Pharmacogenomic landscape of patient-derived tumor cells informs precision oncology therapy

Spatiotemporal genomic architecture informs precision oncology in glioblastoma

(2017) Jin-Ku Lee et al.   NATURE GENETICS

Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients

(2017) Ahmet Zehir et al.   NATURE MEDICINE

A Landscape of Pharmacogenomic Interactions in Cancer

(2016) Francesco Iorio et al.   CELL

Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma

(2016) Michele Ceccarelli et al.   CELL

Multifocal and multicentric glioblastoma: Improved characterisation with FLAIR imaging and prognostic implications

(2016) Arian Lasocki et al.   JOURNAL OF CLINICAL NEUROSCIENCE

Lapatinib in Combination With Capecitabine Plus Oxaliplatin in Human Epidermal Growth Factor Receptor 2–Positive Advanced or Metastatic Gastric, Esophageal, or Gastroesophageal Adenocarcinoma: TRIO-013/LOGiC—A Randomized Phase III Trial

(2016) J. Randolph Hecht et al.   JOURNAL OF CLINICAL ONCOLOGY

A combinatorial strategy for treating KRAS-mutant lung cancer

(2016) Eusebio Manchado et al.   NATURE

Genomic Alterations in Biliary Tract Cancer Using Targeted Sequencing

(2016) Kwai Han Yoo et al.   Translational Oncology

Patient-derived glioblastoma stem cells respond differentially to targeted therapies

(2016) Pratik Kanabur et al.   Oncotarget

Elucidation of Resistance Mechanisms to Second-Generation ALK Inhibitors Alectinib and Ceritinib in Non–Small Cell Lung Cancer Cells

(2016) Xuyuan Dong et al.   NEOPLASIA

Topological Data Analysis Generates High-Resolution, Genome-wide Maps of Human Recombination

(2016) Pablo G. Camara et al.   Cell Systems

Genetic, epigenetic, and molecular landscapes of multifocal and multicentric glioblastoma

(2015) Qun Liu et al.   ACTA NEUROPATHOLOGICA

A randomized phase II study of the MEK1/MEK2 inhibitor trametinib (GSK1120212) compared with docetaxel in KRAS-mutant advanced non-small-cell lung cancer (NSCLC)†

(2015) G. R. Blumenschein et al.   ANNALS OF ONCOLOGY

Activity of ibrutinib in mantle cell lymphoma patients with central nervous system relapse

(2015) S. Bernard et al.   BLOOD

In Silico Prescription of Anticancer Drugs to Cohorts of 28 Tumor Types Reveals Targeting Opportunities

(2015) Carlota Rubio-Perez et al.   CANCER CELL

Prospective Derivation of a Living Organoid Biobank of Colorectal Cancer Patients

(2015) Marc van de Wetering et al.   CELL

Precision medicine: lessons learned from the SHIVA trial

(2015) Apostolia M Tsimberidou et al.   LANCET ONCOLOGY

Mutational landscape and clonal architecture in grade II and III gliomas

(2015) Hiromichi Suzuki et al.   NATURE GENETICS

High-throughput screening using patient-derived tumor xenografts to predict clinical trial drug response

(2015) Hui Gao et al.   NATURE MEDICINE

Subclonal diversification of primary breast cancer revealed by multiregion sequencing

(2015) Lucy R Yates et al.   NATURE MEDICINE

Phase II study of panobinostat in combination with bevacizumab for recurrent glioblastoma and anaplastic glioma

(2015) E. Q. Lee et al.   NEURO-ONCOLOGY

The expression of the PI3K/AKT/mTOR pathway in gastric cancer and its role in gastric cancer prognosis

(2015) Jieer Ying et al.   OncoTargets and Therapy

Predicting Cancer Drug Response: Advancing the DREAM

(2015) R. B. Altman   Cancer Discovery

Combined EGFR/MEK Inhibition Prevents the Emergence of Resistance in EGFR-Mutant Lung Cancer

(2015) E. M. Tricker et al.   Cancer Discovery

Afatinib, an irreversible ErbB family blocker, with protracted temozolomide in recurrent glioblastoma: A case report

(2015) Jad Alshami et al.   Oncotarget

Critical role of Wnt/β-catenin signaling in driving epithelial ovarian cancer platinum resistance

(2015) Anil Belur Nagaraj et al.   Oncotarget

The Human Glioblastoma Cell Culture Resource: Validated Cell Models Representing All Molecular Subtypes

(2015) Yuan Xie et al.   EBioMedicine

CDK4/6 Inhibitor PD0332991 in Glioblastoma Treatment: Does It Have a Future?

(2015) Lisette B. W. Schröder et al.   Frontiers in Oncology

PRADA: pipeline for RNA sequencing data analysis

(2014) Wandaliz Torres-García et al.   BIOINFORMATICS

Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer

(2014) Francesco Abate et al.   BMC Systems Biology

Molecular Pathways: Targeting NRG1 Fusions in Lung Cancer

(2014) L. Fernandez-Cuesta et al.   CLINICAL CANCER RESEARCH

The evolving role of cancer cell line-based screens to define the impact of cancer genomes on drug response

(2014) Mathew J Garnett et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

BYL719, a selective inhibitor of phosphoinositide 3-Kinase α, enhances the effect of selumetinib (AZD6244, ARRY-142886) in KRAS-mutant non-small cell lung cancer

(2014) Bo Mi Ku et al.   INVESTIGATIONAL NEW DRUGS

Selective Antitumor Activity of Ibrutinib in EGFR-Mutant Non–Small Cell Lung Cancer Cells

(2014) Wen Gao et al.   JNCI-Journal of the National Cancer Institute

Comprehensive molecular characterization of gastric adenocarcinoma

(2014) Adam J. Bass et al.   NATURE

A phase II trial of everolimus, temozolomide, and radiotherapy in patients with newly diagnosed glioblastoma: NCCTG N057K

(2014) Daniel J. Ma et al.   NEURO-ONCOLOGY

Phase II trial of sunitinib for recurrent and progressive atypical and anaplastic meningioma

(2014) Thomas J. Kaley et al.   NEURO-ONCOLOGY

Resistance to dual blockade of the kinases PI3K and mTOR in KRAS-mutant colorectal cancer models results in combined sensitivity to inhibition of the receptor tyrosine kinase EGFR

(2014) P. J. Belmont et al.   Science Signaling

The PI3K/AKT/mTOR pathway is activated in gastric cancer with potential prognostic and predictive significance

(2014) Oscar Tapia et al.   VIRCHOWS ARCHIV

HDAC4: mechanism of regulation and biological functions

(2014) Zhengke Wang et al.   Epigenomics

Intrinsic Resistance to MEK Inhibition in KRAS Mutant Lung and Colon Cancer through Transcriptional Induction of ERBB3

(2014) Chong Sun et al.   Cell Reports

Clinical drug response can be predicted using baseline gene expression levels and in vitro drug sensitivity in cell lines

(2014) Paul Geeleher et al.   GENOME BIOLOGY

Early responses predict better outcomes in patients with newly diagnosed chronic myeloid leukemia: results with four tyrosine kinase inhibitor modalities

(2013) P. Jain et al.   BLOOD

MutComFocal: an integrative approach to identifying recurrent and focal genomic alterations in tumor samples

(2013) Vladimir Trifonov et al.   BMC Systems Biology

EGFR Phosphorylates Tumor-Derived EGFRvIII Driving STAT3/5 and Progression in Glioblastoma

(2013) Qi-Wen Fan et al.   CANCER CELL

An Interactive Resource to Identify Cancer Genetic and Lineage Dependencies Targeted by Small Molecules

(2013) Amrita Basu et al.   CELL

The Somatic Genomic Landscape of Glioblastoma

(2013) Cameron W. Brennan et al.   CELL

The Tumor Suppressor Kinase LKB1 Activates the Downstream Kinases SIK2 and SIK3 to Stimulate Nuclear Export of Class IIa Histone Deacetylases

(2013) Donald R. Walkinshaw et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Inhibition of the PI3K/AKT pathway potentiates cytotoxicity of EGFR kinase inhibitors in triple-negative breast cancer cells

(2013) Yong Weon Yi et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

The causes and consequences of genetic heterogeneity in cancer evolution

(2013) Rebecca A. Burrell et al.   NATURE

Mechanism of MEK inhibition determines efficacy in mutant KRAS- versus BRAF-driven cancers

(2013) Georgia Hatzivassiliou et al.   NATURE

Metrics other than potency reveal systematic variation in responses to cancer drugs

(2013) Mohammad Fallahi-Sichani et al.   Nature Chemical Biology

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Coordinate activation of Shh and PI3K signaling in PTEN-deficient glioblastoma: new therapeutic opportunities

(2013) Mariella Gruber Filbin et al.   NATURE MEDICINE

DGIdb: mining the druggable genome

(2013) Malachi Griffith et al.   NATURE METHODS

Mutations in regulators of the epigenome and their connections to global chromatin patterns in cancer

(2013) Christoph Plass et al.   NATURE REVIEWS GENETICS

Ibrutinib in Relapsed Chronic Lymphocytic Leukemia

(2013)   NEW ENGLAND JOURNAL OF MEDICINE

Targeting BTK with Ibrutinib in Relapsed or Refractory Mantle-Cell Lymphoma

(2013) Michael L. Wang et al.   NEW ENGLAND JOURNAL OF MEDICINE

Targeting BTK with Ibrutinib in Relapsed Chronic Lymphocytic Leukemia

(2013) John C. Byrd et al.   NEW ENGLAND JOURNAL OF MEDICINE

The EphB4 Receptor Tyrosine Kinase Promotes Lung Cancer Growth: A Potential Novel Therapeutic Target

(2013) Benjamin D. Ferguson et al.   PLoS One

Targeted Therapy Resistance Mediated by Dynamic Regulation of Extrachromosomal Mutant EGFR DNA

(2013) David A. Nathanson et al.   SCIENCE

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Patient-Specific Orthotopic Glioblastoma Xenograft Models Recapitulate the Histopathology and Biology of Human Glioblastomas In Situ

(2013) Kyeung Min Joo et al.   Cell Reports

EXCAVATOR: detecting copy number variants from whole-exome sequencing data

(2013) Alberto Magi et al.   GENOME BIOLOGY

Pharmacologic synergy between dual phosphoinositide-3-kinase and mammalian target of rapamycin inhibition and 5-Fluorouracil inPIK3CAmutant gastric cancer cells

(2012) Bhaskar Bhattacharya et al.   CANCER BIOLOGY & THERAPY

MET Signaling Regulates Glioblastoma Stem Cells

(2012) K. M. Joo et al.   CANCER RESEARCH

Targeting EGFR for Treatment of Glioblastoma: Molecular Basis to Overcome Resistance

(2012) T. E. Taylor et al.   CURRENT CANCER DRUG TARGETS

Role of Wnt/β-catenin Signaling in Drug Resistance of Pancreatic Cancer

(2012) Jiujie Cui et al.   CURRENT PHARMACEUTICAL DESIGN

Safety, pharmacokinetic, pharmacodynamic, and efficacy data for the oral MEK inhibitor trametinib: a phase 1 dose-escalation trial

(2012) Jeffrey R Infante et al.   LANCET ONCOLOGY

REST Is a Novel Prognostic Factor and Therapeutic Target for Medulloblastoma

(2012) P. Taylor et al.   MOLECULAR CANCER THERAPEUTICS

A Direct HDAC4-MAP Kinase Crosstalk Activates Muscle Atrophy Program

(2012) Moon-Chang Choi et al.   MOLECULAR CELL

MEK inhibitors reverse resistance in epidermal growth factor receptor mutation lung cancer cells with acquired resistance to gefitinib

(2012) Ming-Hung Huang et al.   Molecular Oncology

Systematic identification of genomic markers of drug sensitivity in cancer cells

(2012) Mathew J. Garnett et al.   NATURE

Emergence of KRAS mutations and acquired resistance to anti-EGFR therapy in colorectal cancer

(2012) Sandra Misale et al.   NATURE

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

(2012) Jordi Barretina et al.   NATURE

p16-Cdk4-Rb axis controls sensitivity to a cyclin-dependent kinase inhibitor PD0332991 in glioblastoma xenograft cells

(2012) L. Cen et al.   NEURO-ONCOLOGY

Current clinical development of PI3K pathway inhibitors in glioblastoma

(2012) P. Y. Wen et al.   NEURO-ONCOLOGY

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

Intratumoral heterogeneity of receptor tyrosine kinases EGFR and PDGFRA amplification in glioblastoma defines subpopulations with distinct growth factor response

(2012) N. J. Szerlip et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Different types of K-Ras mutations could affect drug sensitivity and tumour behaviour in non-small-cell lung cancer

(2011) M. C. Garassino et al.   ANNALS OF ONCOLOGY

Glioblastoma: From Molecular Pathology to Targeted Treatment

(2011) Timothy F. Cloughesy et al.   Annual Review of Pathology-Mechanisms of Disease

Comparing Statistical Methods for Quantifying Drug Sensitivity Based on In Vitro Dose–Response Assays

(2011) Shuguang Huang et al.   ASSAY AND DRUG DEVELOPMENT TECHNOLOGIES

ChimeraScan: a tool for identifying chimeric transcription in sequencing data

(2011) Matthew K. Iyer et al.   BIOINFORMATICS

Neuregulin-1-Mediated Autocrine Signaling Underlies Sensitivity to HER2 Kinase Inhibitors in a Subset of Human Cancers

(2011) Timothy R. Wilson et al.   CANCER CELL

Mosaic Amplification of Multiple Receptor Tyrosine Kinase Genes in Glioblastoma

(2011) Matija Snuderl et al.   CANCER CELL

HDAC4 Protein Regulates HIF1α Protein Lysine Acetylation and Cancer Cell Response to Hypoxia

(2011) Hao Geng et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Comprehensive Predictive Biomarker Analysis for MEK Inhibitor GSK1120212

(2011) J. Jing et al.   MOLECULAR CANCER THERAPEUTICS

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Improved Survival with Vemurafenib in Melanoma with BRAF V600E Mutation

(2011) Paul B. Chapman et al.   NEW ENGLAND JOURNAL OF MEDICINE

Topology based data analysis identifies a subgroup of breast cancers with a unique mutational profile and excellent survival

(2011) M. Nicolau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Activated ErbB3/NRG1 Autocrine Loop Supports In Vivo Proliferation in Ovarian Cancer Cells

(2010) Qing Sheng et al.   CANCER CELL

β-Catenin Mediates the Establishment and Drug Resistance of MLL Leukemic Stem Cells

(2010) Jenny Yeung et al.   CANCER CELL

Cell Signaling by Receptor Tyrosine Kinases

(2010) Mark A. Lemmon et al.   CELL

Phase II Evaluation of Gefitinib in Patients With Newly Diagnosed Grade 4 Astrocytoma: Mayo/North Central Cancer Treatment Group Study N0074

(2010) Joon H. Uhm et al.   INTERNATIONAL JOURNAL OF RADIATION ONCOLOGY BIOLOGY PHYSICS

Trastuzumab in combination with chemotherapy versus chemotherapy alone for treatment of HER2-positive advanced gastric or gastro-oesophageal junction cancer (ToGA): a phase 3, open-label, randomised controlled trial

(2010) Yung-Jue Bang et al.   LANCET

ZD6474, a Multitargeted Inhibitor for Receptor Tyrosine Kinases, Suppresses Growth of Gliomas Expressing an Epidermal Growth Factor Receptor Mutant, EGFRvIII, in the Brain

(2010) Jia-Jean Yiin et al.   MOLECULAR CANCER THERAPEUTICS

Analysis of Food and Drug Administration-Approved Anticancer Agents in the NCI60 Panel of Human Tumor Cell Lines

(2010) S. L. Holbeck et al.   MOLECULAR CANCER THERAPEUTICS

The Path to Personalized Medicine

(2010) Margaret A. Hamburg et al.   NEW ENGLAND JOURNAL OF MEDICINE

The Bruton tyrosine kinase inhibitor PCI-32765 blocks B-cell activation and is efficacious in models of autoimmune disease and B-cell malignancy

(2010) L. A. Honigberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A phase I/II trial of GW572016 (lapatinib) in recurrent glioblastoma multiforme: clinical outcomes, pharmacokinetics and molecular correlation

(2009) Brian Thiessen et al.   CANCER CHEMOTHERAPY AND PHARMACOLOGY

Resistance to Targeted Therapies: Refining Anticancer Therapy in the Era of Molecular Oncology

(2009) L. M. Ellis et al.   CLINICAL CANCER RESEARCH

Mechanisms of tumor resistance to EGFR-targeted therapies

(2009) Elizabeth A Hopper-Borge et al.   EXPERT OPINION ON THERAPEUTIC TARGETS

ELDA: Extreme limiting dilution analysis for comparing depleted and enriched populations in stem cell and other assays

(2009) Yifang Hu et al.   JOURNAL OF IMMUNOLOGICAL METHODS

KRAS/BRAF mutation status and ERK1/2 activation as biomarkers for MEK1/2 inhibitor therapy in colorectal cancer

(2009) J. J. Yeh et al.   MOLECULAR CANCER THERAPEUTICS

Combined genomic and gene expression microarray profiling identifies ECOP as an upregulated gene in squamous cell carcinomas independent of DNA amplification

(2009) A Baras et al.   ONCOGENE

Clinical relevance of EGFR- and KRAS-status in colorectal cancer patients treated with monoclonal antibodies directed against the EGFR

(2008) Volker Heinemann et al.   CANCER TREATMENT REVIEWS

New response evaluation criteria in solid tumours: Revised RECIST guideline (version 1.1)

(2008) E.A. Eisenhauer et al.   EUROPEAN JOURNAL OF CANCER

Receiver-operating characteristic curve analysis in diagnostic, prognostic and predictive biomarker research

(2008) K. Soreide   JOURNAL OF CLINICAL PATHOLOGY

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE

Malignant Gliomas in Adults

(2008) Patrick Y. Wen et al.   NEW ENGLAND JOURNAL OF MEDICINE