Optimized detection of homologous recombination deficiency improves the prediction of clinical outcomes in cancer

Pan-cancer analysis of whole genomes

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The repertoire of mutational signatures in human cancer

(2020) Ludmil B. Alexandrov et al.   NATURE

Homologous recombination deficiency status-based classification of high-grade serous ovarian carcinoma

(2020) Hisamitsu Takaya et al.   Scientific Reports

Using whole-genome sequencing data to derive the homologous recombination deficiency scores

(2020) Xavier M. de Luca et al.   npj Breast Cancer

ESMO recommendations on predictive biomarker testing for homologous recombination deficiency and PARP inhibitor benefit in ovarian cancer

(2020) R.E. Miller et al.   ANNALS OF ONCOLOGY

Detecting the mutational signature of homologous recombination deficiency in clinical samples

(2019) Doga C. Gulhan et al.   NATURE GENETICS

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

Whole-genome sequencing of triple-negative breast cancers in a population-based clinical study

(2019) Johan Staaf et al.   NATURE MEDICINE

Niraparib in Patients with Newly Diagnosed Advanced Ovarian Cancer

(2019) Antonio González-Martín et al.   NEW ENGLAND JOURNAL OF MEDICINE

Olaparib plus Bevacizumab as First-Line Maintenance in Ovarian Cancer

(2019) Isabelle Ray-Coquard et al.   NEW ENGLAND JOURNAL OF MEDICINE

Ovarian cancer statistics, 2018

(2018) Lindsey A. Torre et al.   CA-A CANCER JOURNAL FOR CLINICIANS

Genomic and Functional Approaches to Understanding Cancer Aneuploidy

(2018) Alison M. Taylor et al.   CANCER CELL

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

(2018) Jianfang Liu et al.   CELL

Pathogenic Germline Variants in 10,389 Adult Cancers

(2018) Kuan-lin Huang et al.   CELL

Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas

(2018) Theo A. Knijnenburg et al.   Cell Reports

VarSome: the human genomic variant search engine

(2018) Christos Kopanos et al.   BIOINFORMATICS

Contribution of germline deleterious variants in the RAD51 paralogs to breast and ovarian cancers

(2017) Lisa Golmard et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

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

A mutational signature reveals alterations underlying deficient homologous recombination repair in breast cancer

(2017) Paz Polak et al.   NATURE GENETICS

Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes

(2017) Yi Kan Wang et al.   NATURE GENETICS

HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures

(2017) Helen Davies et al.   NATURE MEDICINE

PTEN deficiency sensitizes endometrioid endometrial cancer to compound PARP-PI3K inhibition but not PARP inhibition as monotherapy

(2017) X Bian et al.   ONCOGENE

PARP inhibitors: Synthetic lethality in the clinic

(2017) Christopher J. Lord et al.   SCIENCE

Homologous Recombination Deficiency (HRD) Score Predicts Response to Platinum-Containing Neoadjuvant Chemotherapy in Patients with Triple-Negative Breast Cancer

(2016) M. L. Telli et al.   CLINICAL CANCER RESEARCH

Repair Pathway Choices and Consequences at the Double-Strand Break

(2016) Raphael Ceccaldi et al.   TRENDS IN CELL BIOLOGY

Refinement of Triple-Negative Breast Cancer Molecular Subtypes: Implications for Neoadjuvant Chemotherapy Selection

(2016) Brian D. Lehmann et al.   PLoS One

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology

(2015) Sue Richards et al.   GENETICS IN MEDICINE

Homologous Recombination Deficiency: Exploiting the Fundamental Vulnerability of Ovarian Cancer

(2015) P. A. Konstantinopoulos et al.   Cancer Discovery

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Non-homologous end joining: Emerging themes and unanswered questions

(2014) Sarvan Kumar Radhakrishnan et al.   DNA REPAIR

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

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

Nuclear PTEN Controls DNA Repair and Sensitivity to Genotoxic Stress

(2013) C. Bassi et al.   SCIENCE

Patterns of genomic loss of heterozygosity predict homologous recombination repair defects in epithelial ovarian cancer

(2012) V Abkevich et al.   BRITISH JOURNAL OF CANCER

Ploidy and Large-Scale Genomic Instability Consistently Identify Basal-like Breast Carcinomas with BRCA1/2 Inactivation

(2012) T. Popova et al.   CANCER RESEARCH

Prognostic Value of Residual Tumor Size in Patients With Epithelial Ovarian Cancer FIGO Stages IIA–IV

(2012) Stephan Polterauer et al.   INTERNATIONAL JOURNAL OF GYNECOLOGICAL CANCER

A DNA Repair Pathway–Focused Score for Prediction of Outcomes in Ovarian Cancer Treated With Platinum-Based Chemotherapy

(2012) Josephine Kang et al.   JNCI-Journal of the National Cancer Institute

Telomeric Allelic Imbalance Indicates Defective DNA Repair and Sensitivity to DNA-Damaging Agents

(2012) Nicolai J. Birkbak et al.   Cancer Discovery

High-Throughput Detection of Actionable Genomic Alterations in Clinical Tumor Samples by Targeted, Massively Parallel Sequencing

(2011) Nikhil Wagle et al.   Cancer Discovery

Gene Expression Profile ofBRCAness That Correlates With Responsiveness to Chemotherapy and With Outcome in Patients With Epithelial Ovarian Cancer

(2010) Panagiotis A. Konstantinopoulos et al.   JOURNAL OF CLINICAL ONCOLOGY

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS