Not All Next Generation Sequencing Diagnostics are Created Equal: Understanding the Nuances of Solid Tumor Assay Design for Somatic Mutation Detection

High-density SNP arrays improve detection of HER2 amplification and polyploidy in breast tumors

(2015) Thomas v O Hansen et al.   BMC CANCER

Broad, Hybrid Capture-Based Next-Generation Sequencing Identifies Actionable Genomic Alterations in Lung Adenocarcinomas Otherwise Negative for Such Alterations by Other Genomic Testing Approaches

(2015) A. Drilon et al.   CLINICAL CANCER RESEARCH

PARP inhibitors: A new era of targeted therapy

(2015) Shifalika Tangutoori et al.   MATURITAS

Personalized genomic analyses for cancer mutation discovery and interpretation

(2015) Siân Jones et al.   Science Translational Medicine

Computational methods for detecting copy number variations in cancer genome using next generation sequencing: principles and challenges

(2015) Biao Liu et al.   Oncotarget

Development and validation of a next-generation sequencing–based protocol for 24-chromosome aneuploidy screening of embryos

(2014) Francesco Fiorentino et al.   FERTILITY AND STERILITY

Application of next-generation sequencing technology for comprehensive aneuploidy screening of blastocysts in clinical preimplantation genetic screening cycles

(2014) Francesco Fiorentino et al.   HUMAN REPRODUCTION

Clinical Tumor Sequencing: An Incidental Casualty of the American College of Medical Genetics and Genomics Recommendations for Reporting of Incidental Findings

(2014) D. Williams Parsons et al.   JOURNAL OF CLINICAL ONCOLOGY

The Validation and Clinical Implementation of BRCAplus: A Comprehensive High-Risk Breast Cancer Diagnostic Assay

(2014) Hansook Kim Chong et al.   PLoS One

Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives

(2013) Min Zhao et al.   BMC BIOINFORMATICS

Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation

(2013) J. B. Hiatt et al.   GENOME RESEARCH

Accurately Identifying Low-Allelic Fraction Variants in Single Samples with Next-Generation Sequencing: Applications in Tumor Subclone Resolution

(2013) Lucy F. Stead et al.   HUMAN MUTATION

Recommendations for Human Epidermal Growth Factor Receptor 2 Testing in Breast Cancer: American Society of Clinical Oncology/College of American Pathologists Clinical Practice Guideline Update

(2013) Antonio C. Wolff et al.   JOURNAL OF CLINICAL ONCOLOGY

Validation and Implementation of Targeted Capture and Sequencing for the Detection of Actionable Mutation, Copy Number Variation, and Gene Rearrangement in Clinical Cancer Specimens

(2013) Colin C. Pritchard et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Validation of a Next-Generation Sequencing Assay for Clinical Molecular Oncology

(2013) Catherine E. Cottrell et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

A Multigene Expression Assay to Predict Local Recurrence Risk for Ductal Carcinoma In Situ of the Breast

(2013) L. J. Solin et al.   JNCI-Journal of the National Cancer Institute

Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing

(2013) Garrett M Frampton et al.   NATURE BIOTECHNOLOGY

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Emerging landscape of oncogenic signatures across human cancers

(2013) Giovanni Ciriello et al.   NATURE GENETICS

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

Comparison of Testing Methods for the Detection of BRAF V600E Mutations in Malignant Melanoma: Pre-Approval Validation Study of the Companion Diagnostic Test for Vemurafenib

(2013) Fernando Lopez-Rios et al.   PLoS One

Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers

(2013) Qingguo Wang et al.   Genome Medicine

Current Challenges for HER2 Testing in Diagnostic Pathology: State of the Art and Controversial Issues

(2013) Anna Sapino et al.   Frontiers in Oncology

A comparison of three methods for detecting KRAS mutations in formalin-fixed colorectal cancer specimens

(2012) D Gonzalez de Castro et al.   BRITISH JOURNAL OF CANCER

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

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

Immunohistochemistry in the era of personalised medicine

(2012) Clare Margaret McCourt et al.   JOURNAL OF CLINICAL PATHOLOGY

Molecular inversion probes: a novel microarray technology and its application in cancer research

(2012) Yuker Wang et al.   Cancer Genetics

SEAL: a distributed short read mapping and duplicate removal tool

(2011) L. Pireddu et al.   BIOINFORMATICS

A method for counting PCR template molecules with application to next-generation sequencing

(2011) J. A. Casbon et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Nikhil Wagle et al.   Cancer Discovery

Clinical array-based karyotyping of breast cancer with equivocal HER2 status resolves gene copy number and reveals chromosome 17 complexity

(2010) Shelly Gunn et al.   BMC CANCER

Out of the darkness and into the light: bright field in situ hybridisation for delineation of ERBB2 (HER2) status in breast carcinoma

(2010) A. M Gruver et al.   JOURNAL OF CLINICAL PATHOLOGY

The Vanguard Has Arrived in the Clinical Laboratory

(2010) Shelly R. Gunn   JOURNAL OF MOLECULAR DIAGNOSTICS

A Commercial Real-Time PCR Kit Provides Greater Sensitivity than Direct Sequencing to Detect KRAS Mutations

(2010) Bárbara Angulo et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Target-enrichment strategies for next-generation sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays

(2009) Yuker Wang et al.   BMC Medical Genomics

Optimization of the Affymetrix GeneChip Mapping 10K 2.0 Assay for Routine Clinical Use on Formalin-fixed Paraffin-embedded Tissues

(2009) Maureen Lyons-Weiler et al.   DIAGNOSTIC MOLECULAR PATHOLOGY

Breast cancer and aneusomy 17: implications for carcinogenesis and therapeutic response

(2009) Monica M Reinholz et al.   LANCET ONCOLOGY

The rewards and challenges of array-based karyotyping for clinical oncology applications

(2009) J M Hagenkord et al.   LEUKEMIA

Poor prognostic significance of unamplified chromosome 17 polysomy in invasive breast carcinoma

(2009) Uma Krishnamurti et al.   MODERN PATHOLOGY

A comprehensive catalogue of somatic mutations from a human cancer genome

(2009) Erin D. Pleasance et al.   NATURE

Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes

(2009) Iwanka Kozarewa et al.   NATURE METHODS

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

(2009) Ken Chen et al.   NATURE METHODS

Whole-Genome Scanning by Array Comparative Genomic Hybridization as a Clinical Tool for Risk Assessment in Chronic Lymphocytic Leukemia

(2008) Shelly R. Gunn et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Mechanisms of inherited cancer susceptibility

(2008) Shirley Hodgson   Journal of Zhejiang University-SCIENCE B

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

(2008) Derek Y Chiang et al.   NATURE METHODS

Ataxia-telangiectasia: from a rare disorder to a paradigm for cell signalling and cancer

(2008) Martin F. Lavin   NATURE REVIEWS MOLECULAR CELL BIOLOGY

HER2Status and Benefit from Adjuvant Trastuzumab in Breast Cancer

(2008) Soonmyung Paik et al.   NEW ENGLAND JOURNAL OF MEDICINE