Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas

Cancer statistics, 2015

(2015) Rebecca L. Siegel et al.   CA-A CANCER JOURNAL FOR CLINICIANS

Concurrence of EGFR amplification and sensitizing mutations indicate a better survival benefit from EGFR-TKI therapy in lung adenocarcinoma patients

(2015) Ling Shan et al.   LUNG CANCER

Comprehensive genomic characterization of head and neck squamous cell carcinomas

(2015)   NATURE

Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes

(2015) Sachet A Shukla et al.   NATURE BIOTECHNOLOGY

Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers

(2015) Xiaoyang Zhang et al.   NATURE GENETICS

Clock-like mutational processes in human somatic cells

(2015) Ludmil B Alexandrov et al.   NATURE GENETICS

Systematic discovery of complex insertions and deletions in human cancers

(2015) Kai Ye et al.   NATURE MEDICINE

Nivolumab versus Docetaxel in Advanced Squamous-Cell Non–Small-Cell Lung Cancer

(2015) Julie Brahmer et al.   NEW ENGLAND JOURNAL OF MEDICINE

Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer

(2015) N. A. Rizvi et al.   SCIENCE

EGFR Kinase Domain Duplication (EGFR-KDD) Is a Novel Oncogenic Driver in Lung Cancer That Is Clinically Responsive to Afatinib

(2015) J.-N. Gallant et al.   Cancer Discovery

PRADA: pipeline for RNA sequencing data analysis

(2014) Wandaliz Torres-García et al.   BIOINFORMATICS

Dragging Ras Back in the Ring

(2014) Andrew G. Stephen et al.   CANCER CELL

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

(2014) Katherine A. Hoadley et al.   CELL

Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens

(2014) Matthew M. Gubin et al.   NATURE

Comprehensive molecular profiling of lung adenocarcinoma

(2014) Eric A. Collisson et al.   NATURE

Comprehensive molecular characterization of urothelial bladder carcinoma

(2014)   NATURE

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

The landscape and therapeutic relevance of cancer-associated transcript fusions

(2014) K Yoshihara et al.   ONCOGENE

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

The landscape of kinase fusions in cancer

(2014) Nicolas Stransky et al.   Nature Communications

The Impact of Genomic Changes on Treatment of Lung Cancer

(2013) Stephanie Cardarella et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Combination of Protein Coding and Noncoding Gene Expression as a Robust Prognostic Classifier in Stage I Lung Adenocarcinoma

(2013) Ichiro Akagi et al.   CANCER RESEARCH

Cancer-Derived Mutations in KEAP1 Impair NRF2 Degradation but not Ubiquitination

(2013) B. E. Hast et al.   CANCER RESEARCH

Systematic Identification of Molecular Subtype-Selective Vulnerabilities in Non-Small-Cell Lung Cancer

(2013) Hyun Seok Kim et al.   CELL

New Targetable Oncogenes in Non–Small-Cell Lung Cancer

(2013) Geoffrey R. Oxnard et al.   JOURNAL OF CLINICAL ONCOLOGY

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

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Pan-cancer patterns of somatic copy number alteration

(2013) Travis I Zack et al.   NATURE GENETICS

An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers

(2013) Steven A Roberts et al.   NATURE GENETICS

Oncogenic and drug-sensitive NTRK1 rearrangements in lung cancer

(2013) Aria Vaishnavi et al.   NATURE MEDICINE

Metabolic and Functional Genomic Studies Identify Deoxythymidylate Kinase as a Target in LKB1-Mutant Lung Cancer

(2013) Y. Liu et al.   Cancer Discovery

Deciphering Signatures of Mutational Processes Operative in Human Cancer

(2013) Ludmil B. Alexandrov et al.   Cell Reports

Genomic Landscape of Non-Small Cell Lung Cancer in Smokers and Never-Smokers

(2012) Ramaswamy Govindan et al.   CELL

Mapping the Hallmarks of Lung Adenocarcinoma with Massively Parallel Sequencing

(2012) Marcin Imielinski et al.   CELL

Comprehensive genomic characterization of squamous cell lung cancers

(2012)   NATURE

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer

(2012) Martin Peifer et al.   NATURE GENETICS

Chipping away at the lung cancer genome

(2012) William Pao et al.   NATURE MEDICINE

ContEst: estimating cross-contamination of human samples in next-generation sequencing data

(2011) Kristian Cibulskis et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

The Association of MicroRNA Expression with Prognosis and Progression in Early-Stage, Non-Small Cell Lung Adenocarcinoma: A Retrospective Analysis of Three Cohorts

(2011) M. Saito et al.   CLINICAL CANCER RESEARCH

SOS1 mutations in Noonan syndrome: molecular spectrum, structural insights on pathogenic effects, and genotype-phenotype correlations

(2011) Francesca Lepri et al.   HUMAN MUTATION

New driver mutations in non-small-cell lung cancer

(2011) William Pao et al.   LANCET ONCOLOGY

Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia

(2011) Víctor Quesada et al.   NATURE GENETICS

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

(2011) Mark A DePristo et al.   NATURE GENETICS

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

The Fbw7 Tumor Suppressor Targets KLF5 for Ubiquitin-Mediated Degradation and Suppresses Breast Cell Proliferation

(2010) Dong Zhao et al.   CANCER RESEARCH

Structural and Energetic Mechanisms of Cooperative Autoinhibition and Activation of Vav1

(2010) Bingke Yu et al.   CELL

Conservation of an RNA regulatory map between Drosophila and mammals

(2010) A. N. Brooks et al.   GENOME RESEARCH

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

Derivation of an amino acid similarity matrix for peptide:MHC binding and its application as a Bayesian prior

(2009) Yohan Kim et al.   BMC BIOINFORMATICS

Lung Adenocarcinoma with EGFR Amplification Has Distinct Clinicopathologic and Molecular Features in Never-Smokers

(2009) L. M. Sholl et al.   CANCER RESEARCH

Lung Cancer in Never Smokers: Clinical Epidemiology and Environmental Risk Factors

(2009) J. M. Samet et al.   CLINICAL CANCER RESEARCH

Diagnostic Assay Based on hsa-miR-205 Expression Distinguishes Squamous From Nonsquamous Non–Small-Cell Lung Carcinoma

(2009) Danit Lebanony et al.   JOURNAL OF CLINICAL ONCOLOGY

Kruppel-like factor 5 is required for perinatal lung morphogenesis and function

(2008) H. Wan et al.   DEVELOPMENT

NetMHCpan, a method for MHC class I binding prediction beyond humans

(2008) Ilka Hoof et al.   IMMUNOGENETICS

SOS1 mutations are rare in human malignancies: Implications for Noonan syndrome patients

(2007) Kenneth D. Swanson et al.   GENES CHROMOSOMES & CANCER