Next Generation DNA Sequencing and the Future of Genomic Medicine

NCCN Task Force Report: Molecular Markers in Leukemias and Lymphomas

(2017) Jerald P. Radich et al.   Journal of the National Comprehensive Cancer Network

Structural Variation in the Human Genome and its Role in Disease

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

Ultra deep sequencing detects a low rate of mosaic mutations in tuberous sclerosis complex

(2010) Wei Qin et al.   HUMAN GENETICS

The primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma et al.   NATURE

Transcriptome genetics using second generation sequencing in a Caucasian population

(2010) Stephen B. Montgomery et al.   NATURE

Understanding mechanisms underlying human gene expression variation with RNA sequencing

(2010) Joseph K. Pickrell et al.   NATURE

Whole-Genome Sequencing in a Patient with Charcot–Marie–Tooth Neuropathy

(2010) James R. Lupski et al.   NEW ENGLAND JOURNAL OF MEDICINE

3′-End Sequencing for Expression Quantification (3SEQ) from Archival Tumor Samples

(2010) Andrew H. Beck et al.   PLoS One

Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing

(2010) J. C. Roach et al.   SCIENCE

Development of Personalized Tumor Biomarkers Using Massively Parallel Sequencing

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

Methods for Genomic Partitioning

(2009) Emily H. Turner et al.   Annual Review of Genomics and Human Genetics

Copy Number Variation in Human Health, Disease, and Evolution

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

The HapMap and Genome-Wide Association Studies in Diagnosis and Therapy

(2009) Teri A. Manolio et al.   Annual Review of Medicine

From SNPs to pathways: integration of functional effect of sequence variations on models of cell signalling pathways

(2009) Anna Bauer-Mehren et al.   BMC BIOINFORMATICS

The context and potential of epigenetics in oncology

(2009) J Lopez et al.   BRITISH JOURNAL OF CANCER

Epigenetic Modifiers: Basic Understanding and Clinical Development

(2009) R. L. Piekarz et al.   CLINICAL CANCER RESEARCH

Complexity of CEBPA Dysregulation in Human Acute Myeloid Leukemia

(2009) T. Pabst et al.   CLINICAL CANCER RESEARCH

Counterpoint: Pharmacogenetic-Based Initial Dosing of Warfarin: Not Ready for Prime Time

(2009) C. S. Eby   CLINICAL CHEMISTRY

Metagenomic Pyrosequencing and Microbial Identification

(2009) J. F. Petrosino et al.   CLINICAL CHEMISTRY

Molecular diagnostics of infectious diseases

(2009) Kenneth L Muldrew   CURRENT OPINION IN PEDIATRICS

Pharmacogenetic testing of CYP2C9 and VKORC1 alleles for warfarin

(2009) David A Flockhart et al.   GENETICS IN MEDICINE

The Scientific Foundation for Personal Genomics: Recommendations from a National Institutes of Health–Centers for Disease Control and Prevention Multidisciplinary Workshop

(2009) Muin J Khoury et al.   GENETICS IN MEDICINE

ProPhylER: A curated online resource for protein function and structure based on evolutionary constraint analyses

(2009) J. Binkley et al.   GENOME RESEARCH

SNP detection for massively parallel whole-genome resequencing

(2009) R. Li et al.   GENOME RESEARCH

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Rapid high-throughput human leukocyte antigen typing by massively parallel pyrosequencing for high-resolution allele identification

(2009) Christian Gabriel et al.   HUMAN IMMUNOLOGY

Meta-analysis of genetic association studies: methodologies, between-study heterogeneity and winner's curse

(2009) Hirofumi Nakaoka et al.   JOURNAL OF HUMAN GENETICS

Ultra‐Deep Pyrosequencing of Hepatitis B Virus Quasispecies from Nucleoside and Nucleotide Reverse‐Transcriptase Inhibitor (NRTI)–Treated Patients and NRTI‐Naive Patients

