Coming of age: ten years of next-generation sequencing technologies (original) (raw)

• Watson, J. D. & Crick, F. H. The structure of DNA. Cold Spring Harb. Symp. Quant. Biol. 18, 123–131 (1953).
  Article CAS PubMed Google Scholar
• Mardis, E. R. Next-generation sequencing platforms. Annu. Rev. Anal. Chem. (Palo Alto Calif.) 6, 287–303 (2013). This article provides a concise description of technological advancements supporting NGS.
  Article CAS Google Scholar
• Wetterstrand, K. A. DNA sequencing costs: data from the NHGRI Genome Sequencing Program (GSP). National Human Genome Research Institute [online], http://www.genome.gov/sequencingcosts (updated 15 Jan 2016).
• Kircher, M. & Kelso, J. High-throughput DNA sequencing — concepts and limitations. Bioessays 32, 524–536 (2010).
  Article CAS PubMed Google Scholar
• Veritas Genetics. Veritas genetics launches $999 whole genome and sets new standard for genetic testing — Press Release. Veritas Genetics [online], https://www.veritasgenetics.com/documents/VG-launches-999-whole-genome.pdf (updated 4 Mar 2016).
• Veritas Genetics. Veritas genetics breaks $1,000 whole genome barrier — Press Release. Veritas Genetics [online], https://www.veritasgenetics.com/documents/VG-PGP-Announcement-Final.pdf (29 Sep 2015).
• Liu, L. et al. Comparison of next-generation sequencing systems. J. Biomed. Biotechnol. 2012, 251364 (2012).
  PubMed PubMed Central Google Scholar
• Dressman, D., Yan, H., Traverso, G., Kinzler, K. W. & Vogelstein, B. Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proc. Natl Acad. Sci. USA 100, 8817–8822 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Shendure, J. et al. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309, 1728–1732 (2005).
  Article CAS PubMed Google Scholar
• Kim, J. B. et al. Polony multiplex analysis of gene expression (PMAGE) in mouse hypertrophic cardiomyopathy. Science 316, 1481–1484 (2007).
  Article CAS PubMed Google Scholar
• Leamon, J. H. et al. A massively parallel PicoTiterPlate based platform for discrete picoliter-scale polymerase chain reactions. Electrophoresis 24, 3769–3777 (2003).
  Article CAS PubMed Google Scholar
• Fedurco, M., Romieu, A., Williams, S., Lawrence, I. & Turcatti, G. BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies. Nucleic Acids Res. 34, e22 (2006).
  Article PubMed PubMed Central CAS Google Scholar
• Harris, T. D. et al. Single-molecule DNA sequencing of a viral genome. Science 320, 106–109 (2008).
  Article CAS PubMed Google Scholar
• Drmanac, R. et al. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science 327, 78–81 (2010). This paper describes the use of DNA nanoballs to achieve clonal amplification and the use of cPAL to achieve human genome sequencing as implemented by Complete Genomics (BGI).
  Article CAS PubMed Google Scholar
• Tomkinson, A. E., Vijayakumar, S., Pascal, J. M. & Ellenberger, T. DNA ligases: structure, reaction mechanism, and function. Chem. Rev. 106, 687–699 (2006).
  Article CAS PubMed Google Scholar
• Landegren, U., Kaiser, R., Sanders, J. & Hood, L. A ligase-mediated gene detection technique. Science 241, 1077–1080 (1988).
  Article CAS PubMed Google Scholar
• Valouev, A. et al. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res. 18, 1051–1063 (2008). This paper describes the use of cleavable two-base-encoded probes to achieve genome-wide nucleosome mapping in Caenorhabditis elegans . This technology is implemented by Applied Biosystems (Thermo Fisher) for the SOLiD platform.
  Article CAS PubMed PubMed Central Google Scholar
• Metzker, M. L. Sequencing technologies — the next generation. Nat. Rev. Genet. 11, 31–46 (2010).
  Article CAS PubMed Google Scholar
• Ju, J. et al. Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators. Proc. Natl Acad. Sci. USA 103, 19635–19640 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Guo, J. et al. Four-color DNA sequencing with 3′-_O_-modified nucleotide reversible terminators and chemically cleavable fluorescent dideoxynucleotides. Proc. Natl Acad. Sci. USA 105, 9145–9150 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Timmerman, L. DNA sequencing market will exceed $20 billion, says Illumina CEO Jay Flatley. Forbes [online], http://www.forbes.com/sites/luketimmerman/2015/04/29/qa-with-jay-flatley-ceo-of-illumina-the-genomics-company-pursuing-a-20b-market/#4dbd19943bf5 (29 Apr 2015).
• Karow, J. Qiagen launches GeneReader NGS System at AMP; presents performance evaluation by broad. GenomeWeb [online], https://www.genomeweb.com/molecular-diagnostics/qiagen-launches-genereader-ngs-system-amp-presents-performance-evaluation (4 Nov 2015).
• Smith, D. R. & McKernan, K. Methods of producing and sequencing modified polynucleotides. US Patent 8058030 (2011).
• Margulies, M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376–380 (2005). This paper describes the development of the first NGS technology through the use of pyrosequencing. The authors demonstrate this method through sequencing of the Mycoplasma genitalium genome.
  Article CAS PubMed PubMed Central Google Scholar
• Rothberg, J. M. et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature 475, 348–352 (2011). This paper describes the first non-optical sequencing technology using a massively parallel semi-conductor device to monitor H+ release during DNA synthesis, as implemented by the Ion Torrent platform (Thermo Fisher). The authors demonstrate this technology by sequencing both bacterial and human DNA.
  Article CAS PubMed Google Scholar
• Rieber, N. et al. Coverage bias and sensitivity of variant calling for four whole-genome sequencing technologies. PLoS ONE 8, e66621 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Zook, J. M. et al. Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls. Nat. Biotechnol. 32, 246–251 (2014).
  Article CAS PubMed Google Scholar
• Nothnagel, M. et al. Technology-specific error signatures in the 1000 Genomes Project data. Hum. Genet. 130, 505–516 (2011).
  Article PubMed Google Scholar
• Shen, Y. Sarin, S., Liu, Y., Hobert, O. & Pe'er, I. Comparing platforms for C. elegans mutant identification using high-throughput whole-genome sequencing. PLoS ONE 3, e4012 (2008).
  Article PubMed PubMed Central CAS Google Scholar
• Chan, M. et al. Development of a next-generation sequencing method for BRCA mutation screening: a comparison between a high-throughput and a benchtop platform. J. Mol. Diagnost. 14, 602–612 (2012).
  Article CAS Google Scholar
• Wall, J. D. et al. Estimating genotype error rates from high-coverage next-generation sequence data. Genome Res. 24, 1734–1739 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Harismendy, O. et al. Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol. 10, R32 (2009).
  Article PubMed PubMed Central CAS Google Scholar
• BGI. Revolocity Whole Genome Sequencing Service — Press Release. BGI [online], http://u70g92ptbyk941g21dd41fc4.wpengine.netdna-cdn.com/wp-content/uploads/2015/10/Global-WGSRevolocity-ENG-10-15.pdf (2015).
• Karow, J. BGI halts revolocity launch, cuts complete genomics staff as part of strategic shift. GenomeWeb [online], https://www.genomeweb.com/sequencing-technology/bgi-halts-revolocity-launch-cuts-complete-genomics-staff-part-strategic-shift (23 Nov 2015).
• Bentley, D. R. et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53–59 (2008). This paper demonstrates the use of reversible dye-terminator chemistry for human genome sequencing. This platform is used by the Illumina suite of platforms.
  Article CAS PubMed PubMed Central Google Scholar
• Dohm, J. C., Lottaz, C., Borodina, T. & Himmelbauer, H. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res. 36, e105 (2008).
  Article PubMed PubMed Central CAS Google Scholar
• Nakamura, K. et al. Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res. 39, e90 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Minoche, A. E., Dohm, J. C. & Himmelbauer, H. Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems. Genome Biol. 12, R112 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Ley, T. J. et al. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 456, 66–72 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Sarin, S., Prabhu, S., O'Meara, M. M., Pe'er, I. & Hobert, O. Caenorhabditis elegans mutant allele identification by whole-genome sequencing. Nat. Methods 5, 865–867 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Park, P. J. ChIP–seq: advantages and challenges of a maturing technology. Nat. Rev. Genet. 10, 669–680 (2009). This review provides an overview of ChIP–seq methods for detecting chromatin–DNA interactions and their importance to epigenetics research.
  Article CAS PubMed PubMed Central Google Scholar
• Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y. & Greenleaf, W. J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213–1218 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Brunner, A. L. et al. Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res. 19, 1044–1056 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Wang, Z., Gerstein, M. & Snyder, M. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10, 57–63 (2009). This review provides an overview of advances and challenges in techniques that are used in transcriptomic research with a specific focus in methods that use NGS technologies.
  Article CAS PubMed PubMed Central Google Scholar
• Wang, X. et al. A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing. Bioinformatics 31, 2040–2042 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Qiagen. Oncology insights enabled by knowledge base-guided panel design and the seamless workflow of the GeneReader NGS system — Press Release. Qiagen [online], http://www.genereaderngs.com/PROM-9192-001_1100403_WP_GeneReader_NGS_0116_NA.pdf (2016).
• Forgetta, V. et al. Sequencing of the Dutch elm disease fungus genome using the Roche/454 GS-FLX Titanium System in a comparison of multiple genomics core facilities. J. Biomol. Tech. 24, 39–49 (2013).
  PubMed PubMed Central Google Scholar
• Loman, N. J. et al. Performance comparison of benchtop high-throughput sequencing platforms. Nat. Biotechnol. 30, 434–439 (2012).
  Article CAS PubMed Google Scholar
• GenomeWeb. Roche shutting down 454 sequencing business. GenomeWeb [online], https://www.genomeweb.com/sequencing/roche-shutting-down-454-sequencing-business (15 Oct 2015).
• Malapelle, U. et al. Ion Torrent next-generation sequencing for routine identification of clinically relevant mutations in colorectal cancer patients. J. Clin. Pathol. 68, 64–68 (2015).
  Article PubMed Google Scholar
• Li, S. et al. Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study. Nat. Biotechnol. 32, 915–925 (2014).
  Article PubMed PubMed Central CAS Google Scholar
• Life Technologies. Ion semiconductor sequencing uniquely enables both accurate long reads and paired-end sequencing. Life Technologies [online], https://www3.appliedbiosystems.com/cms/groups/applied_markets_marketing/documents/generaldocuments/cms_098680.pdf (2011)
• Campbell, P. J. et al. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat. Genet. 40, 722–729 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• McCarroll, S. A. & Altshuler, D. M. Copy-number variation and association studies of human disease. Nat. Genet. 39, S37–S42 (2007).
  Article CAS PubMed Google Scholar
• Mirkin, S. M. Expandable DNA repeats and human disease. Nature 447, 932–940 (2007).
  Article CAS PubMed Google Scholar
• Stankiewicz, P. & Lupski, J. R. Structural variation in the human genome and its role in disease. Annu. Rev. Med. 61, 437–455 (2010).
  Article CAS PubMed Google Scholar
• Eid, J. et al. Real-time DNA sequencing from single polymerase molecules. Science 323, 133–138 (2009). The authors describe the development of a real-time sequencing method using their zero-mode waveguide sensors as implemented by the Pacific Biosciences platform. The authors demonstrate the technique by sequencing synthetic DNA templates.
  Article CAS PubMed Google Scholar
• Levene, M. J. et al. Zero-mode waveguides for single-molecule analysis at high concentrations. Science 299, 682–686 (2003).
  Article CAS PubMed Google Scholar
• Loomis, E. W. et al. Sequencing the unsequenceable: expanded CGG-repeat alleles of the fragile X gene. Genome Res. 23, 121–128 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Clarke, J. et al. Continuous base identification for single-molecule nanopore DNA sequencing. Nat. Nanotechnol. 4, 265–270 (2009). The authors demonstrate the use of a mutant alpha-hemolysin for ordered, continuous detection of free nucleotides in solution. This work provides the basis for the approach used by ONT.
  Article CAS PubMed Google Scholar
• Voskoboynik, A. et al. The genome sequence of the colonial chordate, Botryllus schlosseri. eLife 2, e00569 (2013).
  Article PubMed PubMed Central Google Scholar
• McCoy, R. C. et al. Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetitive transposable elements. PLoS ONE 9, e106689 (2014).
  Article PubMed PubMed Central CAS Google Scholar
• Schatz, M. C., Delcher, A. L. & Salzberg, S. L. Assembly of large genomes using second-generation sequencing. Genome Res. 20, 1165–1173 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• English, A. C. et al. Assessing structural variation in a personal genome-towards a human reference diploid genome. BMC Genomics 16, 286 (2015).
  Article PubMed PubMed Central CAS Google Scholar
• Carneiro, M. O. et al. Pacific Biosciences sequencing technology for genotyping and variation discovery in human data. BMC Genomics 13, 375 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Quail, M. A. et al. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 13, 341 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Koren, S. et al. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat. Biotechnol. 30, 693–700 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Larsen, P. A., Heilman, A. M. & Yoder, A. D. The utility of PacBio circular consensus sequencing for characterizing complex gene families in non-model organisms. BMC Genomics 15, 720 (2014).
  Article PubMed PubMed Central Google Scholar
• Heger, M. PacBio launches higher-throughput, lower-cost single-molecule sequencing system. GenomeWeb [online], https://www.genomeweb.com/business-news/pacbio-launches-higher-throughput-lower-cost-single-molecule-sequencing-system (01 Oct 2015).
• Goodwin, S. et al. Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome. Genome Res. 25, 1750–1756 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Jain, M. et al. Improved data analysis for the MinION nanopore sequencer. Nat. Methods 12, 351–356 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Heger, M. 10X Genomics, Pacific Biosciences provide business updates at JP Morgan Healthcare Conference. GenomeWeb [online], https://www.genomeweb.com/sequencing-technology/10x-genomics-pacific-biosciences-provide-business-updates-jp-morgan-healthcare (13 Jan 2016).
• Cirulli, E. T. & Goldstein, D. B. Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nat. Rev. Genet. 11, 415–425 (2010). This review provides a comprehensive overview of advances in, and challenges of using, WGS for variant discovery in human disease.
  Article CAS PubMed Google Scholar
• Ellis, M. J. et al. Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature 486, 353–360 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Prat, A. & Perou, C. M. Mammary development meets cancer genomics. Nat. Med. 15, 842–844 (2009).
  Article CAS PubMed Google Scholar
• 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 467, 1061–1073 (2010).
• 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature 526, 68–74 (2015).
• Sudmant, P. H. et al. An integrated map of structural variation in 2,504 human genomes. Nature 526, 75–81 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• UK10K Consortium. The UK10K project identifies rare variants in health and disease. Nature 526, 82–90 (2015).
• Gudbjartsson, D. F. et al. Large-scale whole-genome sequencing of the Icelandic population. Nat. Genet. 47, 435–444 (2015).
  Article CAS PubMed Google Scholar
• Regalado, A. U.S. to develop DNA study of one million people. MIT Technology Review [online], http://www.technologyreview.com/news/534591/us-to-develop-dna-study-of-one-million-people (30 Jan 2015).
• Sidore, C. et al. Genome sequencing elucidates Sardinian genetic architecture and augments association analyses for lipid and blood inflammatory markers. Nat. Genet. 47, 1272–1281 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Hodges, E. et al. Genome-wide in situ exon capture for selective resequencing. Nat. Genet. 39, 1522–1527 (2015). This paper describes the in situ capture and selective enrichment of human exons for downstream NGS. This manuscript provides the methodological basis for whole-exome and targeted sequencing.
  Article CAS Google Scholar
• Iossifov, I. et al. The contribution of de novo coding mutations to autism spectrum disorder. Nature 515, 216–221 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• O'Roak, B. J. et al. Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature 485, 246–250 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Sanders, S. J. et al. De novo mutations revealed by whole-exome sequencing are strongly associated with autism. Nature 485, 237–241 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Griffith, M. et al. Optimizing cancer genome sequencing and analysis. Cell Syst. 1, 210–223 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Rauch, C. et al. Towards an understanding of DNA recognition by the methyl-CpG binding domain 1. J. Biomol. Struct. Dyn. 22, 695–706 (2005).
  Article CAS PubMed Google Scholar
• Oda, M. et al. High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers. Nucleic Acids Res. 37, 3829–3839 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Irizarry, R. A. et al. Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res. 18, 780–790 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Meissner, A. et al. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 33, 5868–5877 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Flusberg, B. A. et al. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat. Methods 7, 461–465 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Wescoe, Z. L., Schreiber, J. & Akeson, M. Nanopores discriminate among five C5-cytosine variants in DNA. J. Am. Chem. Soc. 136, 16582–16587 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Lam, E. T. et al. Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly. Nat. Biotechnol. 30, 771–776 (2012).
  Article CAS PubMed Google Scholar
• Eichler, E. E., Clark, R. A. & She, X. An assessment of the sequence gaps: unfinished business in a finished human genome. Nat. Rev. Genet. 5, 345–354 (2004).
  Article CAS PubMed Google Scholar
• Chaisson, M. J., Wilson, R. K. & Eichler, E. E. Genetic variation and the de novo assembly of human genomes. Nat. Rev. Genet. 16, 627–640 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Chaisson, M. J. et al. Resolving the complexity of the human genome using single-molecule sequencing. Nature 517, 608–611 (2015). This article provides strong support for the utility of long-read sequencing for generating high-quality reference genomes. The authors demonstrate this by closing and/or extending gaps and resolving structural variants in the GRCh37 human reference genome.
  Article CAS PubMed Google Scholar
• Ritz, A. et al. Characterization of structural variants with single molecule and hybrid sequencing approaches. Bioinformatics 30, 3458–3466 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Snyder, M. W., Adey, A., Kitzman, J. O. & Shendure, J. Haplotype-resolved genome sequencing: experimental methods and applications. Nat. Rev. Genet. 16, 344–358 (2015).
  Article CAS PubMed Google Scholar
• Kuleshov, V. et al. Whole-genome haplotyping using long reads and statistical methods. Nat. Biotechnol. 32, 261–266 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Treutlein, B. et al. Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq. Nature 509, 371–375 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Sharon, D., Tilgner, H., Grubert, F. & Snyder, M. A single-molecule long-read survey of the human transcriptome. Nat. Biotechnol. 31, 1009–1014 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Quick, J. et al. Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella. Genome Biol. 16, 114 (2015).
  Article PubMed PubMed Central CAS Google Scholar
• Quick, J. et al. Real-time, portable genome sequencing for Ebola surveillance. Nature 530, 228–232 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• GenomeWeb. White House announces efforts to accelerate precision medicine initiative. GenomeWeb [online], https://www.genomeweb.com/molecular-diagnostics/white-house-announces-efforts-accelerate-precision-medicine-initiative (25 Feb 2016).
• Illumina. Illumina forms new company to enable early cancer detection via blood-based screening — Press Release. Illumina [online], http://www.illumina.com/company/news-center/press-releases/press-release-details.html?newsid=2127903 (10 Jan 2016).
• Schatz, M. C. & Langmead, B. The DNA data deluge: fast, efficient genome sequencing machines are spewing out more data than geneticists can analyze. IEEE Spectr. 50, 26–33 (2013).
  Article PubMed PubMed Central Google Scholar
• Pop, M. & Salzberg, S. L. Bioinformatics challenges of new sequencing technology. Trends Genet. 24, 142–149 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Sunyaev, S. R. Inferring causality and functional significance of human coding DNA variants. Hum. Mol. Genet. 21, R10–R17 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Gargis, A. S. et al. Assuring the quality of next-generation sequencing in clinical laboratory practice. Nat. Biotechnol. 30, 1033–1036 (2012).
  Article CAS PubMed Google Scholar
• Chrystoja, C. C. & Diamandis, E. P. Whole genome sequencing as a diagnostic test: challenges and opportunities. Clin. Chem. 60, 724–733 (2014).
  Article CAS PubMed Google Scholar
• McGuire, A. L. et al. Point-counterpoint. Ethics and genomic incidental findings. Science 340, 1047–1048 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Bowers, J. et al. Virtual terminator nucleotides for next-generation DNA sequencing. Nat. Methods 6, 593–595 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Heger, M. China's Direct Genomics unveils new targeted NGS system based on Helicos Tech for clinical use. GenomeWeb [online], https://www.genomeweb.com/business-news/chinas-direct-genomics-unveils-new-targeted-ngs-system-based-helicos-tech-clinical-use (27 Oct 2015).
• Karow, J. Oxford Nanopore presents details on new high-throughput sequencer, improvements to MinIon. GenomeWeb [online], https://www.genomeweb.com/sequencing/oxford-nanopore-presents-details-new-high-throughput-sequencer-improvements-mini (16 Sep 2014).
• Karow, J. Sigma-Aldrich enters co-marketing agreement with GenapSys for Genius sequencer. GenomeWeb [online], https://www.genomeweb.com/sequencing-technology/sigma-aldrich-enters-co-marketing-agreement-genapsys-genius-sequencer (1 Jul 2015).
• Roche. Roche acquires Genia Technologies to strengthen next generation sequencing pipeline — Press Release. Roche [online], http://www.roche.com/media/store/releases/med-cor-2014-06-02.htm (2 Jun 2014).
• Heger, M. Illumina unveils mini targeted sequencer, semiconductor sequencing project at JP Morgan Conference. GenomeWeb [online], https://www.genomeweb.com/sequencing-technology/illumina-unveils-mini-targeted-sequencer-semiconductor-sequencing-project-jp (1 Jan 2016).
• NanoString. NanoString Technologies presents proof-of-concept data for novel massively parallel single molecule sequencing chemistry at AGBT meeting — Press Release. NanoString [online], http://investors.nanostring.com/releasedetail.cfm?ReleaseID=954517 (11 Feb 2016).
• Raz, T. & Pascaline, M. Nucleic acid target detection using a detector, a probe and an inhibitor. US Patent 20130344485 (2013).
• Mankos, M. et al. A novel low energy electron microscope for DNA sequencing and surface analysis. Ultramicroscopy 145, 36–49 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Augenlicht, L. H. & Kobrin, D. Cloning and screening of sequences expressed in a mouse colon tumor. Cancer Res. 42, 1088–1093 (1982).
  CAS PubMed Google Scholar
• Dandy, D. S., Wu, P. & Grainger, D. W. Array feature size influences nucleic acid surface capture in DNA microarrays. Proc. Natl Acad. Sci. USA 104, 8223–8228 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Keating, B. J. et al. Concept, design and implementation of a cardiovascular gene-centric 50 k SNP array for large-scale genomic association studies. PLoS ONE 3, e3583 (2008).
  Article PubMed PubMed Central CAS Google Scholar
• DeRisi, J. et al. Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat. Genet. 14, 457–460 (1996).
  Article CAS PubMed Google Scholar
• Alizadeh, A. A. & Staudt, L. M. Genomic-scale gene expression profiling of normal and malignant immune cells. Curr. Opin. Immunol. 12, 219–225 (2000).
  Article CAS PubMed Google Scholar
• Rhodes, D. R. et al. Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proc. Natl Acad. Sci. USA 101, 9309–9314 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Vora, G. J., Meador, C. E., Stenger, D. A. & Andreadis, J. D. Nucleic acid amplification strategies for DNA microarray-based pathogen detection. Appl. Environ. Microbiol. 70, 3047–3054 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Wilson, W. J. et al. Sequence-specific identification of 18 pathogenic microorganisms using microarray technology. Mol. Cell Probes 16, 119–127 (2002).
  Article CAS PubMed Google Scholar
• Imai, K., Kricka, L. J. & Fortina, P. Concordance study of 3 direct-to-consumer genetic-testing services. Clin. Chem. 57, 518–521 (2011).
  Article CAS PubMed Google Scholar
• Dolgin, E. Personalized investigation. Nat. Med. 16, 953–955 (2010).
  Article CAS PubMed Google Scholar
• Jia, P., Wang, L., Meltzer, H. Y. & Zhao, Z. Common variants conferring risk of schizophrenia: a pathway analysis of GWAS data. Schizophr. Res. 122, 38–42 (2010).
  Article PubMed PubMed Central Google Scholar
• Welter, D. et al. The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res. 42, D1001–D1006 (2014).
  Article CAS PubMed Google Scholar
• Carter, N. P. Methods and strategies for analyzing copy number variation using DNA microarrays. Nat. Genet. 39, S16–S21 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Vrijenhoek, T. et al. Recurrent CNVs disrupt three candidate genes in schizophrenia patients. Am. J. Hum. Genet. 83, 504–510 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Marshall, C. R. et al. Structural variation of chromosomes in autism spectrum disorder. Am. J. Hum. Genet. 82, 477–488 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Buck, M. J. & Lieb, J. D. ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 83, 349–360 (2004).
  Article CAS PubMed Google Scholar
• Liang, L. et al. A cross-platform analysis of 14,177 expression quantitative trait loci derived from lymphoblastoid cell lines. Genome Res. 23, 716–726 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Zhao, S., Fung-Leung, W. P., Bittner, A., Ngo, K. & Liu, X. Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells. PLoS ONE 9, e78644 (2014).
  Article PubMed PubMed Central CAS Google Scholar
• Holland, P. M., Abramson, R. D., Watson, R. & Gelfand, D. H. Detection of specific polymerase chain reaction product by utilizing the 5′→3′ exonuclease activity of Thermus aquaticus DNA polymerase. Proc. Natl Acad. Sci. USA 88, 7276–7280 (1991).
  Article CAS PubMed PubMed Central Google Scholar
• Morin, P. A. & McCarthy, M. Highly accurate SNP genotyping from historical and low-quality samples. Mol. Ecol. Notes 7, 937–946 (2007).
  Article CAS Google Scholar
• VanGuilder, H. D., Vrana, K. E. & Freeman, W. M. Twenty-five years of quantitative PCR for gene expression analysis. Biotechniques 44, 619–626 (2008).
  Article CAS PubMed Google Scholar
• Weaver, S. et al. Taking qPCR to a higher level: Analysis of CNV reveals the power of high throughput qPCR to enhance quantitative resolution. Methods 50, 271–276 (2010).
  Article CAS PubMed Google Scholar
• Sedlak, R. H., Cook, L., Cheng, A., Magaret, A. & Jerome, K. R. Clinical utility of droplet digital PCR for human cytomegalovirus. J. Clin. Microbiol. 52, 2844–2848 (2014).
  Article PubMed PubMed Central CAS Google Scholar
• Kulkarni, M. M. in Current Protocols in Molecular Biology Ch. 25 (eds Ausubel, F. M. et al.) (Wiley, 2011).
  Google Scholar
• Nielsen, T. et al. 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. BMC Cancer 14, 177 (2014).
  Article PubMed PubMed Central CAS Google Scholar
• Ku, B. M. et al. High-throughput profiling identifies clinically actionable mutations in salivary duct carcinoma. J. Transl. Med. 12, 299 (2014).
  Article PubMed PubMed Central CAS Google Scholar
• Sailani, M. R. et al. The complex SNP and CNV genetic architecture of the increased risk of congenital heart defects in Down syndrome. Genome Res. 23, 1410–1421 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Lira, M. E. et al. Multiplexed gene expression and fusion transcript analysis to detect ALK fusions in lung cancer. J. Mol. Diagn. 15, 51–61 (2013).
  Article CAS PubMed Google Scholar
• Schwartz, D. C. et al. Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping. Science 262, 110–114 (1993).
  Article CAS PubMed Google Scholar
• Hastie, A. R. et al. Rapid genome mapping in nanochannel arrays for highly complete and accurate de novo sequence assembly of the complex Aegilops tauschii genome. PLoS ONE 8, e55864 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Cao, H. et al. Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology. Gigascience 3, 34 (2014).
  Article PubMed PubMed Central Google Scholar
• Pendleton, M. et al. Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nat. Methods 12, 780–786 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Life Technologies. 5500 W series genetic analyzers. Life Technologies [online], https://tools.thermofisher.com/content/sfs/brochures/5500-w-series-spec-sheet.pdf (2012).
• Yuzuki, D. BGISEQ-500 debuts at the International Congress of Genomics 10. Next Generation Technologist [online], http://www.yuzuki.org/bgiseq-500-debut-at-the-international-congress-of-genomics-10 (24 Oct 2015).
• Winnick, E. Illumina launches four new systems; provides financial, Dx update at JP Morgan. GenomeWeb [online], https://www.genomeweb.com/business-news/illumina-launches-four-new-systems-provides-financial-dx-update-jp-morgan (12 Jan 2015).
• [No authors listed.] Illumina HiSeq 3000 Service Fees. Oregon State University [online], http://cgrb.oregonstate.edu/core/illumina-hiseq-3000/illumina-hiseq-3000-service-fees (updated 1 Jan 2016)
• Heger, M. Thermo Fisher launches new systems to focus on plug and play targeted sequencing. GenomeWeb [online], https://www.genomeweb.com/sequencing-technology/thermo-fisher-launches-new-systems-focus-plug-and-play-targeted-sequencing (1 Sep 2015).
• Ip, C. L. et al. MinION analysis and reference consortium: Phase 1 data release and analysis. F1000Research 4, 1075 (2015).
  Article PubMed PubMed Central Google Scholar
• Glenn, T. C. Field guide to next-generation DNA sequencers. Mol. Ecol. Resour. 11, 759–769 (2011).
  Article CAS PubMed Google Scholar
• Karow, J. At AGBT, 10X Genomics launches GemCode platform; shipments slated for Q2 as firm battles IP lawsuits. GenomeWeb [online], https://www.genomeweb.com/sample-prep/agbt-10x-genomics-launches-gemcode-platform-shipments-slated-q2-firm-battles-ip-lawsuits (2 Mar 2015).