) Samuel F. Bakhoum et al.   NATURE

Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations

(2018) David Tamborero et al.   Genome Medicine

Rucaparib in relapsed, platinum-sensitive high-grade ovarian carcinoma (ARIEL2 Part 1): an international, multicentre, open-label, phase 2 trial

(2017) Elizabeth M Swisher et al.   LANCET ONCOLOGY

Comparative analysis of whole genome sequencing-based telomere length measurement techniques

(2017) Michael Lee et al.   METHODS

Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes

(2017) Yi Kan Wang et al.   NATURE GENETICS

Oncogenic PIK3CA induces centrosome amplification and tolerance to genome doubling

(2017) Inma M. Berenjeno et al.   Nature Communications

Ovarian Cancers Harboring Inactivating Mutations inCDK12Display a Distinct Genomic Instability Pattern Characterized by Large Tandem Duplications

(2016) Tatiana Popova et al.   CANCER RESEARCH

ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization

(2016) Guangchuang Yu et al.   Molecular BioSystems

Landscape of somatic mutations in 560 breast cancer whole-genome sequences

(2016) Serena Nik-Zainal et al.   NATURE

Mutational signatures in esophageal adenocarcinoma define etiologically distinct subgroups with therapeutic relevance

(2016) Maria Secrier et al.   NATURE GENETICS

VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research

(2016) Zhongwu Lai et al.   NUCLEIC ACIDS RESEARCH

The tandem duplicator phenotype as a distinct genomic configuration in cancer

(2016) Francesca Menghi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequencing Structural Variants in Cancer for Precision Therapeutics

(2016) Geoff Macintyre et al.   TRENDS IN GENETICS

Methanol-based fixation is superior to buffered formalin for next-generation sequencing of DNA from clinical cancer samples

(2015) A. M. Piskorz et al.   ANNALS OF ONCOLOGY

Identification of major factors associated with failed clinical molecular oncology testing performed by next generation sequencing (NGS)

(2015) Hussam Al-Kateb et al.   Molecular Oncology

Whole–genome characterization of chemoresistant ovarian cancer

(2015) Ann-Marie Patch et al.   NATURE

Spatial and Temporal Heterogeneity in High-Grade Serous Ovarian Cancer: A Phylogenetic Analysis

(2015) Roland F. Schwarz et al.   PLOS MEDICINE

FlexMix Version 2: Finite Mixtures with Concomitant Variables and Varying and Constant Parameters

(2015) Bettina Grün et al.   Journal of Statistical Software

NbClust: AnRPackage for Determining the Relevant Number of Clusters in a Data Set

(2015) Malika Charrad et al.   Journal of Statistical Software

ShatterProof: operational detection and quantification of chromothripsis

(2014) Shaylan K Govind et al.   BMC BIOINFORMATICS

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

(2014) Katherine A. Hoadley et al.   CELL

Germline Mutation in BRCA1 or BRCA2 and Ten-Year Survival for Women Diagnosed with Epithelial Ovarian Cancer

(2014) Francisco J. Candido-dos-Reis et al.   CLINICAL CANCER RESEARCH

DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly

(2014) Ilari Scheinin et al.   GENOME RESEARCH

Criteria for Inference of Chromothripsis in Cancer Genomes

(2013) Jan O. Korbel et al.   CELL

Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms

(2013) A. Malhotra et al.   GENOME RESEARCH

Integrated genomic characterization of endometrial carcinoma

(2013) Gad Getz et al.   NATURE

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Pan-cancer patterns of somatic copy number alteration

(2013) Travis I Zack et al.   NATURE GENETICS

Emerging landscape of oncogenic signatures across human cancers

(2013) Giovanni Ciriello et al.   NATURE GENETICS

Synthetic lethality between CCNE1 amplification and loss of BRCA1

(2013) D. Etemadmoghadam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An algorithmic approach for breakage-fusion-bridge detection in tumor genomes

(2013) S. Zakov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups

(2012) Christina Curtis et al.   NATURE

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

The role of tandem duplicator phenotype in tumour evolution in high-grade serous ovarian cancer

(2011) Charlotte KY Ng et al.   JOURNAL OF PATHOLOGY

Olaparib in patients with recurrent high-grade serous or poorly differentiated ovarian carcinoma or triple-negative breast cancer: a phase 2, multicentre, open-label, non-randomised study

(2011) Karen A Gelmon et al.   LANCET ONCOLOGY

Telomere dysfunction and chromosome instability

(2011) John P. Murnane   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

Integrated genomic analyses of ovarian carcinoma

(2011) D. Bell et al.   NATURE

A flexible R package for nonnegative matrix factorization

(2010) Renaud Gaujoux et al.   BMC BIOINFORMATICS

Poly(ADP)-Ribose Polymerase Inhibition: Frequent Durable Responses inBRCACarrier Ovarian Cancer Correlating With Platinum-Free Interval

(2010) Peter C. Fong et al.   JOURNAL OF CLINICAL ONCOLOGY

Driver mutations in TP53 are ubiquitous in high grade serous carcinoma of the ovary

(2010) Ahmed Ashour Ahmed et al.   JOURNAL OF PATHOLOGY

Allele-specific copy number analysis of tumors

(2010) P. Van Loo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

Integrated Genome-Wide DNA Copy Number and Expression Analysis Identifies Distinct Mechanisms of Primary Chemoresistance in Ovarian Carcinomas

(2009) D. Etemadmoghadam et al.   CLINICAL CANCER RESEARCH