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

PubWeight™: 2.48‹?› | Rank: Top 2%

🔗 View Article (PMID 27184599)

Published in Nat Rev Genet on May 17, 2016

Authors

Sara Goodwin1, John D McPherson2, W Richard McCombie1

Author Affiliations

1: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
2: Department of Biochemistry and Molecular Medicine; and the Comprehensive Cancer Center, University of California, Davis, California 95817, USA.

Articles citing this

New insights into the generation and role of de novo mutations in health and disease. Genome Biol (2016) 0.88

The Sequences of 1,504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies. Plant Cell (2017) 0.86

How many papillomavirus species can go undetected in papilloma lesions? Sci Rep (2016) 0.86

Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics. F1000Res (2016) 0.84

A Comprehensive Prescription for Plant miRNA Identification. Front Plant Sci (2017) 0.83

Emerging Functions of Circular RNAs. Yale J Biol Med (2016) 0.82

First Complete Genome Sequence of the Skin-Improving Lactobacillus curvatus Strain FBA2, Isolated from Fermented Vegetables, Determined by PacBio Single-Molecule Real-Time Technology. Genome Announc (2016) 0.81

Genomic Instability of iPSCs: Challenges Towards Their Clinical Applications. Stem Cell Rev (2017) 0.81

Contrasting evolutionary genome dynamics between domesticated and wild yeasts. Nat Genet (2017) 0.81

Structural aspects of the inactive X chromosome. Philos Trans R Soc Lond B Biol Sci (2017) 0.81

Genetic Approaches to Understanding Psychiatric Disease. Neurotherapeutics (2017) 0.80

International Standards for Genomes, Transcriptomes, and Metagenomes. J Biomol Tech (2017) 0.79

Clinical and biological insights from viral genome sequencing. Nat Rev Microbiol (2017) 0.78

Fluorescence in situ hybridization in surgical pathology: principles and applications. J Pathol Clin Res (2017) 0.78

Significant loss of sensitivity and specificity in the taxonomic classification occurs when short 16S rRNA gene sequences are used. Heliyon (2016) 0.76

Omics-Based Strategies in Precision Medicine: Toward a Paradigm Shift in Inborn Errors of Metabolism Investigations. Int J Mol Sci (2016) 0.76

Integrating cancer genomic data into electronic health records. Genome Med (2016) 0.76

The complete genome sequence of the phytopathogenic fungus Sclerotinia sclerotiorum reveals insights into the genome architecture of broad host range pathogens. Genome Biol Evol (2017) 0.76

DNA sequencing technologies: 2006-2016. Nat Protoc (2017) 0.76

Human Y-chromosome variation in the genome-sequencing era. Nat Rev Genet (2017) 0.76

SNP Discovery Using a Pangenome: Has the Single Reference Approach Become Obsolete? Biology (Basel) (2017) 0.76

Draft genome sequence of the Tibetan medicinal herb, Rhodiola crenulata. Gigascience (2017) 0.75

Rapid and cost-effective high-throughput sequencing for identification of germline mutations of BRCA1 and BRCA2. J Hum Genet (2017) 0.75

Technological considerations for genome-guided diagnosis and management of cancer. Genome Med (2016) 0.75

Genetic linkage analysis using DNA markers in sweetpotato. Breed Sci (2017) 0.75

Technology: Read the instructions. Nature (2016) 0.75

Gastric Cancer Genomics: Advances and Future Directions. Cell Mol Gastroenterol Hepatol (2017) 0.75

Population and clinical genetics of human transposable elements in the (post) genomic era. Mob Genet Elements (2017) 0.75

Advances in analyzing RNA diversity in eukaryotic transcriptomes: peering through the Omics lens. F1000Res (2016) 0.75

Detection and Enumeration of Spore-Forming Bacteria in Powdered Dairy Products. Front Microbiol (2017) 0.75

Next-Generation Sequencing in Oncology: Genetic Diagnosis, Risk Prediction and Cancer Classification. Int J Mol Sci (2017) 0.75

Microreact: visualizing and sharing data for genomic epidemiology and phylogeography. Microb Genom (2016) 0.75

Opportunities and challenges of whole-genome and -exome sequencing. BMC Genet (2017) 0.75

Screening the Molecular Framework Underlying Local Dendritic mRNA Translation. Front Mol Neurosci (2017) 0.75

Signaling pathways regulating cartilage growth plate formation and activity. Semin Cell Dev Biol (2016) 0.75

Resolving host-pathogen interactions by dual RNA-seq. PLoS Pathog (2017) 0.75

Mate-pair editing: a perspective to double mate-pair sequencing coverage. 3 Biotech (2016) 0.75

Transcriptomics technologies. PLoS Comput Biol (2017) 0.75

Robust long-read native DNA sequencing using the ONT CsgG Nanopore system. Wellcome Open Res (2017) 0.75

Magnetowetting of Ferrofluidic Thin Liquid Films. Sci Rep (2017) 0.75

De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms. Sci Rep (2017) 0.75

High-resolution analysis of multi-copy variant surface glycoprotein gene expression sites in African trypanosomes. BMC Genomics (2016) 0.75

Multidimensional Integrative Genomics Approaches to Dissecting Cardiovascular Disease. Front Cardiovasc Med (2017) 0.75

A Survey of Computational Tools to Analyze and Interpret Whole Exome Sequencing Data. Int J Genomics (2016) 0.75

A Review of Bioinformatics Tools for Bio-Prospecting from Metagenomic Sequence Data. Front Genet (2017) 0.75

Deep Assessment of Genomic Diversity in Cassava for Herbicide Tolerance and Starch Biosynthesis. Comput Struct Biotechnol J (2017) 0.75

From Sequence Data to Returnable Results: Ethical Issues in Variant Calling and Interpretation. Genet Test Mol Biomarkers (2017) 0.75

MathIOmica: An Integrative Platform for Dynamic Omics. Sci Rep (2016) 0.75

Primer Sets Developed for Functional Genes Reveal Shifts in Functionality of Fungal Community in Soils. Front Microbiol (2016) 0.75

Molecular Population Genetics. Genetics (2017) 0.75

Next-Generation Sequencing in Cardiovascular Disease: Present Clinical Applications and the Horizon of Precision Medicine. Circulation (2017) 0.75

DNA Sequencing Sensors: An Overview. Sensors (Basel) (2017) 0.75

PRECISION MEDICINE - The Golden Gate for Detection, Treatment and Prevention of Alzheimer's Disease. J Prev Alzheimers Dis (2016) 0.75

[Genetic methods for analysis of autoinflammatory diseases]. Z Rheumatol (2017) 0.75

SP174 Antibody Lacks Specificity for NRAS Q61R and Cross-Reacts With HRAS and KRAS Q61R Mutant Proteins in Malignant Melanoma. Appl Immunohistochem Mol Morphol (2018) 0.75

Validation and Implementation of Clinical Laboratory Improvements Act (CLIA)-Compliant Whole Genome Sequencing in Public Health Microbiology Laboratory. J Clin Microbiol (2017) 0.75

Global survey of mRNA levels and decay rates of Chlamydia trachomatis trachoma and lymphogranuloma venereum biovars. Heliyon (2017) 0.75

A primer to clinical genome sequencing. Curr Opin Pediatr (2017) 0.75

Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area. Hum Cell (2017) 0.75

Towards precision medicine: discovering novel gynecological cancer biomarkers and pathways using linked data. J Biomed Semantics (2017) 0.75

The Case for Laboratory Developed Procedures: Quality and Positive Impact on Patient Care. Acad Pathol (2017) 0.75

Topological methods for genomics: present and future directions. Curr Opin Syst Biol (2016) 0.75

Genome-Wide Association Studies In Plant Pathosystems: Toward an Ecological Genomics Approach. Front Plant Sci (2017) 0.75

Interpreting Microbial Biosynthesis in the Genomic Age: Biological and Practical Considerations. Mar Drugs (2017) 0.75

Scalability and Validation of Big Data Bioinformatics Software. Comput Struct Biotechnol J (2017) 0.75

Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis. Clin Microbiol Rev (2017) 0.75

A Comprehensive Quality Evaluation System for Complex Herbal Medicine Using PacBio Sequencing, PCR-Denaturing Gradient Gel Electrophoresis, and Several Chemical Approaches. Front Plant Sci (2017) 0.75

stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage. Genome Biol (2017) 0.75

Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing. Gigascience (2017) 0.75

STEAK: A specific tool for transposable elements and retrovirus detection in high-throughput sequencing data. Virus Evol (2017) 0.75

Whole-Genome Restriction Mapping by "Subhaploid"-Based RAD Sequencing: An Efficient and Flexible Approach for Physical Mapping and Genome Scaffolding. Genetics (2017) 0.75

Commentary: CRISPR-Cas Encoding of a Digital Movie into the Genomes of a Population of Living Bacteria. Front Bioeng Biotechnol (2017) 0.75

Beyond editing to writing large genomes. Nat Rev Genet (2017) 0.75

Diversity of Functionally Permissive Sequences in the Receptor-Binding Site of Influenza Hemagglutinin. Cell Host Microbe (2017) 0.75

Using omics approaches to understand pulmonary diseases. Respir Res (2017) 0.75

A high-fidelity method for genomic sequencing of single somatic cells reveals a very high mutational burden. Exp Biol Med (Maywood) (2017) 0.75

DUDE-Seq: Fast, flexible, and robust denoising for targeted amplicon sequencing. PLoS One (2017) 0.75

A clinician's guide to microbiome analysis. Nat Rev Gastroenterol Hepatol (2017) 0.75

Characterization of the Rosellinia necatrix Transcriptome and Genes Related to Pathogenesis by Single-Molecule mRNA Sequencing. Plant Pathol J (2017) 0.75

Ultra-sensitive Sequencing Identifies High Prevalence of Clonal Hematopoiesis-Associated Mutations throughout Adult Life. Am J Hum Genet (2017) 0.75

Sequencing DNA for the Oxidatively Modified Base 8-Oxo-7,8-Dihydroguanine. Methods Enzymol (2017) 0.75

A transcriptomic approach to study the effect of long-term starvation and diet composition on the expression of mitochondrial oxidative phosphorylation genes in gilthead sea bream (Sparus aurata). BMC Genomics (2017) 0.75

The Grapevine and Wine Microbiome: Insights from High-Throughput Amplicon Sequencing. Front Microbiol (2017) 0.75

Food Safety in the Age of Next Generation Sequencing, Bioinformatics, and Open Data Access. Front Microbiol (2017) 0.75

ChimericSeq: An open-source, user-friendly interface for analyzing NGS data to identify and characterize viral-host chimeric sequences. PLoS One (2017) 0.75

Dissecting evolution and disease using comparative vertebrate genomics. Nat Rev Genet (2017) 0.75

Calculating quality of public high-throughput sequencing data to obtain suitable subset for reanalysis from the Sequence Read Archive. Gigascience (2017) 0.75

Articles cited by this

(truncated to the top 100)

Genome sequencing in microfabricated high-density picolitre reactors. Nature (2005) 150.21

A map of human genome variation from population-scale sequencing. Nature (2010) 121.13

Accurate whole human genome sequencing using reversible terminator chemistry. Nature (2008) 90.20

RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77

Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet (2008) 43.63

Sequencing technologies - the next generation. Nat Rev Genet (2009) 40.57

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature (2008) 38.13

Real-time DNA sequencing from single polymerase molecules. Science (2008) 29.53

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res (2008) 26.36

Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science (2009) 21.24

Accurate multiplex polony sequencing of an evolved bacterial genome. Science (2005) 20.91

An integrated semiconductor device enabling non-optical genome sequencing. Nature (2011) 20.85

Genome-wide in situ exon capture for selective resequencing. Nat Genet (2007) 19.97

Detection of specific polymerase chain reaction product by utilizing the 5'----3' exonuclease activity of Thermus aquaticus DNA polymerase. Proc Natl Acad Sci U S A (1991) 16.94

Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat Genet (1996) 15.73

Structural variation of chromosomes in autism spectrum disorder. Am J Hum Genet (2008) 15.51

The structure of DNA. Cold Spring Harb Symp Quant Biol (1953) 15.08

Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature (2012) 14.76

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res (2013) 14.23

De novo mutations revealed by whole-exome sequencing are strongly associated with autism. Nature (2012) 13.61

ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet (2009) 13.12

Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proc Natl Acad Sci U S A (2003) 12.91

A global reference for human genetic variation. Nature (2015) 12.85

Single-molecule DNA sequencing of a viral genome. Science (2008) 11.66

Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotechnol (2012) 10.31

A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics (2012) 9.97

Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat Methods (2010) 9.75

Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol (2009) 9.59

Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nat Rev Genet (2010) 9.53

Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proc Natl Acad Sci U S A (2004) 9.42

Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol (2012) 8.99

Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res (2005) 8.69

Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res (2008) 8.62

Copy-number variation and association studies of human disease. Nat Genet (2007) 8.50

A massively parallel PicoTiterPlate based platform for discrete picoliter-scale polymerase chain reactions. Electrophoresis (2003) 8.29

Continuous base identification for single-molecule nanopore DNA sequencing. Nat Nanotechnol (2009) 8.09

Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature (2012) 8.03

Structural variation in the human genome and its role in disease. Annu Rev Med (2010) 7.85

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res (2008) 7.77

Zero-mode waveguides for single-molecule analysis at high concentrations. Science (2003) 7.69

A ligase-mediated gene detection technique. Science (1988) 7.61

ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics (2004) 7.21

Concept, design and implementation of a cardiovascular gene-centric 50 k SNP array for large-scale genomic association studies. PLoS One (2008) 7.16

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods (2013) 7.06

Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res (2011) 6.88

Assembly of large genomes using second-generation sequencing. Genome Res (2010) 5.94

The contribution of de novo coding mutations to autism spectrum disorder. Nature (2014) 5.94

Field guide to next-generation DNA sequencers. Mol Ecol Resour (2011) 5.93

Methods and strategies for analyzing copy number variation using DNA microarrays. Nat Genet (2007) 5.64

Expandable DNA repeats and human disease. Nature (2007) 5.50

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq. Nature (2014) 5.47

Bioinformatics challenges of new sequencing technology. Trends Genet (2008) 5.34

Polony multiplex analysis of gene expression (PMAGE) in mouse hypertrophic cardiomyopathy. Science (2007) 5.19

Twenty-five years of quantitative PCR for gene expression analysis. Biotechniques (2008) 5.08

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems. Genome Biol (2011) 4.98

BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies. Nucleic Acids Res (2006) 4.93

Caenorhabditis elegans mutant allele identification by whole-genome sequencing. Nat Methods (2008) 4.71

Comparison of next-generation sequencing systems. J Biomed Biotechnol (2012) 4.56

Large-scale whole-genome sequencing of the Icelandic population. Nat Genet (2015) 4.54

Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res (2009) 4.11

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls. Nat Biotechnol (2014) 4.07

Improved data analysis for the MinION nanopore sequencer. Nat Methods (2015) 3.90

The UK10K project identifies rare variants in health and disease. Nature (2015) 3.89

High-throughput DNA sequencing--concepts and limitations. Bioessays (2010) 3.77

Assuring the quality of next-generation sequencing in clinical laboratory practice. Nat Biotechnol (2012) 3.62

Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping. Science (1993) 3.54

Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly. Nat Biotechnol (2012) 3.43

An integrated map of structural variation in 2,504 human genomes. Nature (2015) 3.30

Real-time, portable genome sequencing for Ebola surveillance. Nature (2016) 3.30

Resolving the complexity of the human genome using single-molecule sequencing. Nature (2014) 2.96

Pacific biosciences sequencing technology for genotyping and variation discovery in human data. BMC Genomics (2012) 2.92

Virtual terminator nucleotides for next-generation DNA sequencing. Nat Methods (2009) 2.83

Point-counterpoint. Ethics and genomic incidental findings. Science (2013) 2.73

Sequence-specific identification of 18 pathogenic microorganisms using microarray technology. Mol Cell Probes (2002) 2.70

Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells. PLoS One (2014) 2.67

Recurrent CNVs disrupt three candidate genes in schizophrenia patients. Am J Hum Genet (2008) 2.61

Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators. Proc Natl Acad Sci U S A (2006) 2.58

DNA ligases: structure, reaction mechanism, and function. Chem Rev (2006) 2.57

An assessment of the sequence gaps: unfinished business in a finished human genome. Nat Rev Genet (2004) 2.51

Concordance study of 3 direct-to-consumer genetic-testing services. Clin Chem (2010) 2.33

Taking qPCR to a higher level: Analysis of CNV reveals the power of high throughput qPCR to enhance quantitative resolution. Methods (2010) 2.27

Comparing platforms for C. elegans mutant identification using high-throughput whole-genome sequencing. PLoS One (2008) 2.24

A single-molecule long-read survey of the human transcriptome. Nat Biotechnol (2013) 2.24

Whole-genome haplotyping using long reads and statistical methods. Nat Biotechnol (2014) 2.11

Next-generation sequencing platforms. Annu Rev Anal Chem (Palo Alto Calif) (2013) 2.11

Sequencing the unsequenceable: expanded CGG-repeat alleles of the fragile X gene. Genome Res (2012) 2.04

Mammary development meets cancer genomics. Nat Med (2009) 2.04

Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella. Genome Biol (2015) 1.99

MinION Analysis and Reference Consortium: Phase 1 data release and analysis. F1000Res (2015) 1.95

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome. Genome Res (2015) 1.89

The genome sequence of the colonial chordate, Botryllus schlosseri. Elife (2013) 1.86

Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nat Methods (2015) 1.83

High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers. Nucleic Acids Res (2009) 1.80

Common variants conferring risk of schizophrenia: a pathway analysis of GWAS data. Schizophr Res (2010) 1.79

Nucleic acid amplification strategies for DNA microarray-based pathogen detection. Appl Environ Microbiol (2004) 1.76

Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetitive transposable elements. PLoS One (2014) 1.74

A cross-platform analysis of 14,177 expression quantitative trait loci derived from lymphoblastoid cell lines. Genome Res (2013) 1.72

Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study. Nat Biotechnol (2014) 1.68

Four-color DNA sequencing with 3'-O-modified nucleotide reversible terminators and chemically cleavable fluorescent dideoxynucleotides. Proc Natl Acad Sci U S A (2008) 1.64

Genome sequencing elucidates Sardinian genetic architecture and augments association analyses for lipid and blood inflammatory markers. Nat Genet (2015) 1.52