Integrative genomic and transcriptomic analysis of leiomyosarcoma

Spectrum of mutations in leiomyosarcomas identified by clinical targeted next-generation sequencing

(2017) Paul J Lee et al.   EXPERIMENTAL AND MOLECULAR PATHOLOGY

PARP1 expression drives the synergistic antitumor activity of trabectedin and PARP1 inhibitors in sarcoma preclinical models

(2017) Ymera Pignochino et al.   Molecular Cancer

Systematic analysis of telomere length and somatic alterations in 31 cancer types

(2017) Floris P Barthel et al.   NATURE GENETICS

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Enhancing the Cytotoxic Effects of PARP Inhibitors with DNA Demethylating Agents – A Potential Therapy for Cancer

(2016) Nidal E. Muvarak et al.   CANCER CELL

FANCD2 limits BLM-dependent telomere instability in the alternative lengthening of telomeres pathway

(2016) Heather Root et al.   HUMAN MOLECULAR GENETICS

Olaratumab and doxorubicin versus doxorubicin alone for treatment of soft-tissue sarcoma: an open-label phase 1b and randomised phase 2 trial

(2016) William D Tap et al.   LANCET

The Role of Aneuploidy in Cancer Evolution

(2016) Laurent Sansregret et al.   Cold Spring Harbor Perspectives in Medicine

Exome Sequencing of Uterine Leiomyosarcomas Identifies Frequent Mutations in TP53, ATRX, and MED12

(2016) Netta Mäkinen et al.   PLoS Genetics

Tetraploidy and CIN: a dangerous combination

(2015) Sally Dewhurst et al.   CELL CYCLE

Clinically Relevant Molecular Subtypes in Leiomyosarcoma

(2015) X. Guo et al.   CLINICAL CANCER RESEARCH

Targeted exome sequencing profiles genetic alterations in leiomyosarcoma

(2015) Narasimhan P. Agaram et al.   GENES CHROMOSOMES & CANCER

Alternative lengthening of telomeres renders cancer cells hypersensitive to ATR inhibitors

(2015) R. L. Flynn et al.   SCIENCE

Suppression of the alternative lengthening of telomere pathway by the chromatin remodelling factor ATRX

(2015) David Clynes et al.   Nature Communications

Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data

(2014) F. Favero et al.   ANNALS OF ONCOLOGY

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Therapeutic Targeting of Cancers with Loss of PTEN Function

(2014) Lloye Dillon et al.   CURRENT DRUG TARGETS

Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes

(2014) Mark D M Leiserson et al.   NATURE GENETICS

Systemic treatment of soft-tissue sarcoma—gold standard and novel therapies

(2014) Mark Linch et al.   Nature Reviews Clinical Oncology

Tolerance of Whole-Genome Doubling Propagates Chromosomal Instability and Accelerates Cancer Genome Evolution

(2014) S. M. Dewhurst et al.   Cancer Discovery

A Small Molecule Inhibitor of the BLM Helicase Modulates Chromosome Stability in Human Cells

(2013) Giang Huong Nguyen et al.   CHEMISTRY & BIOLOGY

Genetic Profiling Identifies Two Classes of Soft-Tissue Leiomyosarcomas with Distinct Clinical Characteristics

(2013) A. Italiano et al.   CLINICAL CANCER RESEARCH

Chromothripsis and beyond: rapid genome evolution from complex chromosomal rearrangements

(2013) C.-Z. Zhang et al.   GENES & DEVELOPMENT

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

Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma

(2013) David T W Jones et al.   NATURE GENETICS

Nuclear PTEN Controls DNA Repair and Sensitivity to Genotoxic Stress

(2013) C. Bassi et al.   SCIENCE

Drugging Topoisomerases: Lessons and Challenges

(2012) Yves Pommier   ACS Chemical Biology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Genome Sequencing of Pediatric Medulloblastoma Links Catastrophic DNA Rearrangements with TP53 Mutations

(2012) Tobias Rausch et al.   CELL

cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate

(2012) Günter Klambauer et al.   NUCLEIC ACIDS RESEARCH

Loss of ATRX, Genome Instability, and an Altered DNA Damage Response Are Hallmarks of the Alternative Lengthening of Telomeres Pathway

(2012) Courtney A. Lovejoy et al.   PLoS Genetics

PML body meets telomere

(2012) Inn Chung et al.   Nucleus

Parent-specific copy number in paired tumor–normal studies using circular binary segmentation

(2011) Adam B. Olshen et al.   BIOINFORMATICS

Sarcomas in TP53 germline mutation carriers

(2011) Simona Ognjanovic et al.   CANCER

Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development

(2011) Philip J. Stephens et al.   CELL

Algorithms for Detecting Significantly Mutated Pathways in Cancer

(2011) Fabio Vandin et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The underlying mechanism for the PARP and BRCA synthetic lethality: Clearing up the misunderstandings

(2011) Thomas Helleday   Molecular Oncology

Exome sequencing identifies MAX mutations as a cause of hereditary pheochromocytoma

(2011) Iñaki Comino-Méndez et al.   NATURE GENETICS

Altered Telomeres in Tumors with ATRX and DAXX Mutations

(2011) C. M. Heaphy et al.   SCIENCE

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

Constant p53 Pathway Inactivation in a Large Series of Soft Tissue Sarcomas with Complex Genetics

(2010) Gaëlle Pérot et al.   AMERICAN JOURNAL OF PATHOLOGY

Testing new regimens in patients with advanced soft tissue sarcoma: analysis of publications from the last 10 years

(2010) N. Penel et al.   ANNALS OF ONCOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Comprehensive Mapping of p53 Pathway Alterations Reveals an Apparent Role for Both SNP309 and MDM2 Amplification in Sarcomagenesis

(2010) M. Ito et al.   CLINICAL CANCER RESEARCH

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Validated prediction of clinical outcome in sarcomas and multiple types of cancer on the basis of a gene expression signature related to genome complexity

(2010) Frédéric Chibon et al.   NATURE MEDICINE

Alternative lengthening of telomeres: models, mechanisms and implications

(2010) Anthony J. Cesare et al.   NATURE REVIEWS GENETICS

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Synthetic lethal targeting ofPTENmutant cells with PARP inhibitors

(2009) Ana M. Mendes-Pereira et al.   EMBO Molecular Medicine

DNA C-circles are specific and quantifiable markers of alternative-lengthening-of-telomeres activity

(2009) Jeremy D Henson et al.   NATURE BIOTECHNOLOGY

A gene expression signature classifying telomerase and ALT immortalization reveals an hTERT regulatory network and suggests a mesenchymal stem cell origin for ALT

(2009) K Lafferty-Whyte et al.   ONCOGENE

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

(2009) Bryan N. Howie et al.   PLoS Genetics

A quantitative real-time PCR method for absolute telomere length

(2008) Nathan J. O'Callaghan et al.   BIOTECHNIQUES

Genetic aberrations in soft tissue leiomyosarcoma

(2008) Jilong Yang et al.   CANCER LETTERS