Using large-scale genomics data to identify driver mutations in lung cancer: methods and challenges

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Personalized genomic analyses for cancer mutation discovery and interpretation

(2015) Siân Jones et al.   Science Translational Medicine

Discrepancies in Cancer Genomic Sequencing Highlight Opportunities for Driver Mutation Discovery

(2014) A. M. Hudson et al.   CANCER RESEARCH

R102Q Mutation Shifts the Salt-Bridge Network and Reduces the Structural Flexibility of Human Neuronal Calcium Sensor-1 Protein

(2014) Yuzhen Zhu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

ARID1B is a specific vulnerability in ARID1A-mutant cancers

(2014) Katherine C Helming et al.   NATURE MEDICINE

ROS1 — Targeting the One Percent in Lung Cancer

(2014) Kathryn A. Gold   NEW ENGLAND JOURNAL OF MEDICINE

First-Line Crizotinib versus Chemotherapy in ALK-Positive Lung Cancer

(2014) Benjamin J. Solomon et al.   NEW ENGLAND JOURNAL OF MEDICINE

Crizotinib in ROS1-Rearranged Non–Small-Cell Lung Cancer

(2014) Alice T. Shaw et al.   NEW ENGLAND JOURNAL OF MEDICINE

Only three driver gene mutations are required for the development of lung and colorectal cancers

(2014) Cristian Tomasetti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Intratumor heterogeneity in localized lung adenocarcinomas delineated by multiregion sequencing

(2014) J. Zhang et al.   SCIENCE

Spatial and temporal diversity in genomic instability processes defines lung cancer evolution

(2014) E. C. de Bruin et al.   SCIENCE

Functional characterization of a novel missense mutation, His147Arg, in A1 domain of FV protein causing type II deficiency

(2014) Hsiang-Chun Liu et al.   THROMBOSIS RESEARCH

P-loop Conformation Governed Crizotinib Resistance in G2032R-Mutated ROS1 Tyrosine Kinase: Clues from Free Energy Landscape

(2014) Huiyong Sun et al.   PLoS Computational Biology

Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies

(2014) Glenn S Cowley et al.   Scientific Data

Mutation incidence and coincidence in non small-cell lung cancer: meta-analyses by ethnicity and histology (mutMap)

(2013) S. Dearden et al.   ANNALS OF ONCOLOGY

OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes

(2013) David Tamborero et al.   BIOINFORMATICS

Molecular dynamics and docking simulation of a natural variant of Activated Protein C with impaired protease activity: implications for integrin-mediated antiseptic function

(2013) Pasqualina D’Ursi et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Relationship between a point mutation S97C in CK1δ protein and its affect on ATP-binding affinity

(2013) Ambuj Kumar et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Phase III Study of Afatinib or Cisplatin Plus Pemetrexed in Patients With Metastatic Lung Adenocarcinoma WithEGFRMutations

(2013) Lecia V. Sequist et al.   JOURNAL OF CLINICAL ONCOLOGY

Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers

(2013) J. Reimand et al.   Molecular Systems Biology

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

Inconsistency in large pharmacogenomic studies

(2013) Benjamin Haibe-Kains et al.   NATURE

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

A panoramic view of acute myeloid leukemia

(2013) Sai-Juan Chen et al.   NATURE GENETICS

Network-based stratification of tumor mutations

(2013) Matan Hofree et al.   NATURE METHODS

Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

(2013)   NEW ENGLAND JOURNAL OF MEDICINE

Two-state dynamics of the SH3–SH2 tandem of Abl kinase and the allosteric role of the N-cap

(2013) Carles Corbi-Verge et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeted genetic dependency screen facilitates identification of actionable mutations in FGFR4, MAP3K9, and PAK5 in lung cancer

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

Effects of oncogenic mutations on the conformational free-energy landscape of EGFR kinase

(2013) L. Sutto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic Screens in Human Cells Using the CRISPR-Cas9 System

(2013) Tim Wang et al.   SCIENCE

Differential Relationship of DNA Replication Timing to Different Forms of Human Mutation and Variation

(2012) Amnon Koren et al.   AMERICAN JOURNAL OF HUMAN GENETICS

β-Catenin-Driven Cancers Require a YAP1 Transcriptional Complex for Survival and Tumorigenesis

(2012) Joseph Rosenbluh et al.   CELL

Inhibition of MEK and PI3K/mTOR Suppresses Tumor Growth but Does Not Cause Tumor Regression in Patient-Derived Xenografts of RAS-Mutant Colorectal Carcinomas

(2012) G. Migliardi et al.   CLINICAL CANCER RESEARCH

Molecular Epidemiology of EGFR and KRAS Mutations in 3,026 Lung Adenocarcinomas: Higher Susceptibility of Women to Smoking-Related KRAS-Mutant Cancers

(2012) S. Dogan et al.   CLINICAL CANCER RESEARCH

MuSiC: Identifying mutational significance in cancer genomes

(2012) N. D. Dees et al.   GENOME RESEARCH

Erlotinib versus standard chemotherapy as first-line treatment for European patients with advanced EGFR mutation-positive non-small-cell lung cancer (EURTAC): a multicentre, open-label, randomised phase 3 trial

(2012) Rafael Rosell et al.   LANCET ONCOLOGY

Selumetinib plus docetaxel for KRAS-mutant advanced non-small-cell lung cancer: a randomised, multicentre, placebo-controlled, phase 2 study

(2012) Pasi A Jänne et al.   LANCET ONCOLOGY

Unresponsiveness of colon cancer to BRAF(V600E) inhibition through feedback activation of EGFR

(2012) Anirudh Prahallad et al.   NATURE

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

(2012) Jordi Barretina et al.   NATURE

Predicting the Functional Effect of Amino Acid Substitutions and Indels

(2012) Yongwook Choi et al.   PLoS One

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1.

(2012) Ethan Cerami et al.   Cancer Discovery

Identification of Molecular Vulnerabilities in Human Multiple Myeloma Cells by RNA Interference Lethality Screening of the Druggable Genome

(2011) R. E. Tiedemann et al.   CANCER RESEARCH

Cancer-Associated Loss-of-Function Mutations Implicate DAPK3 as a Tumor-Suppressing Kinase

(2011) J. Brognard et al.   CANCER RESEARCH

Oncogene addiction as a foundational rationale for targeted anti-cancer therapy: promises and perils

(2011) Davide Torti et al.   EMBO Molecular Medicine

Clinical Characteristics of Patients With Lung Adenocarcinomas HarboringBRAFMutations

(2011) Paul K. Paik et al.   JOURNAL OF CLINICAL ONCOLOGY

New driver mutations in non-small-cell lung cancer

(2011) William Pao et al.   LANCET ONCOLOGY

High-throughput RNAi Screening Identifies a Role for TNK1 in Growth and Survival of Pancreatic Cancer Cells

(2011) M. C. Henderson et al.   MOLECULAR CANCER RESEARCH

Predicting the functional impact of protein mutations: application to cancer genomics

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer

(2011) H. W. Cheung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The BATTLE Trial: Personalizing Therapy for Lung Cancer

(2011) Edward S. Kim et al.   Cancer Discovery

Randomized Phase II Multicenter Trial of Two Schedules of Lapatinib as First- or Second-Line Monotherapy in Patients with Advanced or Metastatic Non-Small Cell Lung Cancer

(2010) H. J. Ross et al.   CLINICAL CANCER RESEARCH

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

Gefitinib or Chemotherapy for Non–Small-Cell Lung Cancer with Mutated EGFR

(2010) Makoto Maemondo et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

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

Clinical Features and Outcome of Patients With Non–Small-Cell Lung Cancer Who Harbor EML4-ALK

(2009) Alice T. Shaw et al.   JOURNAL OF CLINICAL ONCOLOGY

Gefitinib versus cisplatin plus docetaxel in patients with non-small-cell lung cancer harbouring mutations of the epidermal growth factor receptor (WJTOG3405): an open label, randomised phase 3 trial

(2009) Tetsuya Mitsudomi et al.   LANCET ONCOLOGY

p16INK4A inactivation mechanisms in non-small-cell lung cancer patients occupationally exposed to asbestos

(2009) Pascal Andujar et al.   LUNG CANCER

Small interfering RNA library screen of human kinases and phosphatases identifies polo-like kinase 1 as a promising new target for the treatment of pediatric rhabdomyosarcomas

(2009) K. Hu et al.   MOLECULAR CANCER THERAPEUTICS

Identification of Survival Genes in Human Glioblastoma Cells by Small Interfering RNA Screening

(2009) N. G. Thaker et al.   MOLECULAR PHARMACOLOGY

A small-cell lung cancer genome with complex signatures of tobacco exposure

(2009) Erin D. Pleasance et al.   NATURE

Human mutation rate associated with DNA replication timing

(2009) John A Stamatoyannopoulos et al.   NATURE GENETICS

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols

Gefitinib or Carboplatin–Paclitaxel in Pulmonary Adenocarcinoma

(2009) Tony S. Mok et al.   NEW ENGLAND JOURNAL OF MEDICINE

Oncogene Addiction

(2008) I. B. Weinstein et al.   CANCER RESEARCH

RNAi-Mediated Silencing of Nuclear Factor Erythroid-2-Related Factor 2 Gene Expression in Non-Small Cell Lung Cancer Inhibits Tumor Growth and Increases Efficacy of Chemotherapy

(2008) A. Singh et al.   CANCER RESEARCH

Transcription-coupled DNA repair: two decades of progress and surprises

(2008) Philip C. Hanawalt et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY