Overview of Next‐Generation Sequencing Technologies

High throughput DNA sequencing methodology (next generation sequencing; NGS) has rapidly evolved over the past 15 years and new methods are continually being commercialized. As the technology develops, so do increases in the number of corresponding applications for basic and applied science. The purpose of this review is to provide a compendium of NGS methodologies and associated applications. Each brief discussion is followed by web links to the manufacturer and/or web‐based visualizations. Keyword searches, such as with Google, may also provide helpful internet links and information. © 2018 by John Wiley & Sons, Inc.

[1]  E. Mardis Next-generation DNA sequencing methods. , 2008, Annual review of genomics and human genetics.

[2]  Kin-Fan Au,et al.  PacBio Sequencing and Its Applications , 2015, Genom. Proteom. Bioinform..

[3]  Mark Akeson,et al.  Single-molecule analysis of DNA-protein complexes using nanopores , 2007, Nature Methods.

[4]  Doug Stryke,et al.  Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis , 2015, Genome Medicine.

[5]  M. Metzker Sequencing technologies — the next generation , 2010, Nature Reviews Genetics.

[6]  Joanna Bybee,et al.  Adapting capillary gel electrophoresis as a sensitive, high-throughput method to accelerate characterization of nucleic acid metabolic enzymes , 2015, Nucleic acids research.

[7]  R. Contreras,et al.  Glycome mapping on DNA sequencing equipment , 2006, Nature Protocols.

[8]  R. Contreras,et al.  Ultrasensitive profiling and sequencing of N-linked oligosaccharides using standard DNA-sequencing equipment. , 2001, Glycobiology.

[9]  George M. Church,et al.  Genomes for all. , 2006, Scientific American.

[10]  D. Schwartz,et al.  Optical mapping of lambda bacteriophage clones using restriction endonucleases , 1995, Nature Genetics.

[11]  F. Sanger,et al.  DNA sequencing with chain-terminating inhibitors. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[12]  Hanlee P. Ji,et al.  Next-generation DNA sequencing , 2008, Nature Biotechnology.

[13]  W. Gilbert,et al.  Sequencing end-labeled DNA with base-specific chemical cleavages. , 1980, Methods in enzymology.

[14]  Radoje Drmanac,et al.  Sequencing by hybridization (SBH): advantages, achievements, and opportunities. , 2002, Advances in biochemical engineering/biotechnology.

[15]  Chengqi Yi,et al.  Analysis of RNA base modification and structural rearrangement by single-molecule real-time detection of reverse transcription , 2013, Journal of Nanobiotechnology.

[16]  Z. Kelman,et al.  The Roles of Family B and D DNA Polymerases in Thermococcus Species 9°N Okazaki Fragment Maturation* , 2015, The Journal of Biological Chemistry.

[17]  P. Kwok,et al.  Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly , 2012, Nature Biotechnology.

[18]  Richard J. Roberts,et al.  The methylomes of six bacteria , 2012, Nucleic acids research.

[19]  D. Schwartz,et al.  Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping. , 1993, Science.

[20]  T. Furey ChIP – seq and beyond : new and improved methodologies to detect and characterize protein – DNA interactions , 2012 .

[21]  A. Mirzabekov,et al.  DNA sequencing by hybridization--a megasequencing method and a diagnostic tool? , 1994, Trends in biotechnology.

[22]  F. Sanger,et al.  A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. , 1975, Journal of molecular biology.

[23]  P. Kwok,et al.  A Hybrid Approach for de novo Human Genome Sequence Assembly and Phasing , 2016, Nature Methods.

[24]  Bernard P. Puc,et al.  An integrated semiconductor device enabling non-optical genome sequencing , 2011, Nature.

[25]  O. Ito,et al.  Preparation of Composite Films of a Conjugated Polymer and C60NWs and Their Photovoltaic Application , 2016 .

[26]  T. Deng,et al.  Solid-State Nanopore-Based DNA Sequencing Technology , 2016 .

[27]  Minh Duc Cao,et al.  Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinIONTM sequencing , 2015, bioRxiv.

[28]  A. F. Gardner,et al.  Pre-steady-state Kinetic Analysis of a Family D DNA Polymerase from Thermococcus sp. 9°N Reveals Mechanisms for Archaeal Genomic Replication and Maintenance* , 2015, The Journal of Biological Chemistry.

[29]  Kevin Y. Yip,et al.  Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays , 2015, Genetics.

[30]  T. C. Evans,et al.  DNA damage is a major cause of sequencing errors, directly confounding variant identification , 2016, bioRxiv.

[31]  Sergey Koren,et al.  De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing[CC-BY] , 2017, Plant Cell.

[32]  D. Branton,et al.  Characterization of individual polynucleotide molecules using a membrane channel. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[33]  D. Branton,et al.  The potential and challenges of nanopore sequencing , 2008, Nature Biotechnology.

[34]  H. Aburatani,et al.  Ordered restriction endonuclease maps of yeast artificial chromosomes created by optical mapping on surfaces. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[35]  T. Anantharaman,et al.  Automated high resolution optical mapping using arrayed, fluid-fixed DNA molecules. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[36]  Tyson A. Clark,et al.  Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing , 2012, Nature Biotechnology.

[37]  F. Westerlund,et al.  Optical DNA mapping in nanofluidic devices: principles and applications. , 2017, Lab on a chip.

[38]  D. Deamer,et al.  Sequence-specific detection of individual DNA polymerase complexes in real time using a nanopore. , 2007, Nature nanotechnology.

[39]  M. Ronaghi,et al.  Real-time DNA sequencing using detection of pyrophosphate release. , 1996, Analytical biochemistry.

[40]  J. Hofkens,et al.  Optical mapping of DNA: Single‐molecule‐based methods for mapping genomes , 2011, Biopolymers.

[41]  Timothy D. Harris,et al.  The challenges of sequencing by synthesis , 2009, Nature Biotechnology.

[42]  Tyson A. Clark,et al.  Direct detection of DNA methylation during single-molecule, real-time sequencing , 2010, Nature Methods.

[43]  H. Swerdlow,et al.  A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers , 2012, BMC Genomics.

[44]  D. Richman,et al.  Comparison of Sequencing by Hybridization and Cycle Sequencing for Genotyping of Human Immunodeficiency Virus Type 1 Reverse Transcriptase , 2000, Journal of Clinical Microbiology.

[45]  Pingfang Liu,et al.  DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification , 2017, Science.

[46]  C. Manaia,et al.  Applications of optical DNA mapping in microbiology. , 2017, BioTechniques.

[47]  Heping Zhang,et al.  Short communication: Single molecule, real-time sequencing technology revealed species- and strain-specific methylation patterns of 2 Lactobacillus strains. , 2015, Journal of dairy science.

[48]  J. Shendure,et al.  DNA sequencing at 40: past, present and future , 2017, Nature.

[49]  Gary D Bader,et al.  Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes. , 2015, F1000Research.

[50]  M. Brenner,et al.  Sequencing by Hybridization of Long Targets , 2012, PloS one.