Semin Thromb Hemost 2019; 45(07): 661-673
DOI: 10.1055/s-0039-1688446
Review Article
Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

Next-Generation Sequencing and Emerging Technologies

1   Translational Genomics Group, Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
2   Department of Neurogenetics, Kolling Institute, University of Sydney and Royal North Shore Hospital, St Leonards, New South Wales, Australia
3   Molecular Medicine Laboratory, Concord Hospital, Sydney, Australia
,
1   Translational Genomics Group, Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
4   Computational Biology Group, Children's Cancer Institute, University of New South Wales, Randwick, New South Wales, Australia
,
1   Translational Genomics Group, Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
2   Department of Neurogenetics, Kolling Institute, University of Sydney and Royal North Shore Hospital, St Leonards, New South Wales, Australia
› Author Affiliations
Further Information

Publication History

Publication Date:
16 May 2019 (online)

Abstract

Genetic sequencing technologies are evolving at a rapid pace with major implications for research and clinical practice. In this review, the authors provide an updated overview of next-generation sequencing (NGS) and emerging methodologies. NGS has tremendously improved sequencing output while being more time and cost-efficient in comparison to Sanger sequencing. The authors describe short-read sequencing approaches, such as sequencing by synthesis, ion semiconductor sequencing, and nanoball sequencing. Third-generation long-read sequencing now promises to overcome many of the limitations of short-read sequencing, such as the ability to reliably resolve repeat sequences and large genomic rearrangements. By combining complementary methods with massively parallel DNA sequencing, a greater insight into the biological context of disease mechanisms is now possible. Emerging methodologies, such as advances in nanopore technology, in situ nucleic acid sequencing, and microscopy-based sequencing, will continue the rapid evolution of this area. These new technologies hold many potential applications for hematological disorders, with the promise of precision and personalized medical care in the future.

 
  • References

  • 1 Wetterstrand KA. DNA Sequencing Costs: Data from the NHGRI Genome Sequencing Program (GSP). Available at: https://www.genome.gov/sequencingcostsdata . Accessed December 12, 2018
  • 2 Watson JD, Crick FH. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 1953; 171 (4356): 737-738
  • 3 Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 1977; 74 (12) 5463-5467
  • 4 Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010; 11 (01) 31-46
  • 5 Schadt EE, Turner S, Kasarskis A. A window into third-generation sequencing. Hum Mol Genet 2010; 19 (R2): R227-R240
  • 6 Schloss JA. How to get genomes at one ten-thousandth the cost. Nat Biotechnol 2008; 26 (10) 1113-1115
  • 7 Muzzey D, Evans EA, Lieber C. Understanding the basics of NGS: from mechanism to variant calling. Curr Genet Med Rep 2015; 3 (04) 158-165
  • 8 van Dijk EL, Auger H, Jaszczyszyn Y, Thermes C. Ten years of next-generation sequencing technology. Trends Genet 2014; 30 (09) 418-426
  • 9 Zappala Z, Montgomery SB. Non-coding loss-of-function variation in human genomes. Hum Hered 2016; 81 (02) 78-87
  • 10 Deveson IW, Hardwick SA, Mercer TR, Mattick JS. The dimensions, dynamics, and relevance of the mammalian noncoding transcriptome. Trends Genet 2017; 33 (07) 464-478
  • 11 Gloss BS, Dinger ME. Realizing the significance of noncoding functionality in clinical genomics. Exp Mol Med 2018; 50 (08) 97
  • 12 Meyerson M, Gabriel S, Getz G. Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet 2010; 11 (10) 685-696
  • 13 Goodwin S, McPherson JD, McCombie WR. Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 2016; 17 (06) 333-351
  • 14 Liu L, Li Y, Li S. , et al. Comparison of next-generation sequencing systems. J Biomed Biotechnol 2012; 2012: 251364
  • 15 Mardis ER. The impact of next-generation sequencing technology on genetics. Trends Genet 2008; 24 (03) 133-141
  • 16 Raine A, Liljedahl U, Nordlund J. Data quality of whole genome bisulfite sequencing on Illumina platforms. PLoS One 2018; 13 (04) e0195972
  • 17 Merriman B, Rothberg JM, Rothberg JM. ; Ion Torrent R&D Team. Progress in ion torrent semiconductor chip based sequencing. Electrophoresis 2012; 33 (23) 3397-3417
  • 18 Drmanac R, Sparks AB, Callow MJ. , et al. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science 2010; 327 (5961): 78-81
  • 19 Huang J, Liang X, Xuan Y. , et al. A reference human genome dataset of the BGISEQ-500 sequencer. Gigascience 2017; 6 (05) 1-9
  • 20 Poplin R, Chang PC, Alexander D. , et al. A universal SNP and small-indel variant caller using deep neural networks. Nat Biotechnol 2018; 36 (10) 983-987
  • 21 Heger M. BGI Launches New Sequencer as Customers Report Data From Earlier Instruments. 2018 . Available at: https://www.genomeweb.com/sequencing/bgi-launches-new-sequencer-customers-report-data-earlier-instruments#.W-jL9-JxWUk . Accessed November 2, 2018
  • 22 Rhoads A, Au KF. PacBio sequencing and its applications. Genomics Proteomics Bioinformatics 2015; 13 (05) 278-289
  • 23 Ardui S, Ameur A, Vermeesch JR, Hestand MS. Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics. Nucleic Acids Res 2018; 46 (05) 2159-2168
  • 24 Travers KJ, Chin CS, Rank DR, Eid JS, Turner SW. A flexible and efficient template format for circular consensus sequencing and SNP detection. Nucleic Acids Res 2010; 38 (15) e159
  • 25 Levene MJ, Korlach J, Turner SW, Foquet M, Craighead HG, Webb WW. Zero-mode waveguides for single-molecule analysis at high concentrations. Science 2003; 299 (5607): 682-686
  • 26 Flusberg BA, Webster DR, Lee JH. , et al. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat Methods 2010; 7 (06) 461-465
  • 27 Eid J, Fehr A, Gray J. , et al. Real-time DNA sequencing from single polymerase molecules. Science 2009; 323 (5910): 133-138
  • 28 Nakano K, Shiroma A, Shimoji M. , et al. Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area. Hum Cell 2017; 30 (03) 149-161
  • 29 Pacific Biosciences Releases Highest-Quality, Most Contiguous Individual Human Genome Assembly to Date. 2018. Available at: https://www.pacb.com/press_releases/pacific-biosciences-releases-highest-quality-most-contiguous-individual-human-genome-assembly-to-date/ . Accessed October 10, 2018
  • 30 Illumina to Acquire Pacific Biosciences for $1.2 Billion. 2018. Available at: https://www.genomeweb.com/sequencing/illumina-acquire-pacific-biosciences-12-billion#.W9_EWuJxWUk . Accessed November 2, 2018
  • 31 Lu H, Giordano F, Ning Z. Oxford Nanopore MinION sequencing and genome assembly. Genomics Proteomics Bioinformatics 2016; 14 (05) 265-279
  • 32 Quick J, Loman NJ, Duraffour S. , et al. Real-time, portable genome sequencing for Ebola surveillance. Nature 2016; 530 (7589): 228-232
  • 33 Castro-Wallace SL, Chiu CY, John KK. , et al. Nanopore DNA sequencing and genome assembly on the international space station. Sci Rep 2017; 7 (01) 18022
  • 34 Payne A, Holmes N, Rakyan V, Loose M. Whale watching with BulkVis: a graphical viewer for Oxford Nanopore bulk fast5 files. bioRxiv 2018 (e-pub ahead of print). doi:10.1101/312256
  • 35 Jonkhout N, Tran J, Smith MA, Schonrock N, Mattick JS, Novoa EM. The RNA modification landscape in human disease. RNA 2017; 23 (12) 1754-1769
  • 36 Garalde DR, Snell EA, Jachimowicz D. , et al. Highly parallel direct RNA sequencing on an array of nanopores. Nat Methods 2018; 15 (03) 201-206
  • 37 Van der Auwera GA, Carneiro MO, Hartl C. , et al. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinformatics 2013; 43: 1-33
  • 38 Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res 2010; 38 (06) 1767-1771
  • 39 Auton A, Brooks LD, Durbin RM. , et al; 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature 2015; 526 (7571): 68-74
  • 40 Sequence Alignment/Map Format Specification. 2018 . Available at: https://samtools.github.io/hts-specs/SAMv1.pdf . Accessed October 10, 2018
  • 41 Robinson JT, Thorvaldsdóttir H, Winckler W. , et al. Integrative genomics viewer. Nat Biotechnol 2011; 29 (01) 24-26
  • 42 Thorvaldsdóttir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 2013; 14 (02) 178-192
  • 43 The Variant Call Format (VCF) Version 4.2 Specification. 2018 . Available at: https://samtools.github.io/hts-specs/VCFv4.2.pdf . Accessed November 7, 2018
  • 44 Pickrell WO, Rees MI, Chung SK. Next generation sequencing methodologies--an overview. Adv Protein Chem Struct Biol 2012; 89: 1-26
  • 45 Jaratlerdsiri W, Chan EKF, Petersen DC. , et al. Next generation mapping reveals novel large genomic rearrangements in prostate cancer. Oncotarget 2017; 8 (14) 23588-23602
  • 46 Mak AC, Lai YY, Lam ET. , et al. Genome-wide structural variation detection by genome mapping on nanochannel arrays. Genetics 2016; 202 (01) 351-362
  • 47 Mostovoy Y, Levy-Sakin M, Lam J. , et al. A hybrid approach for de novo human genome sequence assembly and phasing. Nat Methods 2016; 13 (07) 587-590
  • 48 Hastie AR, Lam ET, Pang AW. , et al. Rapid automated large structural variation detection in a diploid genome by NanoChannel based next-generation mapping. bioRxiv 2017 (e-pub ahead of print). doi:10.1101/102764
  • 49 Barseghyan H, Tang W, Wang RT. , et al. Next-generation mapping: a novel approach for detection of pathogenic structural variants with a potential utility in clinical diagnosis. Genome Med 2017; 9 (01) 90
  • 50 Oxford Nanopore Technologies. SmidgION. Available at: https://nanoporetech.com/products/smidgion . Accessed November 7, 2018
  • 51 Miller JR, Zhou P, Mudge J. , et al. Hybrid assembly with long and short reads improves discovery of gene family expansions. BMC Genomics 2017; 18 (01) 541
  • 52 Minei R, Hoshina R, Ogura A. De novo assembly of middle-sized genome using MinION and Illumina sequencers. BMC Genomics 2018; 19 (01) 700
  • 53 Jain M, Olsen HE, Turner DJ. , et al. Linear assembly of a human centromere on the Y chromosome. Nat Biotechnol 2018; 36 (04) 321-323
  • 54 Koepfli KP, Paten B, O'Brien SJ. ; Genome 10K Community of Scientists. The Genome 10K Project: a way forward. Annu Rev Anim Biosci 2015; 3: 57-111
  • 55 Tsang HF, Xue VW, Koh SP, Chiu YM, Ng LP, Wong SC. NanoString, a novel digital color-coded barcode technology: current and future applications in molecular diagnostics. Expert Rev Mol Diagn 2017; 17 (01) 95-103
  • 56 Veldman-Jones MH, Brant R, Rooney C. , et al. Evaluating robustness and sensitivity of the NanoString Technologies nCounter platform to enable multiplexed gene expression analysis of clinical samples. Cancer Res 2015; 75 (13) 2587-2593
  • 57 NanoString. NanoString Showcases Groundbreaking New Platforms at 2018 Advances in Genome Biology and Technology (AGBT) Conference. 2018 . Available at: https://globenewswire.com/news-release/2018/02/12/1338884/0/en/NanoString-Showcases-Groundbreaking-New-Platforms-at-2018-Advances-in-Genome-Biology-and-Technology-AGBT-Conference.html . Accessed November 12, 2018
  • 58 Byron SA, Van Keuren-Jensen KR, Engelthaler DM, Carpten JD, Craig DW. Translating RNA sequencing into clinical diagnostics: opportunities and challenges. Nat Rev Genet 2016; 17 (05) 257-271
  • 59 Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008; 5 (07) 621-628
  • 60 Vilfan ID, Tsai YC, Clark TA. , et al. Analysis of RNA base modification and structural rearrangement by single-molecule real-time detection of reverse transcription. J Nanobiotechnology 2013; 11: 8
  • 61 Fischer N, Indenbirken D, Meyer T. , et al. Evaluation of unbiased next-generation sequencing of RNA (RNA-seq) as a diagnostic method in influenza virus-positive respiratory samples. J Clin Microbiol 2015; 53 (07) 2238-2250
  • 62 Cummings BB, Marshall JL, Tukiainen T. , et al; Genotype-Tissue Expression Consortium. Improving genetic diagnosis in Mendelian disease with transcriptome sequencing. Sci Transl Med 2017; 9 (386) eaal5209
  • 63 Ambrosini G, Dreos R, Kumar S, Bucher P. The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data. BMC Genomics 2016; 17 (01) 938
  • 64 Huang L, Ma F, Chapman A, Lu S, Xie XS. Single-cell whole-genome amplification and sequencing: methodology and applications. Annu Rev Genomics Hum Genet 2015; 16: 79-102
  • 65 Chen D, Zhen H, Qiu Y. , et al. Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms. Sci Rep 2018; 8 (01) 4963
  • 66 Sanchez-Cespedes M, Cairns P, Jen J, Sidransky D. Degenerate oligonucleotide-primed PCR (DOP-PCR): evaluation of its reliability for screening of genetic alterations in neoplasia. Biotechniques 1998; 25 (06) 1036-1038
  • 67 Chen F, Liu P, Gu Y. , et al. Isolation and whole genome sequencing of fetal cells from maternal blood towards the ultimate non-invasive prenatal testing. Prenat Diagn 2017; 37 (13) 1311-1321
  • 68 Bakker B, Taudt A, Belderbos ME. , et al. Single-cell sequencing reveals karyotype heterogeneity in murine and human malignancies. Genome Biol 2016; 17 (01) 115
  • 69 Goto Y, Yanagi I, Matsui K, Yokoi T, Takeda K. Integrated solid-state nanopore platform for nanopore fabrication via dielectric breakdown, DNA-speed deceleration and noise reduction. Sci Rep 2016; 6: 31324
  • 70 Fanget A, Traversi F, Khlybov S. , et al. Nanopore integrated nanogaps for DNA detection. Nano Lett 2014; 14 (01) 244-249
  • 71 Morikawa T, Yokota K, Tanimoto S, Tsutsui M, Taniguchi M. Detecting single-nucleotides by tunneling current measurements at sub-MHz temporal resolution. Sensors (Basel) 2017; 17 (04) E885
  • 72 Garaj S, Hubbard W, Reina A, Kong J, Branton D, Golovchenko JA. Graphene as a subnanometre trans-electrode membrane. Nature 2010; 467 (7312): 190-193
  • 73 Heerema SJ, Dekker C. Graphene nanodevices for DNA sequencing. Nat Nanotechnol 2016; 11 (02) 127-136
  • 74 Wang Y, Yang Q, Wang Z. The evolution of nanopore sequencing. Front Genet 2015; 5: 449
  • 75 Ke R, Mignardi M, Pacureanu A. , et al. In situ sequencing for RNA analysis in preserved tissue and cells. Nat Methods 2013; 10 (09) 857-860
  • 76 Lee JH, Daugharthy ER, Scheiman J. , et al. Highly multiplexed subcellular RNA sequencing in situ. Science 2014; 343 (6177): 1360-1363
  • 77 Wang X, Allen WE, Wright MA. , et al. Three-dimensional intact-tissue sequencing of single-cell transcriptional states. Science 2018; 361 (6400): 5691
  • 78 Chen X, Sun YC, Church GM, Lee JH, Zador AM. Efficient in situ barcode sequencing using padlock probe-based BaristaSeq. Nucleic Acids Res 2018; 46 (04) e22
  • 79 Kühnemund M, Wei Q, Darai E. , et al. Targeted DNA sequencing and in situ mutation analysis using mobile phone microscopy. Nat Commun 2017; 8: 13913
  • 80 Mankos M, Shadman K, Persson HH, N'Diaye AT, Schmid AK, Davis RW. A novel low energy electron microscope for DNA sequencing and surface analysis. Ultramicroscopy 2014; 145: 36-49
  • 81 Mankos M, Persson HH, N'Diaye AT, Shadman K, Schmid AK, Davis RW. Nucleotide-specific contrast for DNA sequencing by electron spectroscopy. PLoS One 2016; 11 (05) e0154707
  • 82 Quantum steps to better sequencing. Nat Nanotechnol 2010; 5 (12) 823
  • 83 Di Ventra M, Taniguchi M. Decoding DNA, RNA and peptides with quantum tunnelling. Nat Nanotechnol 2016; 11 (02) 117-126
  • 84 Tanaka H, Kawai T. Partial sequencing of a single DNA molecule with a scanning tunnelling microscope. Nat Nanotechnol 2009; 4 (08) 518-522
  • 85 Tanaka H, Taniguchi M. Sequencing of adenine in DNA by scanning tunneling microscopy. Jpn J Appl Phys 2017 ;56(8)
  • 86 Alekseyev YO, Fazeli R, Yang S. , et al. A next-generation sequencing primer—how does it work and what can it do?. Acad Pathol 2018; 5: 2374289518766521
  • 87 Caspar SM, Dubacher N, Kopps AM, Meienberg J, Henggeler C, Matyas G. Clinical sequencing: from raw data to diagnosis with lifetime value. Clin Genet 2018; 93 (03) 508-519
  • 88 Kumar KR, Wali GM, Kamate M. , et al. Defining the genetic basis of early onset hereditary spastic paraplegia using whole genome sequencing. Neurogenetics 2016; 17 (04) 265-270
  • 89 Mattick JS, Dinger M, Schonrock N, Cowley M. Whole genome sequencing provides better diagnostic yield and future value than whole exome sequencing. Med J Aust 2018; 209 (05) 197-199
  • 90 Freedman ML, Monteiro AN, Gayther SA. , et al. Principles for the post-GWAS functional characterization of cancer risk loci. Nat Genet 2011; 43 (06) 513-518
  • 91 Meienberg J, Bruggmann R, Oexle K, Matyas G. Clinical sequencing: is WGS the better WES?. Hum Genet 2016; 135 (03) 359-362
  • 92 Mallawaarachchi AC, Hort Y, Cowley MJ. , et al. Whole-genome sequencing overcomes pseudogene homology to diagnose autosomal dominant polycystic kidney disease. Eur J Hum Genet 2016; 24 (11) 1584-1590
  • 93 Minoche AE, Horvat C, Johnson R. , et al. Genome sequencing as a first-line genetic test in familial dilated cardiomyopathy. Genet Med 2019; 21 (03) 650-662
  • 94 Belkadi A, Bolze A, Itan Y. , et al. Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants. Proc Natl Acad Sci U S A 2015; 112 (17) 5473-5478
  • 95 Bagnall RD, Ingles J, Dinger ME. , et al. Whole genome sequencing improves outcomes of genetic testing in patients with hypertrophic cardiomyopathy. J Am Coll Cardiol 2018; 72 (04) 419-429
  • 96 Chaisson MJ, Huddleston J, Dennis MY. , et al. Resolving the complexity of the human genome using single-molecule sequencing. Nature 2015; 517 (7536): 608-611
  • 97 Freson K, Turro E. High-throughput sequencing approaches for diagnosing hereditary bleeding and platelet disorders. J Thromb Haemost 2017; 15 (07) 1262-1272
  • 98 Heremans J, Freson K. High-throughput sequencing for diagnosing platelet disorders: lessons learned from exploring the causes of bleeding disorders. Int J Lab Hematol 2018; 40 (Suppl. 01) 89-96
  • 99 Simeoni I, Stephens JC, Hu F. , et al. A high-throughput sequencing test for diagnosing inherited bleeding, thrombotic, and platelet disorders. Blood 2016; 127 (23) 2791-2803
  • 100 Clark BE, Shooter C, Smith F, Brawand D, Thein SL. Next-generation sequencing as a tool for breakpoint analysis in rearrangements of the globin gene clusters. Int J Lab Hematol 2017; 39 (Suppl. 01) 111-120
  • 101 Konkle BA, Johnsen JM, Wheeler M, Watson C, Skinner M, Pierce GF. ; My Life Our Future programme. Genotypes, phenotypes and whole genome sequence: approaches from the My Life Our Future haemophilia project. Haemophilia 2018; 24 (Suppl. 06) 87-94