Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine

Nozzle: a report generation toolkit for data analysis pipelines

(2013) Nils Gehlenborg et al.   BIOINFORMATICS

Lessons from the Cancer Genome

(2013) Levi A. Garraway et al.   CELL

DNA-Mutation Inventory to Refine and Enhance Cancer Treatment (DIRECT): A Catalog of Clinically Relevant Cancer Mutations to Enable Genome-Directed Anticancer Therapy

(2013) P. Yeh et al.   CLINICAL CANCER RESEARCH

Rebooting Cancer Tissue Handling in the Sequencing Era

(2013) Laura Goetz et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Genomics-Driven Oncology: Framework for an Emerging Paradigm

(2013) Levi A. Garraway   JOURNAL OF CLINICAL ONCOLOGY

Comparison of Clinical Targeted Next-Generation Sequence Data from Formalin-Fixed and Fresh-Frozen Tissue Specimens

(2013) David H. Spencer et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

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

(2012) Ramaswamy Govindan et al.   CELL

A Landscape of Driver Mutations in Melanoma

(2012) Eran Hodis et al.   CELL

Mapping the Hallmarks of Lung Adenocarcinoma with Massively Parallel Sequencing

(2012) Marcin Imielinski et al.   CELL

Targeted Next-generation Sequencing of Advanced Prostate Cancer Identifies Potential Therapeutic Targets and Disease Heterogeneity

(2012) Himisha Beltran et al.   EUROPEAN UROLOGY

Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability

(2012) Y. Drier et al.   GENOME RESEARCH

The CRKL gene encoding an adaptor protein is amplified, overexpressed, and a possible therapeutic target in gastric cancer

(2012) Hiroko Natsume et al.   Journal of Translational Medicine

Genome and Transcriptome Sequencing in Prospective Metastatic Triple-Negative Breast Cancer Uncovers Therapeutic Vulnerabilities

(2012) D. W. Craig et al.   MOLECULAR CANCER THERAPEUTICS

Sequence analysis of mutations and translocations across breast cancer subtypes

(2012) Shantanu Banerji et al.   NATURE

Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer

(2012) Christopher E Barbieri et al.   NATURE GENETICS

Identification of new ALK and RET gene fusions from colorectal and lung cancer biopsies

(2012) Doron Lipson et al.   NATURE MEDICINE

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

(2012) Marco Gerlinger et al.   NEW ENGLAND JOURNAL OF MEDICINE

Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing

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

Circumventing Cancer Drug Resistance in the Era of Personalized Medicine

(2012) Levi A. Garraway et al.   Cancer Discovery

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

(2012) Ethan Cerami et al.   Cancer Discovery

Targeted high throughput sequencing in clinical cancer Settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity

(2011) Martin Kerick et al.   BMC Medical Genomics

The Mutational Landscape of Head and Neck Squamous Cell Carcinoma

(2011) N. Stransky et al.   SCIENCE

Personalized Oncology Through Integrative High-Throughput Sequencing: A Pilot Study

(2011) S. Roychowdhury et al.   Science Translational Medicine

Amplification of CRKL Induces Transformation and Epidermal Growth Factor Receptor Inhibitor Resistance in Human Non-Small Cell Lung Cancers

(2011) H. W. Cheung 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

A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries

(2011) Sheila Fisher et al.   GENOME BIOLOGY

A Synthetic Lethal Interaction between K-Ras Oncogenes and Cdk4 Unveils a Therapeutic Strategy for Non-small Cell Lung Carcinoma

(2010) Marta Puyol et al.   CANCER CELL

Integrative Genomic and Proteomic Analyses Identify Targets for Lkb1-Deficient Metastatic Lung Tumors

(2010) Julian Carretero et al.   CANCER CELL

Genomic and Biological Characterization of Exon 4 KRAS Mutations in Human Cancer

(2010) M. Janakiraman et al.   CANCER RESEARCH

Rapid targeted mutational analysis of human tumours: a clinical platform to guide personalized cancer medicine

(2010) Dora Dias-Santagata et al.   EMBO Molecular Medicine

Future of Personalized Medicine in Oncology: A Systems Biology Approach

(2010) Ana Maria Gonzalez-Angulo et al.   JOURNAL OF CLINICAL ONCOLOGY

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

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

Profiling Critical Cancer Gene Mutations in Clinical Tumor Samples

(2009) Laura E. MacConaill et al.   PLoS One

Activating mutations in human acute megakaryoblastic leukemia

(2008) S. Malinge et al.   BLOOD

Somatic mutations affect key pathways in lung adenocarcinoma

(2008) Li Ding et al.   NATURE

High-resolution mapping of copy-number alterations with massively parallel sequencing

(2008) Derek Y Chiang et al.   NATURE METHODS

NCBI Reference Sequences: current status, policy and new initiatives

(2008) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH