Secuenciación de nueva generación (NGS) de ADN: presente y futuro en la práctica clínica Presente y futuro en la práctica clínica
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abr 2, 2020
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Santiago Rubio
http://orcid.org/0000-0002-5857-4272
Rafael Adrián Pacheco-Orozco
http://orcid.org/0000-0002-1114-7812
Ana Milena Gómez
http://orcid.org/0000-0002-4739-5260
Sandra Perdomo
http://orcid.org/0000-0001-7740-8141
Reggie García-Robles
http://orcid.org/0000-0002-6804-0979
http://orcid.org/0000-0002-5857-4272
Rafael Adrián Pacheco-Orozco
http://orcid.org/0000-0002-1114-7812
Ana Milena Gómez
http://orcid.org/0000-0002-4739-5260
Sandra Perdomo
http://orcid.org/0000-0001-7740-8141
Reggie García-Robles
http://orcid.org/0000-0002-6804-0979
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Resumen
Introducción: el término secuenciación de nueva generación (NGS) hace referencia a las tecnologías diseñadas para analizar gran cantidad de ADN de forma masiva y paralela. Abordamos en esta revisión los conceptos básicos de estas tecnologías, las consideraciones de su uso clínico actual y perspectivas a futuro. Desarrollo: las pruebas basadas en NGS han revolucionado el estudio de los genomas pues permiten la lectura de millones de secuencias de ADN de forma masiva y paralela en un menor lapso de tiempo y a menor costo por base. Estas pruebas incluyen la secuenciación de panel de genes, la secuenciación completa del exoma y la secuenciación completa del genoma. El análisis de sus resultados es complejo y requiere de un proceso bioinformático y clínico exhaustivo para su adecuada interpretación. Las limitaciones de las pruebas NGS incluyen aspectos técnicos como la cobertura, profundidad y longitud de las secuencias, las cuales se pueden solventar implementando buenas prácticas de laboratorio. Conclusiones: las pruebas basadas en la secuenciación por NGS son herramientas diagnósticas que deben partir de una aproximación clínica adecuada para su uso razonado, correcta interpretación y toma de decisiones acertadas. Es de gran trascendencia que los médicos tengan la información básica para poder solicitar e interpretar estas pruebas dada su relevancia clínica actual.
Keywords
High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA, Mutation, Variant interpretationSecuenciación de Nucleótidos de Alto Rendimiento, Análisis de Secuencia de ADN, Mutación, Interpretación de variantes
References
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35. O’Roak BJ, Deriziotis P, Lee C, Vives L, Schwartz JJ, Girirajan S, et al. Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations. Nat Genet. 2011;43(6):585-9.
36. Lam HYK, Clark MJ, Chen R, Chen R, Natsoulis G, O’Huallachain M, et al. Performance comparison of whole-genome sequencing platforms. Nat Biotechnol. 2011;30(1):78-82.
37. Tavtigian S V, Greenblatt MS, Lesueur F, Byrnes GB. In silico analysis of missense substitutions using sequence-alignment based methods. Hum Mutat. 2008;29(11):1327-36.
38. Thompson BA, Greenblatt MS, Vallee MP, Herkert JC, Tessereau C, Young EL, et al. Calibration of multiple in silico tools for predicting pathogenicity of mismatch repair gene missense substitutions. Hum Mutat. 2013 Jan;34(1):255-65.
39. Thusberg J, Olatubosun A, Vihinen M. Performance of mutation pathogenicity prediction methods on missense variants. Hum Mutat. 2011 Apr;32(4):358-68.
40. Ahram M, Soubani M, Abu Salem L, Saker H, Ahmad M. Knowledge, Attitudes, and Practice Regarding Genetic Testing and Genetic Counselors in Jordan: A Population-Based Survey. J Genet Couns. 2015;24(6):1001-10.
41. Roach JC, Glusman G, Smit AFA, Huff CD, Hubley R, Shannon PT, et al. Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science. 2010;328(5978):636-9.
42. Strom SP, Lee H, Das K, Vilain E, Nelson SF, Grody WW, et al. Assessing the necessity of confirmatory testing for exome-sequencing results in a clinical molecular diagnostic laboratory. Genet Med. 2014;16(7):510-5.
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46. Berliner JL, Fay AM. Risk assessment and genetic counseling for hereditary breast and ovarian cancer: recommendations of the National Society of Genetic Counselors. J Genet Couns. 2007;16(3):241-60.
47. Laine C, Davidoff F. Patient-centered medicine: a professional evolution. JAMA. 1996;275(2):152-6.
48. Vig HS, Wang C. The evolution of personalized cancer genetic counseling in the era of personalized medicine. Fam Cancer. 2012;11:539-44.
49. Sukenik-Halevy R, Ludman MD, Ben-Shachar S, Raas-Rothschild A. The time-consuming demands of the practice of medical genetics in the era of advanced genomic testing. Genet Med. 2016;18(4):372-7.
50. Chen Y-C, Liu T, Yu C-H, Chiang T-Y, Hwang C-C. Effects of GC bias in next-generation-sequencing data on de novo genome assembly. PLoS One. 2013;8(4):e62856.
51. Ulahannan D, Kovac MB, Mulholland PJ, Cazier J-B, Tomlinson I. Technical and implementation issues in using next-generation sequencing of cancers in clinical practice. Br J Cancer. 2013;109(4):827-35.
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53. Gibbs RA, Boerwinkle E, Doddapaneni H, Han Y, Korchina V, Kovar C, et al. A global reference for human genetic variation. Nature [Internet]. 2015;526(7571):68-74. Disponible en: http://www.nature.com/articles/nature15393
54. Ministerio de Salud y Protección Social. Resolución 5851 del 21 de diciembre de 2018, por la cual se establece la Clasificación Única de Procedimientos en Salud-CUPS [Internet]. Disponible en: https://www.minsalud.gov.co/Normatividad_Nuevo/Resolución5851de2018.pdf
55. Liu Z, Zhu L, Roberts R, Tong W. Toward clinical implementation of next-generation sequencing-based genetic testing in rare diseases: where are we? Trends Genet. 2019;35(11):852-67.
56. Jin Y, Zhang L, Ning B, Hong H, Xiao W, Tong W, et al. Application of genome analysis strategies in the clinical testing for pediatric diseases. Pediatr Investig. 2018 Jul 16;2(2):72-81.
57. Van Dijk EL, Jaszczyszyn Y, Naquin D, Thermes C. The third revolution in sequencing technology. Trends Genet. 2018 Sep;34(9):666-81.
2. Lander ES. Initial impact of the sequencing of the human genome. Nature. 2011;470(7333):187-97.
3. Zhang W, Cui H, Wong L-JC. Application of next generation sequencing to molecular diagnosis of inherited diseases. Top Curr Chem. 2014;336(1):19-45.
4. Santillán S, Álvarez D, Buades C, Romera-López A, Pérez-Cabornero L, Valero-Hervás D, et al. Diagnóstico molecular de enfermedades genéticas: del diagnóstico genético al diagnóstico genómico con la secuenciación masiva. Rev Médica Clínica Las Condes. 2015;26(4):458-69.
5. Van Dijk EL, Auger H, Jaszczyszyn Y, Thermes C. Ten years of next-generation sequencing technology. Trends Genet. 2014;30(9):418-26.
6. Gallo JE. Actualidad de la genómica clínica en el área cardiovascular en Colombia. Rev Colomb Cardiol. 2017;24(1):1-2.
7. Faure D, Joly D. Next-generation sequencing as a powerful motor for advances in the biological and environmental sciences. Genetica. 2015;143:129-32.
8. Tucker T, Marra M, Friedman JM. Massively parallel sequencing: the next big thing in genetic medicine. Am J Hum Genet. 2009;85(2):142-54.
9. Heather JM, Chain B. The sequence of sequencers: The history of sequencing DNA. Genomics [Internet]. 2016;107(1):1-8. https://doi.org/10.1016/j.ygeno.2015.11.003.
10. Voelkerding K, Dames SA, Durtschi JD. Next-generation sequencing: from basic research to diagnostics. Clin Chem. 2009;55(4):641-58.
11. Mardis ER. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet. 2008;9:387-402.
12. Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol. 2008;26(10):1135-45.
13. Lewis T. Human Genome Project Marks 10th Anniversary. Live Science. 2013;1-7.
14. Sims D, Sudbery I, Ilott NE, Heger A, Ponting CP. Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet. 2014;15:121.
15. Rodríguez-Santiago B, Armengol L. Tecnologías de secuenciación de nueva generación en diagnóstico genético pre- y postnatal. Diagnóstico Prenat. 2012;23(2):56-66.
16. Morozova O, Marra MA. Applications of next-generation sequencing technologies in functional genomics. Genomics. 2008;92(5):255-64.
17. Goodwin S, McPherson JD, McCombie WR. Coming of age: Ten years of next-generation sequencing technologies. Nat Rev Genet. 2016;17(6):333-51.
18. Illumina. Illumina Sequencing Technology; 2015. Disponible en: http://illumina.com
19. Buermans HPJ, den Dunnen JT. Next generation sequencing technology: advances and applications. Biochim Biophys Acta - Mol Basis Dis. 2014;1842(10):1932-41.
20. Pennisi E. Genomics: SEMICONDUCTORS inspire new sequencing technologies. Science. 2010;327(5970):1190.
21. Hulick PJ. Next-generation DNA sequencing (NGS): principles and clinical applications [internet]. UpToDate. 2018. Disponible en: https://www.uptodate.com/contents/next-generation-dna-sequencing-ngs-principles-and-clinical-applications
22. Briceño Balcázar I. Medicina genómica en Cardiología. Rev Colomb Cardiol. 2017;24(1):3-4.
23. Rubinstein WS, Maglott DR, Lee JM, Kattman BL, Malheiro AJ, Ovetsky M, et al. The NIH genetic testing registry: a new, centralized database of genetic tests to enable access to comprehensive information and improve transparency. Nucleic Acids Res. 2013;41(1): 925-35.
24. Hereditary Cancer Solution™ by Sophia Genetics [Internet]. Sophia Genetics; 2019 [citado 2 dic 2019]. Disponible en: https://www.sophiagenetics.com/hospitals/solutions/hereditary-cancer-solution.html
25. Choi M, Scholl UI, Ji W, Liu T, Tikhonova IR, Zumbo P, et al. Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc Natl Acad Sci U S A. 2009;106(45):19096-101.
26. Worthey EA, Mayer AN, Syverson GD, Helbling D, Bonacci BB, Decker B, et al. Making a definitive diagnosis: successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease. Genet Med. 2011;13(3):255-62.
27. Biesecker LG, Green RC. Diagnostic clinical genome and exome sequencing. N Engl J Med. 2014;371:1170.
28. Srivastava S, Love-Nichols JA, Dies KA, Ledbetter DH, Martin CL, Chung WK, et al. Meta-analysis and multidisciplinary consensus statement: exome sequencing is a first-tier clinical diagnostic test for individuals with neurodevelopmental disorders. Genet Med. 2019;21(11):2413-21.
29. Bainbridge MN, Wiszniewski W, Murdock DR, Friedman J, Gonzaga-Jauregui C, Newsham I, et al. Whole-genome sequencing for optimized patient management. Sci Transl Med. 2011;3(87):87re3.
30. Kuhlenbaumer G, Hullmann J, Appenzeller S. Novel genomic techniques open new avenues in the analysis of monogenic disorders. Hum Mutat. 2011;32(2):144-51.
31. Smith HS, Swint JM, Lalani SR, Yamal J-M, de Oliveira Otto MC, Castellanos S, et al. Clinical Application of Genome and Exome Sequencing as a Diagnostic Tool for Pediatric Patients: a Scoping Review of the Literature. Genet Med. 2019;21(1):3-16.
32. Endrullat C, Glökler J, Franke P, Frohme M. Standardization and quality management in next-generation sequencing. Appl Transl Genomics. 2016;10:2-9.
33. Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, et al. Standards and guidelines for the interpretation of sequence variants: A joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17(5):405-24.
34. Taylor JC, Martin HC, Lise S, Broxholme J, Cazier J-B, Rimmer A, et al. Factors influencing success of clinical genome sequencing across a broad spectrum of disorders. Nat Genet. 2015;47(7):717-26.
35. O’Roak BJ, Deriziotis P, Lee C, Vives L, Schwartz JJ, Girirajan S, et al. Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations. Nat Genet. 2011;43(6):585-9.
36. Lam HYK, Clark MJ, Chen R, Chen R, Natsoulis G, O’Huallachain M, et al. Performance comparison of whole-genome sequencing platforms. Nat Biotechnol. 2011;30(1):78-82.
37. Tavtigian S V, Greenblatt MS, Lesueur F, Byrnes GB. In silico analysis of missense substitutions using sequence-alignment based methods. Hum Mutat. 2008;29(11):1327-36.
38. Thompson BA, Greenblatt MS, Vallee MP, Herkert JC, Tessereau C, Young EL, et al. Calibration of multiple in silico tools for predicting pathogenicity of mismatch repair gene missense substitutions. Hum Mutat. 2013 Jan;34(1):255-65.
39. Thusberg J, Olatubosun A, Vihinen M. Performance of mutation pathogenicity prediction methods on missense variants. Hum Mutat. 2011 Apr;32(4):358-68.
40. Ahram M, Soubani M, Abu Salem L, Saker H, Ahmad M. Knowledge, Attitudes, and Practice Regarding Genetic Testing and Genetic Counselors in Jordan: A Population-Based Survey. J Genet Couns. 2015;24(6):1001-10.
41. Roach JC, Glusman G, Smit AFA, Huff CD, Hubley R, Shannon PT, et al. Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science. 2010;328(5978):636-9.
42. Strom SP, Lee H, Das K, Vilain E, Nelson SF, Grody WW, et al. Assessing the necessity of confirmatory testing for exome-sequencing results in a clinical molecular diagnostic laboratory. Genet Med. 2014;16(7):510-5.
43. U. S. Food and Drug Administration. Use of public human genetic variant databases to support clinical validity for genetic and genomic-based in vitro diagnostics guidance for stakeholders and food and drug administration staff [internet]. 2018. Disponible en: https://www.fda.gov/media/99200/download.
44. U. S. Food and Drug Administration. Considerations for design, development, and analytical validation of next generation sequencing (NGS) - based in vitro diagnostics (IVDs) intended to aid in the diagnosis of suspected germline diseases. Guidance [Internet]. 2018;(April). Disponible en: https://www.fda.gov/downloads/MedicalDevices/DeviceRegulationandGuidance/GuidanceDocuments/UCM509838.pdf?utm_campaign=FDAfinalizesguidancesforNextGenerationSequencingTests&utm_medium=email&utm_source=Eloqua&elqTrackId=2E86C2A3704E9129.
45. Houfek JF, Soltis-vaughan BS, Atwood JR, Reiser GM, Schaefer GB. Adults’ perceptions of genetic counseling and genetic testing. App Nurs Res. 2015;28(1):25-30. https://doi.org/10.1016/j.apnr.2014.03.001
46. Berliner JL, Fay AM. Risk assessment and genetic counseling for hereditary breast and ovarian cancer: recommendations of the National Society of Genetic Counselors. J Genet Couns. 2007;16(3):241-60.
47. Laine C, Davidoff F. Patient-centered medicine: a professional evolution. JAMA. 1996;275(2):152-6.
48. Vig HS, Wang C. The evolution of personalized cancer genetic counseling in the era of personalized medicine. Fam Cancer. 2012;11:539-44.
49. Sukenik-Halevy R, Ludman MD, Ben-Shachar S, Raas-Rothschild A. The time-consuming demands of the practice of medical genetics in the era of advanced genomic testing. Genet Med. 2016;18(4):372-7.
50. Chen Y-C, Liu T, Yu C-H, Chiang T-Y, Hwang C-C. Effects of GC bias in next-generation-sequencing data on de novo genome assembly. PLoS One. 2013;8(4):e62856.
51. Ulahannan D, Kovac MB, Mulholland PJ, Cazier J-B, Tomlinson I. Technical and implementation issues in using next-generation sequencing of cancers in clinical practice. Br J Cancer. 2013;109(4):827-35.
52. Basho RK, Eterovic AK, FundaMeric-Bernstam. Clinical applications and limitations of next-generation sequencing. Am J Hematol Oncol. 2015;11(3):17-22.
53. Gibbs RA, Boerwinkle E, Doddapaneni H, Han Y, Korchina V, Kovar C, et al. A global reference for human genetic variation. Nature [Internet]. 2015;526(7571):68-74. Disponible en: http://www.nature.com/articles/nature15393
54. Ministerio de Salud y Protección Social. Resolución 5851 del 21 de diciembre de 2018, por la cual se establece la Clasificación Única de Procedimientos en Salud-CUPS [Internet]. Disponible en: https://www.minsalud.gov.co/Normatividad_Nuevo/Resolución5851de2018.pdf
55. Liu Z, Zhu L, Roberts R, Tong W. Toward clinical implementation of next-generation sequencing-based genetic testing in rare diseases: where are we? Trends Genet. 2019;35(11):852-67.
56. Jin Y, Zhang L, Ning B, Hong H, Xiao W, Tong W, et al. Application of genome analysis strategies in the clinical testing for pediatric diseases. Pediatr Investig. 2018 Jul 16;2(2):72-81.
57. Van Dijk EL, Jaszczyszyn Y, Naquin D, Thermes C. The third revolution in sequencing technology. Trends Genet. 2018 Sep;34(9):666-81.
Cómo citar
Rubio, S., Pacheco-Orozco, R. A., Gómez, A. M., Perdomo, S., & García-Robles, R. (2020). Secuenciación de nueva generación (NGS) de ADN: presente y futuro en la práctica clínica: Presente y futuro en la práctica clínica. Universitas Medica, 61(2). https://doi.org/10.11144/Javeriana.umed61-2.sngs
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