Clinical Analysis and Interpretation of Cancer Genome Data

The prognostic signficance of pretreatment leukocytosis in patients with anal cancer treated with radical chemoradiotherapy or radiotherapy.

(2017) Robyn Banerjee et al.   JOURNAL OF CLINICAL ONCOLOGY

Detection of Somatic Copy Number Alterations in Cancer Using Targeted Exome Capture Sequencing

(2015) Robert J. Lonigro et al.   NEOPLASIA

Identification of recurrent NAB2-STAT6 gene fusions in solitary fibrous tumor by integrative sequencing

(2013) Dan R Robinson et al.   NATURE GENETICS

Discovery and Statistical Genotyping of Copy-Number Variation from Whole-Exome Sequencing Depth

(2012) Menachem Fromer et al.   AMERICAN JOURNAL OF HUMAN GENETICS

JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data

(2012) Andrew Roth et al.   BIOINFORMATICS

Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS

(2012) Anne-Katrin Emde et al.   BIOINFORMATICS

Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

SOAP3: ultra-fast GPU-based parallel alignment tool for short reads

(2012) C.-M. Liu et al.   BIOINFORMATICS

An integrative variant analysis suite for whole exome next-generation sequencing data

(2012) Danny Challis et al.   BMC BIOINFORMATICS

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

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

The legal risks of returning results of genomics research

(2012) Ellen Wright Clayton et al.   GENETICS IN MEDICINE

Managing incidental findings and research results in genomic research involving biobanks and archived data sets

(2012) Susan M. Wolf et al.   GENETICS IN MEDICINE

Translating genomic information into clinical medicine: Lung cancer as a paradigm

(2012) M. A. Levy et al.   GENOME RESEARCH

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

Copy number variation detection and genotyping from exome sequence data

(2012) N. Krumm et al.   GENOME RESEARCH

SOAPindel: Efficient identification of indels from short paired reads

(2012) S. Li et al.   GENOME RESEARCH

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Feasibility of real time next generation sequencing of cancer genes linked to drug response: Results from a clinical trial

(2012) Ben Tran et al.   INTERNATIONAL JOURNAL OF CANCER

Pretreatment Epidermal Growth Factor Receptor (EGFR) T790M Mutation Predicts Shorter EGFR Tyrosine Kinase Inhibitor Response Duration in Patients With Non–Small-Cell Lung Cancer

(2012) Kang-Yi Su et al.   JOURNAL OF CLINICAL ONCOLOGY

Individual genetic and genomic research results and the tradition of informed consent: exploring US review board guidance

(2012) Christian Simon et al.   JOURNAL OF MEDICAL ETHICS

wANNOVAR: annotating genetic variants for personal genomes via the web

(2012) Xiao Chang et al.   JOURNAL OF MEDICAL GENETICS

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

Cancer biomarkers

(2012) N. Lynn Henry et al.   Molecular Oncology

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

(2012) Anirudh Prahallad et al.   NATURE

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

(2012) Doron Lipson et al.   NATURE MEDICINE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Mutation Discovery in Regions of Segmental Cancer Genome Amplifications with CoNAn-SNV: A Mixture Model for Next Generation Sequencing of Tumors

(2012) Anamaria Crisan 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

Comparative analysis of algorithms for next-generation sequencing read alignment

(2011) M. Ruffalo et al.   BIOINFORMATICS

SomaticSniper: identification of somatic point mutations in whole genome sequencing data

(2011) David E. Larson et al.   BIOINFORMATICS

From pharmacogenomic knowledge acquisition to clinical applications: the PharmGKB as a clinical pharmacogenomic biomarker resource

(2011) Ellen M McDonagh et al.   Biomarkers in Medicine

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

(2011) A. Abyzov et al.   GENOME RESEARCH

The GeneInsight suite: a platform to support laboratory and provider use of DNA-based genetic testing

(2011) Samuel J. Aronson et al.   HUMAN MUTATION

Monitoring of Minimal Residual Disease in NPM1-Mutated Acute Myeloid Leukemia: A Study From the German-Austrian Acute Myeloid Leukemia Study Group

(2011) Jan Krönke et al.   JOURNAL OF CLINICAL ONCOLOGY

A Platform for Rapid Detection of Multiple Oncogenic Mutations With Relevance to Targeted Therapy in Non–Small-Cell Lung Cancer

(2011) Zengliu Su et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Initial genome sequencing and analysis of multiple myeloma

(2011) Michael A. Chapman et al.   NATURE

Improved Survival with Vemurafenib in Melanoma with BRAF V600E Mutation

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

Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery

(2011) F. Zhu et al.   NUCLEIC ACIDS RESEARCH

STITCH 3: zooming in on protein-chemical interactions

(2011) M. Kuhn et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

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

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

High-Throughput Detection of Actionable Genomic Alterations in Clinical Tumor Samples by Targeted, Massively Parallel Sequencing

(2011) Nikhil Wagle et al.   Cancer Discovery

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts

(2011) Daehwan Kim et al.   GENOME BIOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

A survey of sequence alignment algorithms for next-generation sequencing

(2010) H. Li et al.   BRIEFINGS IN BIOINFORMATICS

A Novel, Highly Sensitive Antibody Allows for the Routine Detection of ALK-Rearranged Lung Adenocarcinomas by Standard Immunohistochemistry

(2010) M. Mino-Kenudson et al.   CLINICAL CANCER RESEARCH

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

Dindel: Accurate indel calls from short-read data

(2010) C. A. Albers et al.   GENOME RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Clinical Implications of the Cancer Genome

(2010) Laura E. MacConaill et al.   JOURNAL OF CLINICAL ONCOLOGY

mrsFAST: a cache-oblivious algorithm for short-read mapping

(2010) Faraz Hach et al.   NATURE METHODS

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

MutationTaster evaluates disease-causing potential of sequence alterations

(2010) Jana Marie Schwarz et al.   NATURE METHODS

Advances in understanding cancer genomes through second-generation sequencing

(2010) Matthew Meyerson et al.   NATURE REVIEWS GENETICS

IDH1 or IDH2 mutations predict longer survival and response to temozolomide in low-grade gliomas

(2010) C. Houillier et al.   NEUROLOGY

DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs

(2010) C. Knox et al.   NUCLEIC ACIDS RESEARCH

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

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

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

American Society of Clinical Oncology Provisional Clinical Opinion: Testing forKRASGene Mutations in Patients With Metastatic Colorectal Carcinoma to Predict Response to Anti–Epidermal Growth Factor Receptor Monoclonal Antibody Therapy

(2009) Carmen J. Allegra et al.   JOURNAL OF CLINICAL ONCOLOGY

Use of Archived Specimens in Evaluation of Prognostic and Predictive Biomarkers

(2009) R. M. Simon et al.   JNCI-Journal of the National Cancer Institute

Transcriptome sequencing to detect gene fusions in cancer

(2009) Christopher A. Maher et al.   NATURE

Personalized copy number and segmental duplication maps using next-generation sequencing

(2009) Can Alkan et al.   NATURE GENETICS

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

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

(2009) Prateek Kumar et al.   Nature Protocols

Profiling Critical Cancer Gene Mutations in Clinical Tumor Samples

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

SHRiMP: Accurate Mapping of Short Color-space Reads

(2009) Stephen M. Rumble et al.   PLoS Computational Biology

Changing interpretations, stable genes: responsibilities of patients, professionals, and policy makers in the clinical interpretation of complex genetic information

(2008) Brian H Shirts et al.   GENETICS IN MEDICINE

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

(2008) Derek Y Chiang et al.   NATURE METHODS

Mutations and Treatment Outcome in Cytogenetically Normal Acute Myeloid Leukemia

(2008) Richard F. Schlenk et al.   NEW ENGLAND JOURNAL OF MEDICINE