(2009) Severine Margeridon‐Thermet et al.   JOURNAL OF INFECTIOUS DISEASES

Transcriptome sequencing to detect gene fusions in cancer

(2009) Christopher A. Maher 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

Single-molecule sequencing of an individual human genome

(2009) Dmitry Pushkarev et al.   NATURE BIOTECHNOLOGY

Exome sequencing identifies the cause of a mendelian disorder

(2009) Sarah B Ng et al.   NATURE GENETICS

Virtual terminator nucleotides for next-generation DNA sequencing

(2009) Jayson Bowers et al.   NATURE METHODS

Sense from sequence reads: methods for alignment and assembly

(2009) Paul Flicek et al.   NATURE METHODS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Estimation of the Warfarin Dose with Clinical and Pharmacogenetic Data

(2009)   NEW ENGLAND JOURNAL OF MEDICINE

Pharmacogenetics — Tailoring Treatment for the Outliers

(2009) Janet Woodcock et al.   NEW ENGLAND JOURNAL OF MEDICINE

Recurring Mutations Found by Sequencing an Acute Myeloid Leukemia Genome

(2009) Elaine R. Mardis et al.   NEW ENGLAND JOURNAL OF MEDICINE

Mutation ofFOXL2in Granulosa-Cell Tumors of the Ovary

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

Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances

(2009) T. LaFramboise   NUCLEIC ACIDS RESEARCH

Low-Abundance HIV Drug-Resistant Viral Variants in Treatment-Experienced Persons Correlate with Historical Antiretroviral Use

(2009) Thuy Le et al.   PLoS One

Repertoire of microRNAs in Epithelial Ovarian Cancer as Determined by Next Generation Sequencing of Small RNA cDNA Libraries

(2009) Stacia K. Wyman et al.   PLoS One

ThemiR-17∼92cluster collaborates with the Sonic Hedgehog pathway in medulloblastoma

(2009) Tamar Uziel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays

(2009) R. Drmanac et al.   SCIENCE

Measurement and Clinical Monitoring of Human Lymphocyte Clonality by Massively Parallel V-D-J Pyrosequencing

(2009) S. D. Boyd et al.   Science Translational Medicine

High-resolution, high-throughput HLA genotyping by next-generation sequencing

(2009) G. Bentley et al.   TISSUE ANTIGENS

Identifying Relationships among Genomic Disease Regions: Predicting Genes at Pathogenic SNP Associations and Rare Deletions

(2009) Soumya Raychaudhuri et al.   PLoS Genetics

Circulating Tumor Cell Analysis: Technical and Statistical Considerations for Application to the Clinic

(2009) Alison L. Allan et al.   Journal of Oncology

Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing

(2008) Ryan D. Morin et al.   BIOTECHNIQUES

Translation of the Philadelphia chromosome into therapy for CML

(2008) B. J. Druker   BLOOD

Nested Patch PCR enables highly multiplexed mutation discovery in candidate genes

(2008) K. E. Varley et al.   GENOME RESEARCH

Analysis of Mixed Sequencing Chromatograms and Its Application in Direct 16S rRNA Gene Sequencing of Polymicrobial Samples

(2008) O. Kommedal et al.   JOURNAL OF CLINICAL MICROBIOLOGY

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

(2008) Timothy J. Ley et al.   NATURE

Genome-scale DNA methylation maps of pluripotent and differentiated cells

(2008) Alexander Meissner et al.   NATURE

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley 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

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

(2008) Michael A Quail et al.   NATURE METHODS

SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries

(2008) Curtis P Van Tassell et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

A New Arenavirus in a Cluster of Fatal Transplant-Associated Diseases

(2008) Gustavo Palacios et al.   NEW ENGLAND JOURNAL OF MEDICINE

Reactome knowledgebase of human biological pathways and processes

(2008) L. Matthews et al.   NUCLEIC ACIDS RESEARCH

A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

(2008) M. Sultan et al.   SCIENCE

Single-Molecule DNA Sequencing of a Viral Genome

(2008) T. D. Harris et al.   SCIENCE

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE