Caracterización de las tecnologías de secuenciación genética de segunda y tercera generación
Barra lateral del artículo
Contenido principal del artículo
Resumen
El avance en la secuenciación de material genético ha favorecido el estudio de nuevas áreas de investigación relacionadas a la genómica, transcriptómica y demás ciencias -ómicas. Esto creó la necesidad de desarrollar nuevas tecnologías más accesibles y eficientes, como las tecnologías de segunda y tercera generación. Por ello, esta revisión caracterizó las principales metodologías de secuenciación de segunda y tercera generación. Las tecnologías de segunda generación se ven representadas por la secuenciación por síntesis fragmentos cortos con alta calidad y precisión. En la tercera generación se especializan en lecturas largas secuenciadas por nanoporos y secuenciación de una sola molécula en tiempo real. Las empresas Illumina y PacBio poseen una mayor calidad y precisión en las lecturas, en comparación a Oxford Nanopore Technologies (ONT). Sin embargo, las lecturas de ONT solucionan problemas del ensamblaje genómico propios de lecturas cortas. Todas las tecnologías analizadas poseen secuenciadores para proyectos de producción a escala; Illumina y ONT también poseen secuenciadores sobremesa, y solamente la última presenta dispositivos portátiles. Con respecto a la accesibilidad, los países centroamericanos poseen poca cobertura por parte de estas empresas, siendo Illumina la única con una distribuidora radicada en la región. Cada tecnología de secuenciación posee ventajas y desventajas asociadas, lo cual impulsa a su uso en conjunto, lo que permite análisis más convenientes y completos. Por lo cual el desarrollo de nuevos programas bioinformáticos para la mejora del análisis corresponde a consideraciones que deben ser abordadas con la intención de fortalecer el uso de las técnicas de secuenciación.
Detalles del artículo
Esta obra está bajo una licencia internacional Creative Commons Atribución-NoComercial-SinDerivadas 4.0.
Los autores conservan los derechos de autor y ceden a la revista el derecho de la primera publicación y pueda editarlo, reproducirlo, distribuirlo, exhibirlo y comunicarlo en el país y en el extranjero mediante medios impresos y electrónicos. Asimismo, asumen el compromiso sobre cualquier litigio o reclamación relacionada con derechos de propiedad intelectual, exonerando de responsabilidad a la Editorial Tecnológica de Costa Rica. Además, se establece que los autores pueden realizar otros acuerdos contractuales independientes y adicionales para la distribución no exclusiva de la versión del artículo publicado en esta revista (p. ej., incluirlo en un repositorio institucional o publicarlo en un libro) siempre que indiquen claramente que el trabajo se publicó por primera vez en esta revista.
Citas
F. Sanger, S. Nicklen, and A. R. Coulson, “DNA sequencing with chain-terminating inhibitors,” Proceedings of the National Academy of Sciences, vol. 74, no. 12, pp. 5463–5467, Dec. 1977, doi: 10.1073/PNAS.74.12.5463.
C. R. Gade, M. Dixit, and N. K. Sharma, “Dideoxy nucleoside triphosphate (ddNTP) analogues: Synthesis and polymerase substrate activities of pyrrolidinyl nucleoside triphosphates (prNTPs),” Bioorg Med Chem, vol. 24, no. 18, pp. 4016–4022, Sep. 2016, doi: 10.1016/J.BMC.2016.06.043.
J. Craig Venter et al., “The sequence of the human genome,” Science (1979), vol. 291, no. 5507, pp. 1304–1351, Feb. 2001, doi: 10.1126/SCIENCE.1058040/SUPPL_FILE/1058040S3-7_LARGE.JPEG.
R. A. Gibbs, “The Human Genome Project changed everything,” Nat Rev Genet, vol. 21, no. 10, pp. 575–576, Aug. 2020, doi: 10.1038/S41576-020-0275-3.
S. Nurk et al., “The complete sequence of a human genome,” Science (1979), vol. 376, no. 6588, pp. 44–53, Apr. 2022, doi: 10.1126/SCIENCE.ABJ6987.
B. Amer and E. E. K. Baidoo, “Omics-Driven Biotechnology for Industrial Applications,” Front Bioeng Biotechnol, vol. 9, p. 30, Feb. 2021, doi: 10.3389/FBIOE.2021.613307/BIBTEX.
R. Bhattacharjya, A. Tiwari, T. K. Marella, H. Bansal, and S. Srivastava, “New paradigm in diatom omics and genetic manipulation,” Bioresour Technol, vol. 325, p. 124708, Apr. 2021, doi: 10.1016/J.BIORTECH.2021.124708.
M. A. Wörheide, J. Krumsiek, G. Kastenmüller, and M. Arnold, “Multi-omics integration in biomedical research – A metabolomics-centric review,” Anal Chim Acta, vol. 1141, pp. 144–162, Jan. 2021, doi: 10.1016/J.ACA.2020.10.038.
J. M. Heather and B. Chain, “The sequence of sequencers: The history of sequencing DNA,” Genomics, vol. 107, no. 1, pp. 1–8, Jan. 2016, doi: 10.1016/J.YGENO.2015.11.003.
W. Huang, L. Li, J. R. Myers, and G. T. Marth, “ART: a next-generation sequencing read simulator,” Bioinformatics, vol. 28, no. 4, pp. 593–594, 2012.
S. Goodwin, J. D. McPherson, and R. McCombie, “Coming of age: ten years of next-generation sequencing technologies,” Nat Rev Genet, vol. 17, no. 6, pp. 333–351, 2016, doi: 10.1038/nrg.2016.49.
W. de Coster, S. D’hert, D. T. Schultz, M. Cruts, and C. van Broeckhoven, “NanoPack: visualizing and processing long-read sequencing data,” Bioinformatics, vol. 34, no. 15, pp. 2666–2669, 2018.
J. Brown, M. Pirrung, and L. A. McCue, “FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool,” Bioinformatics, vol. 33, no. 19, pp. 3137–3139, 2017.
S. F. Yang, C. W. Lu, C. te Yao, and C. M. Hung, “To Trim or Not to Trim: Effects of Read Trimming on the De Novo Genome Assembly of a Widespread East Asian Passerine, the Rufous-Capped Babbler (Cyanoderma ruficeps Blyth),” Genes (Basel), vol. 10, no. 10, Oct. 2019, doi: 10.3390/GENES10100737.
R. R. Wick, L. M. Judd, C. L. Gorrie, and K. E. Holt, “Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads,” PLoS Comput Biol, vol. 13, no. 6, Jun. 2017, doi: 10.1371/JOURNAL.PCBI.1005595.
M. Alser et al., “Accelerating genome analysis: A primer on an ongoing journey,” IEEE Micro, vol. 40, no. 5, 2020.
M. T. Swain, I. J. Tsai, S. A. Assefa, C. Newbold, M. Berriman, and T. D. Otto, “A Post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs,” Nat Protoc, vol. 7, no. 7, p. 1260, Jul. 2012, doi: 10.1038/NPROT.2012.068.
M. Imelfort and D. Edwards, “De novo sequencing of plant genomes using second-generation technologies,” Brief Bioinform, vol. 10, no. 6, pp. 609–618, Nov. 2009, doi: 10.1093/BIB/BBP039.
Illumina, “An introduction to Next-Generation Sequencing Technology.” www.illumina.com/technology/next-generation-sequencing.html (accessed Oct. 03, 2022).
E. R. Mardis, “Next-Generation Sequencing Platforms,” Annual Review of Analytical Chemistry, vol. 6, pp. 287–303, Jun. 2013, doi: 10.1146/ANNUREV-ANCHEM-062012-092628.
M. Molnar and L. Ilie, “Correcting Illumina data,” Brief Bioinform, vol. 16, no. 4, pp. 588–599, Jul. 2015, doi: 10.1093/bib/bbu029.
J. M. Valderrama Martín, F. Ortigosa, and R. Cañas, “Métodos de secuenciación: tercera generación,” Encuentros en la Biología, vol. 13, no. 175, pp. 15–21, 2020.
D. Lang et al., “Comparison of the two up-to-date sequencing technologies for genome assembly: HiFi reads of Pacific Biosciences Sequel II system and ultralong reads of Oxford Nanopore,” Gigascience, vol. 9, no. 12, pp. 1–7, Nov. 2020, doi: 10.1093/GIGASCIENCE/GIAA123.
D. Buck et al., “Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis,” F1000Res, vol. 6, 2017, doi: 10.12688/F1000RESEARCH.10571.2.
C. Delahaye and J. Nicolas, “Sequencing DNA with nanopores: Troubles and biases,” PLoS One, vol. 16, no. 10, p. e0257521, Oct. 2021, doi: 10.1371/JOURNAL.PONE.0257521.
B. Lin, J. Hui, and H. Mao, “Nanopore Technology and Its Applications in Gene Sequencing,” Biosensors 2021, Vol. 11, Page 214, vol. 11, no. 7, p. 214, Jun. 2021, doi: 10.3390/BIOS11070214.
E. E. Schadt, S. Turner, and A. Kasarskis, “A window into third-generation sequencing,” Hum Mol Genet, vol. 19, no. R2, pp. R227–R240, Oct. 2010, doi: 10.1093/hmg/ddq416.
J. Eid et al., “Real-Time DNA Sequencing from Single Polymerase Molecules,” Science (1979), vol. 323, no. 5910, pp. 133–138, Jan. 2009, doi: 10.1126/science.1162986.
E. B. Fichot and R. S. Norman, “Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform,” Microbiome, vol. 1, no. 1, pp. 1–5, Mar. 2013, doi: 10.1186/2049-2618-1-10/FIGURES/4.
PacBio, “How HiFi sequencing works - PacBio.” https://www.pacb.com/technology/hifi-sequencing/how-it-works/ (accessed Oct. 02, 2022).
M. Schirmer, R. D’Amore, U. Z. Ijaz, N. Hall, and C. Quince, “Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data,” BMC Bioinformatics, vol. 17, no. 1, p. 125, Dec. 2016, doi: 10.1186/s12859-016-0976-y.
D. Tshiabuila et al., “Comparison of SARS-CoV-2 sequencing using the ONT GridION and the Illumina MiSeq,” BMC Genomics, vol. 23, no. 1, pp. 1–17, Dec. 2022, doi: 10.1186/S12864-022-08541-5/FIGURES/8.
K. Thys, P. Verhasselt, J. Reumers, B. M. P. Verbist, B. Maes, and J. Aerssens, “Performance assessment of the Illumina massively parallel sequencing platform for deep sequencing analysis of viral minority variants,” J Virol Methods, vol. 221, pp. 29–38, 2015, doi: https://doi.org/10.1016/j.jviromet.2015.04.022.
S. S. T. Mak et al., “Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing,” Gigascience, vol. 6, no. 8, Jun. 2017, doi: 10.1093/gigascience/gix049.
A. Pecman et al., “Systematic Comparison of Nanopore and Illumina Sequencing for the Detection of Plant Viruses and Viroids Using Total RNA Sequencing Approach,” Front Microbiol, vol. 13, 2022, doi: 10.3389/fmicb.2022.883921.
A. P. Heikema et al., “Comparison of Illumina versus Nanopore 16S rRNA Gene Sequencing of the Human Nasal Microbiota,” Genes (Basel), vol. 11, no. 9, 2020, doi: 10.3390/genes11091105.
E. S. Wright and K. H. Vetsigian, “Quality filtering of Illumina index reads mitigates sample cross-talk,” BMC Genomics, vol. 17, no. 1, p. 876, 2016, doi: 10.1186/s12864-016-3217-x.
A. Cacho, E. Smirnova, S. Huzurbazar, and X. Cui, “A Comparison of Base-calling Algorithms for Illumina Sequencing Technology,” Brief Bioinform, vol. 17, no. 5, pp. 786–795, Sep. 2016, doi: 10.1093/bib/bbv088.
S. Goldstein, L. Beka, J. Graf, and J. L. Klassen, “Evaluation of strategies for the assembly of diverse bacterial genomes using MinION long-read sequencing,” BMC Genomics, vol. 20, no. 1, pp. 1–17, Jan. 2019, doi: 10.1186/S12864-018-5381-7/FIGURES/7.
M. A. Madoui et al., “Genome assembly using Nanopore-guided long and error-free DNA reads,” BMC Genomics, vol. 16, no. 1, pp. 1–11, Dec. 2015, doi: 10.1186/S12864-015-1519-Z/TABLES/3.
I. Kirov et al., “Nanopore RNA Sequencing Revealed Long Non-Coding and LTR Retrotransposon-Related RNAs Expressed at Early Stages of Triticale SEED Development,” Plants, vol. 9, no. 12, p. 1794, Dec. 2020, doi: 10.3390/PLANTS9121794.
T. Wongsurawat et al., “Rapid sequencing of multiple RNA viruses in their native form,” Front Microbiol, vol. 10, no. FEB, p. 260, 2019, doi: 10.3389/FMICB.2019.00260/BIBTEX.
A. Bayega et al., “Nanopore long-read RNA-seq and absolute quantification delineate transcription dynamics in early embryo development of an insect pest,” Sci Rep, vol. 11, no. 1, Dec. 2021, doi: 10.1038/S41598-021-86753-7.
G. Wang et al., “A strategy for complete telomere-to-telomere assembly of ciliate macronuclear genome using ultra-high coverage Nanopore data,” Comput Struct Biotechnol J, vol. 19, pp. 1928–1932, Jan. 2021, doi: 10.1016/J.CSBJ.2021.04.007.
Y. Wang, X. Cai, and Y. Mao, “The first complete genome sequence of species Shewanella decolorationis, from a bioremediation competent strain Ni1-3,” G3 Genes|Genomes|Genetics, vol. 11, no. 10, Sep. 2021, doi: 10.1093/G3JOURNAL/JKAB261.
E. L. Moss, D. G. Maghini, and A. S. Bhatt, “Complete, closed bacterial genomes from microbiomes using nanopore sequencing,” Nat Biotechnol, vol. 38, no. 6, pp. 701–707, Jun. 2020, doi: 10.1038/S41587-020-0422-6.
A. Bruno, J. M. Aury, and S. Engelen, “BoardION: real-time monitoring of Oxford Nanopore sequencing instruments,” BMC Bioinformatics, vol. 22, no. 1, pp. 1–8, Dec. 2021, doi: 10.1186/S12859-021-04161-0/FIGURES/5.
J. R. Revollo, J. A. Miranda, and V. N. Dobrovolsky, “PacBio sequencing detects genome-wide ultra-low-frequency substitution mutations resulting from exposure to chemical mutagens,” Environ Mol Mutagen, vol. 62, no. 8, pp. 438–445, Oct. 2021, doi: 10.1002/EM.22462.
Y. Zeng, X. Wang, and J. Zhang, “Single-cell biomedicine: roles of single-cell nuclear elements,” Cell Biol Toxicol, vol. 36, no. 1, Feb. 2020, doi: 10.1007/S10565-020-09515-7.
S. B. Kingan et al., “A High-Quality De novo Genome Assembly from a Single Mosquito Using PacBio Sequencing,” Genes (Basel), vol. 10, no. 1, p. 62, Jan. 2019, doi: 10.3390/GENES10010062.
Illumina, “Sequencing Platforms | Compare NGS platform applications & specifications.” https://www.illumina.com/systems/sequencing-platforms.html (accessed Oct. 03, 2022).
M. A. Quail et al., “A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers,” BMC Genomics, vol. 13, no. 1, p. 341, 2012, doi: 10.1186/1471-2164-13-341.
Oxford Nanopore Technologies, “Products | Oxford Nanopore Technologies.” https://nanoporetech.com/products (accessed Oct. 01, 2022).
Oxford Nanopore Technologies, “Store | Oxford Nanopore Technologies.” https://store.nanoporetech.com/devices.html (accessed Oct. 01, 2022).
PacBio, “Sequel systems - PacBio.” https://www.pacb.com/technology/hifi-sequencing/sequel-system/ (accessed Oct. 01, 2022).
University of Wasington, “University of Washington PacBio Sequencing Services.” https://pacbio.gs.washington.edu/ (accessed Oct. 01, 2022).
Illimina, “Office Locations | Contact information.” https://www.illumina.com/company/contact-us/locations.html (accessed Oct. 03, 2022).
Oxford Nanopore Technologies, “Contact us | Oxford Nanopore Technologies.” https://nanoporetech.com/contact (accessed Oct. 01, 2022).
Oxford Nanopore Technologies, “Nanopore Distributors directory.” https://nanoporetech.com/services/distributors (accessed Oct. 01, 2022).
PacBio, “Contact us - PacBio.” https://www.pacb.com/contact-us/ (accessed Oct. 01, 2022).
C. Perea et al., “Bioinformatic analysis of genotype by sequencing (GBS) data with NGSEP,” BMC Genomics, vol. 17, Aug. 2016, doi: 10.1186/S12864-016-2827-7.
A. Prjibelski, D. Antipov, D. Meleshko, A. Lapidus, and A. Korobeynikov, “Using SPAdes De Novo Assembler,” Curr Protoc Bioinformatics, vol. 70, no. 1, p. e102, Jun. 2020, doi: 10.1002/CPBI.102.
A. Khezri, E. Avershina, and R. Ahmad, “Hybrid Assembly Provides Improved Resolution of Plasmids, Antimicrobial Resistance Genes, and Virulence Factors in Escherichia coli and Klebsiella pneumoniae Clinical Isolates,” Microorganisms, vol. 9, no. 12, Dec. 2021, doi: 10.3390/MICROORGANISMS9122560.
M. Santos et al., “Increasing access to next-generation sequencing in oncology for Brazil,” Lancet Oncology, vol. 20, pp. 20–23, 2019, doi: 10.1016/S1470-2045(18)30822-2.
W. A. Mantilla, M. C. Sanabria-Salas, A. M. Baldion, L. F. Sua, D. M. Gonzalez, and M. Lema, “NGS in Lung, Breast, and Unknown Primary Cancer in Colombia: A Multidisciplinary Consensus on Challenges and Opportunities,” JCO Glob Oncol, no. 7, pp. 1012–1023, Dec. 2021, doi: 10.1200/go.21.00046.
M. Helmy, M. Awad, and K. A. Mosa, “Limited resources of genome sequencing in developing countries: Challenges and solutions,” Appl Transl Genom, vol. 9, pp. 15–19, Jun. 2016, doi: 10.1016/J.ATG.2016.03.003.
S. A. Vishnopolska et al., “Genetics and genomic medicine in Argentina,” Mol Genet Genomic Med, vol. 6, no. 4, pp. 481–491, Jul. 2018, doi: 10.1002/MGG3.455.
M. Chand and R. L. Tung, “Skilled immigration to fill talent gaps: A comparison of the immigration policies of the United States, Canada, and Australia,” Journal of International Business Policy, vol. 2, no. 4, pp. 333–355, Dec. 2019, doi: 10.1057/S42214-019-00039-4/TABLES/3.