Coming of age: ten years of next-generation sequencing technologies

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing: Fig. 1.

(2015) Xuefeng Wang et al.   BIOINFORMATICS

Assessing structural variation in a personal genome—towards a human reference diploid genome

(2015) Adam C English et al.   BMC GENOMICS

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome

(2015) Sara Goodwin et al.   GENOME RESEARCH

An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

The UK10K project identifies rare variants in health and disease

(2015)   NATURE

Genome sequencing elucidates Sardinian genetic architecture and augments association analyses for lipid and blood inflammatory markers

(2015) Carlo Sidore et al.   NATURE GENETICS

Large-scale whole-genome sequencing of the Icelandic population

(2015) Daniel F Gudbjartsson et al.   NATURE GENETICS

Assembly and diploid architecture of an individual human genome via single-molecule technologies

(2015) Matthew Pendleton et al.   NATURE METHODS

Improved data analysis for the MinION nanopore sequencer

(2015) Miten Jain et al.   NATURE METHODS

Haplotype-resolved genome sequencing: experimental methods and applications

(2015) Matthew W. Snyder et al.   NATURE REVIEWS GENETICS

Genetic variation and the de novo assembly of human genomes

(2015) Mark J. P. Chaisson et al.   NATURE REVIEWS GENETICS

Optimizing Cancer Genome Sequencing and Analysis

(2015) Malachi Griffith et al.   Cell Systems

Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology

(2015) Hongzhi Cao et al.   GigaScience

Characterization of structural variants with single molecule and hybrid sequencing approaches

(2014) Anna Ritz et al.   BIOINFORMATICS

Analytical validation of the PAM50-based Prosigna Breast Cancer Prognostic Gene Signature Assay and nCounter Analysis System using formalin-fixed paraffin-embedded breast tumor specimens

(2014) Torsten Nielsen et al.   BMC CANCER

The utility of PacBio circular consensus sequencing for characterizing complex gene families in non-model organisms

(2014) Peter A Larsen et al.   BMC GENOMICS

Estimating genotype error rates from high-coverage next-generation sequence data

(2014) Jeffrey D. Wall et al.   GENOME RESEARCH

Clinical Utility of Droplet Digital PCR for Human Cytomegalovirus

(2014) R. H. Sedlak et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Ion Torrent next-generation sequencing for routine identification of clinically relevant mutations in colorectal cancer patients

(2014) Umberto Malapelle et al.   JOURNAL OF CLINICAL PATHOLOGY

Nanopores Discriminate among Five C5-Cytosine Variants in DNA

(2014) Zachary L. Wescoe et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

High-throughput profiling identifies clinically actionable mutations in salivary duct carcinoma

(2014) Bo Mi Ku et al.   Journal of Translational Medicine

Resolving the complexity of the human genome using single-molecule sequencing

(2014) Mark J. P. Chaisson et al.   NATURE

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

(2014) Barbara Treutlein et al.   NATURE

The contribution of de novo coding mutations to autism spectrum disorder

(2014) Ivan Iossifov et al.   NATURE

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study

(2014) Sheng Li et al.   NATURE BIOTECHNOLOGY

Whole-genome haplotyping using long reads and statistical methods

(2014) Volodymyr Kuleshov et al.   NATURE BIOTECHNOLOGY

Comparison of RNA-Seq and Microarray in Transcriptome Profiling of Activated T Cells

(2014) Shanrong Zhao et al.   PLoS One

Illumina TruSeq Synthetic Long-Reads Empower De Novo Assembly and Resolve Complex, Highly-Repetitive Transposable Elements

(2014) Rajiv C. McCoy et al.   PLoS One

A novel low energy electron microscope for DNA sequencing and surface analysis

(2014) M. Mankos et al.   ULTRAMICROSCOPY

Next-Generation Sequencing Platforms

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

Whole Genome Sequencing as a Diagnostic Test: Challenges and Opportunities

(2013) C. C. Chrystoja et al.   CLINICAL CHEMISTRY

A cross-platform analysis of 14,177 expression quantitative trait loci derived from lymphoblastoid cell lines

(2013) L. Liang et al.   GENOME RESEARCH

The complex SNP and CNV genetic architecture of the increased risk of congenital heart defects in Down syndrome

(2013) M. R. Sailani et al.   GENOME RESEARCH

The DNA data deluge

(2013) M. C. Schatz et al.   IEEE SPECTRUM

A single-molecule long-read survey of the human transcriptome

(2013) Donald Sharon et al.   NATURE BIOTECHNOLOGY

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

Rapid Genome Mapping in Nanochannel Arrays for Highly Complete and Accurate De Novo Sequence Assembly of the Complex Aegilops tauschii Genome

(2013) Alex R. Hastie et al.   PLoS One

Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies

(2013) Nora Rieber et al.   PLoS One

Ethics and Genomic Incidental Findings

(2013) A. L. McGuire et al.   SCIENCE

The genome sequence of the colonial chordate, Botryllus schlosseri

(2013) Ayelet Voskoboynik et al.   eLife

Pacific biosciences sequencing technology for genotyping and variation discovery in human data

(2012) Mauricio O Carneiro et al.   BMC GENOMICS

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

Sequencing the unsequenceable: Expanded CGG-repeat alleles of the fragile X gene

(2012) E. W. Loomis et al.   GENOME RESEARCH

Inferring causality and functional significance of human coding DNA variants

(2012) S. R. Sunyaev   HUMAN MOLECULAR GENETICS

Development of a Next-Generation Sequencing Method for BRCA Mutation Screening

(2012) Maurice Chan et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Multiplexed Gene Expression and Fusion Transcript Analysis to Detect ALK Fusions in Lung Cancer

(2012) Maruja E. Lira et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

De novo mutations revealed by whole-exome sequencing are strongly associated with autism

(2012) Stephan J. Sanders et al.   NATURE

Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations

(2012) Brian J. O’Roak et al.   NATURE

Performance comparison of benchtop high-throughput sequencing platforms

(2012) Nicholas J Loman et al.   NATURE BIOTECHNOLOGY

Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly

(2012) Ernest T Lam et al.   NATURE BIOTECHNOLOGY

Assuring the quality of next-generation sequencing in clinical laboratory practice

(2012) Amy S Gargis et al.   NATURE BIOTECHNOLOGY

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Technology-specific error signatures in the 1000 Genomes Project data

(2011) Michael Nothnagel et al.   HUMAN GENETICS

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

An integrated semiconductor device enabling non-optical genome sequencing

(2011) Jonathan M. Rothberg et al.   NATURE

Sequence-specific error profile of Illumina sequencers

(2011) Kensuke Nakamura et al.   NUCLEIC ACIDS RESEARCH

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

(2011) André E Minoche et al.   GENOME BIOLOGY

Structural Variation in the Human Genome and its Role in Disease

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

High-throughput DNA sequencing - concepts and limitations

(2010) Martin Kircher et al.   BIOESSAYS

Concordance Study of 3 Direct-to-Consumer Genetic-Testing Services

(2010) K. Imai et al.   CLINICAL CHEMISTRY

Assembly of large genomes using second-generation sequencing

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

Taking qPCR to a higher level: Analysis of CNV reveals the power of high throughput qPCR to enhance quantitative resolution

(2010) Suzanne Weaver et al.   METHODS

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Personalized investigation

(2010) Elie Dolgin   NATURE MEDICINE

Direct detection of DNA methylation during single-molecule, real-time sequencing

(2010) Benjamin A Flusberg et al.   NATURE METHODS

Uncovering the roles of rare variants in common disease through whole-genome sequencing

(2010) Elizabeth T. Cirulli et al.   NATURE REVIEWS GENETICS

Common variants conferring risk of schizophrenia: A pathway analysis of GWAS data

(2010) Peilin Jia et al.   SCHIZOPHRENIA RESEARCH

Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver

(2009) A. L. Brunner et al.   GENOME RESEARCH

Mammary development meets cancer genomics

(2009) Aleix Prat et al.   NATURE MEDICINE

Virtual terminator nucleotides for next-generation DNA sequencing

(2009) Jayson Bowers et al.   NATURE METHODS

Continuous base identification for single-molecule nanopore DNA sequencing

(2009) James Clarke et al.   Nature Nanotechnology

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers

(2009) Mayumi Oda et al.   NUCLEIC ACIDS RESEARCH

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

(2009) R. Drmanac et al.   SCIENCE

Evaluation of next generation sequencing platforms for population targeted sequencing studies

(2009) Olivier Harismendy et al.   GENOME BIOLOGY

Structural Variation of Chromosomes in Autism Spectrum Disorder

(2008) Christian R. Marshall et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Recurrent CNVs Disrupt Three Candidate Genes in Schizophrenia Patients

(2008) Terry Vrijenhoek et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Twenty-five years of quantitative PCR for gene expression analysis

(2008) Heather D. VanGuilder et al.   BIOTECHNIQUES

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning

(2008) A. Valouev et al.   GENOME RESEARCH

Comprehensive high-throughput arrays for relative methylation (CHARM)

(2008) R. A. Irizarry et al.   GENOME RESEARCH

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

(2008) Timothy J. Ley et al.   NATURE

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

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

(2008) Peter J Campbell et al.   NATURE GENETICS

Caenorhabditis elegans mutant allele identification by whole-genome sequencing

(2008) Sumeet Sarin et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH

Concept, Design and Implementation of a Cardiovascular Gene-Centric 50 K SNP Array for Large-Scale Genomic Association Studies

(2008) Brendan J. Keating et al.   PLoS One

Comparing Platforms for C. elegans Mutant Identification Using High-Throughput Whole-Genome Sequencing

(2008) Yufeng Shen et al.   PLoS One

Four-color DNA sequencing with 3'-O-modified nucleotide reversible terminators and chemically cleavable fluorescent dideoxynucleotides

(2008) J. Guo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Bioinformatics challenges of new sequencing technology

(2008) Mihai Pop et al.   TRENDS IN GENETICS