Clinical Applications of Next-Generation Sequencing in Cancer Diagnosis

Next-Generation Sequencing Platforms

(2013) Elaine R. Mardis   Annual Review of Analytical Chemistry

WaveCNV: allele-specific copy number alterations in primary tumors and xenograft models from next-generation sequencing

(2013) Carson Holt et al.   BIOINFORMATICS

Technical and implementation issues in using next-generation sequencing of cancers in clinical practice

(2013) D Ulahannan et al.   BRITISH JOURNAL OF CANCER

A glimpse into past, present, and future DNA sequencing

(2013) Marcos Morey et al.   MOLECULAR GENETICS AND METABOLISM

Key Principles and Clinical Applications of "Next-Generation" DNA Sequencing

(2012) J. M. Rizzo et al.   Cancer Prevention Research

Next-generation sequencing: ready for the clinics?

(2012) AN Desai et al.   CLINICAL GENETICS

Long-Range PCR and Next-Generation Sequencing of BRCA1 and BRCA2 in Breast Cancer

(2012) Hilmi Ozcelik et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Detection of Genomic Variations in BRCA1 and BRCA2 Genes by Long-Range PCR and Next-Generation Sequencing

(2012) Imma Hernan et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate

(2012) Günter Klambauer et al.   NUCLEIC ACIDS RESEARCH

Whole Cancer Genome Sequencing by Next-Generation Methods

(2011) Jeffrey S. Ross et al.   AMERICAN JOURNAL OF CLINICAL PATHOLOGY

Comprehensive next-generation cancer genome sequencing in the era of targeted therapy and personalized oncology

(2011) Maureen Cronin et al.   Biomarkers in Medicine

Cancer statistics, 2011

(2011) Rebecca Siegel et al.   CA-A CANCER JOURNAL FOR CLINICIANS

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

Massive parallel amplicon sequencing of the breast cancer genes BRCA1 and BRCA2: opportunities, challenges, and limitations

(2011) Kim De Leeneer et al.   HUMAN MUTATION

Comparison of Effect Sizes Associated With Biomarkers Reported in Highly Cited Individual Articles and in Subsequent Meta-analyses

(2011) John P. A. Ioannidis   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

The genomic complexity of primary human prostate cancer

(2011) Michael F. Berger et al.   NATURE

A decade’s perspective on DNA sequencing technology

(2011) Elaine R. Mardis   NATURE

Detecting common copy number variants in high-throughput sequencing data by using JointSLM algorithm

(2011) Alberto Magi 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

Whole-Exome-Sequencing-Based Discovery of Human FADD Deficiency

(2010) Alexandre Bolze et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Structural Variation in the Human Genome and its Role in Disease

(2010) Paweł Stankiewicz et al.   Annual Review of Medicine

CNAseg—a novel framework for identification of copy number changes in cancer from second-generation sequencing data

(2010) Sergii Ivakhno et al.   BIOINFORMATICS

rSW-seq: Algorithm for detection of copy number alterations in deep sequencing data

(2010) Tae-Min Kim et al.   BMC BIOINFORMATICS

Use of cancer-specific genomic rearrangements to quantify disease burden in plasma from patients with solid tumors

(2010) David J. McBride et al.   GENES CHROMOSOMES & CANCER

Copy number and targeted mutational analysis reveals novel somatic events in metastatic prostate tumors

(2010) C. M. Robbins et al.   GENOME RESEARCH

A window into third-generation sequencing

(2010) E. E. Schadt et al.   HUMAN MOLECULAR GENETICS

Genetic diagnosis of familial breast cancer using clonal sequencing

(2010) Joanne E. Morgan et al.   HUMAN MUTATION

Gene Expression-Based Prognostic Signatures in Lung Cancer: Ready for Clinical Use?

(2010) J. Subramanian et al.   JNCI-Journal of the National Cancer Institute

The mutation spectrum revealed by paired genome sequences from a lung cancer patient

(2010) William Lee et al.   NATURE

The patterns and dynamics of genomic instability in metastatic pancreatic cancer

(2010) Peter J. Campbell et al.   NATURE

Genome remodelling in a basal-like breast cancer metastasis and xenograft

(2010) Li Ding et al.   NATURE

Distant metastasis occurs late during the genetic evolution of pancreatic cancer

(2010) Shinichi Yachida et al.   NATURE

International network of cancer genome projects

(2010) Thomas J. Hudson (Chairperson) et al.   NATURE

Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin

(2010) Ryan D Morin et al.   NATURE GENETICS

Mutations in the guanine nucleotide exchange factor gene IQSEC2 cause nonsyndromic intellectual disability

(2010) Cheryl Shoubridge et al.   NATURE GENETICS

Advances in understanding cancer genomes through second-generation sequencing

(2010) Matthew Meyerson et al.   NATURE REVIEWS GENETICS

ARID1AMutations in Endometriosis-Associated Ovarian Carcinomas

(2010) Kimberly C. Wiegand et al.   NEW ENGLAND JOURNAL OF MEDICINE

Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing

(2010) Tom Walsh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Development of Personalized Tumor Biomarkers Using Massively Parallel Sequencing

(2010) R. J. Leary et al.   Science Translational Medicine

The $1,000 genome, the $100,000 analysis?

(2010) Elaine R Mardis   Genome Medicine

Systematic Inference of Copy-Number Genotypes from Personal Genome Sequencing Data Reveals Extensive Olfactory Receptor Gene Content Diversity

(2010) Sebastian M. Waszak et al.   PLoS Computational Biology

Cancer genomics identifies determinants of tumor biology

(2010) Elaine R Mardis   GENOME BIOLOGY

Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors

(2010) Steven JM Jones et al.   GENOME BIOLOGY

Copy Number Variation in Human Health, Disease, and Evolution

(2009) Feng Zhang et al.   Annual Review of Genomics and Human Genetics

CNV-seq, a new method to detect copy number variation using high-throughput sequencing

(2009) Chao Xie et al.   BMC BIOINFORMATICS

High-throughput resequencing in the diagnosis of BRCA1/2 mutations using oligonucleotide resequencing microarrays

(2009) Christopher Schroeder et al.   BREAST CANCER RESEARCH AND TREATMENT

Sensitive and accurate detection of copy number variants using read depth of coverage

(2009) S. Yoon et al.   GENOME RESEARCH

Microarray-based multicycle-enrichment of genomic subsets for targeted next-generation sequencing

(2009) D. Summerer et al.   GENOME RESEARCH

Cancer genome sequencing: a review

(2009) E. R. Mardis et al.   HUMAN MOLECULAR GENETICS

Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution

(2009) Sohrab P. Shah et al.   NATURE

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

(2009) Erin D. Pleasance et al.   NATURE

A comprehensive catalogue of somatic mutations from a human cancer genome

(2009) Erin D. Pleasance et al.   NATURE

Complex landscapes of somatic rearrangement in human breast cancer genomes

(2009) Philip J. Stephens et al.   NATURE

Computational methods for discovering structural variation with next-generation sequencing

(2009) Paul Medvedev et al.   NATURE METHODS

Mutation ofFOXL2in Granulosa-Cell Tumors of the Ovary

(2009) Sohrab P. Shah et al.   NEW ENGLAND JOURNAL OF MEDICINE

Improved fabrication of zero-mode waveguides for single-molecule detection

(2008) Mathieu Foquet et al.   JOURNAL OF APPLIED PHYSICS

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

(2008) Timothy J. Ley et al.   NATURE

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE

The potential and challenges of nanopore sequencing

(2008) Daniel Branton et al.   NATURE BIOTECHNOLOGY

Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing

(2008) Peter J Campbell et al.   NATURE GENETICS

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

(2008) Derek Y Chiang et al.   NATURE METHODS

A large genome center's improvements to the Illumina sequencing system

(2008) Michael A Quail et al.   NATURE METHODS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Epigenetics in Cancer

(2008) Manel Esteller   NEW ENGLAND JOURNAL OF MEDICINE

Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses

(2008) S. Jones et al.   SCIENCE

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE