scholarly journals Fundamentos y aplicaciones biomédicas de las principales tecnologías de secuenciación: una revisión de literatura

Author(s):  
Anny Jineth Camargo Mancipe ◽  
Karen Nattaly Valero González ◽  
Alida Marcela Gómez Rodriguez ◽  
Diego Fernando Camargo Mancipe ◽  
Carlos Fernando Suárez Martínez ◽  
...  

Introducción. La secuenciación tiene como finalidad determinar la composición de los nucleótidos presentes en el ADN o ARN. Desde la finalización del proyecto genoma humano, surgieron diversas tecnologías de secuenciación como Roche 454, SOLID, Illumina, Ion torrent, Pacbio y Oxford nanopore como herramientas para secuenciar rápidamente, con mayor precisión y costo-eficiencia, permitiendo el desarrollo de proyectos a gran escala y el estudio de genes y genomas, la composición de microbiomas, enfermedades metabólicas y enfermedades genéticas que afectan la población. Objetivo. Describir los fundamentos de los métodos de secuenciación de ADN y sus aplicaciones en las ciencias biomédicas. Métodos. Revisión descriptiva de las principales estrategias de secuenciación de ADN de primera, segunda y tercera generación y su aplicación en el entorno biomédico. Esta revisión se realizó a partir de la búsqueda de artículos en bases de datos electrónicas especializadas en investigación científica. Se encontraron 118 documentos, de los cuales se excluyeron 6 por no cumplir con los criterios de inclusión y se seleccionaron 112 por cumplir con todos los requisitos. Conclusiones. La secuenciación de ADN y ARN ha permitido avances en los estudios de organismos biológicos, el surgimiento de los métodos de secuenciación de siguiente generación arroja una gran cantidad de datos, incluidos genomas secuenciados completamente de varias especies, con un rendimiento extenso, tiempos reducidos y costo-eficiencia que lleva a la transformación por completo de las ciencias de la vida, logrando un progreso sin precedentes en el análisis de genomas, la evaluación de ecología microbiana y el diagnóstico de enfermedades.

2013 ◽  
Vol 137 (9) ◽  
pp. 1296-1303 ◽  
Author(s):  
Colleen T. Harrington ◽  
Elaine I. Lin ◽  
Matthew T. Olson ◽  
James R. Eshleman

Context.—DNA sequencing is critical to identifying many human genetic disorders caused by DNA mutations, including cancer. Pyrosequencing is less complex, involves fewer steps, and has a superior limit of detection compared with Sanger sequencing. The fundamental basis of pyrosequencing is that pyrophosphate is released when a deoxyribonucleotide triphosphate is added to the end of a nascent strand of DNA. Because deoxyribonucleotide triphosphates are sequentially added to the reaction and because the pyrophosphate concentration is continuously monitored, the DNA sequence can be determined. Objective.—To demonstrate the fundamental principles of pyrosequencing. Data Sources.—Salient features of pyrosequencing are demonstrated using the free software program Pyromaker (http://pyromaker.pathology.jhmi.edu), through which users can input DNA sequences and other pyrosequencing parameters to generate the expected pyrosequencing results. Conclusions.—We demonstrate how mutant and wild-type DNA sequences result in different pyrograms. Using pyrograms of established mutations in tumors, we explain how to analyze the pyrogram peaks generated by different dispensation sequences. Further, we demonstrate some limitations of pyrosequencing, including how some complex mutations can be indistinguishable from single base mutations. Pyrosequencing is the basis of the Roche 454 next-generation sequencer and many of the same principles also apply to the Ion Torrent hydrogen ion-based next-generation sequencers.


2014 ◽  
Vol 81 (1) ◽  
pp. 106-116 ◽  
Author(s):  
Frido Welker ◽  
Elza Duijm ◽  
Kristiaan J. van der Gaag ◽  
Bas van Geel ◽  
Peter de Knijff ◽  
...  

AbstractHumans colonized the Balearic Islands 5–4 ka ago. They arrived in a uniquely adapted ecosystem with the Balearic mountain goat Myotragus balearicus (Bovidae, Antilopinae, Caprini) as the only large mammal. This mammal went extinct rapidly after human arrival. Several hypotheses have been proposed to explain the extinction of M. balearicus. For the present study ancient DNA analysis (Sanger sequencing, Roche-454, Ion Torrent), and pollen and macrofossil analyses were performed on preserved coprolites from M. balearicus, providing information on its diet and paleo-environment. The information retrieved shows that M. balearicus was heavily dependent on the Balearic box species Buxus balearica during at least part of the year, and that it was most probably a browser. Hindcast ecological niche modelling of B. balearica shows that local distribution of this plant species was affected by climate changes. This suggests that the extinction of M. balearicus can be related to the decline and regional extinction of a plant species that formed a major component of its diet. The vegetation change is thought to be caused by increased aridity occurring throughout the Mediterranean. Previous hypotheses relating the extinction of M. balearicus directly to the arrival of humans on the islands must therefore be adjusted.


PLoS ONE ◽  
2017 ◽  
Vol 12 (2) ◽  
pp. e0171983 ◽  
Author(s):  
Sarah Sandmann ◽  
Aniek O. de Graaf ◽  
Bert A. van der Reijden ◽  
Joop H. Jansen ◽  
Martin Dugas

2017 ◽  
Author(s):  
Chris Wymant ◽  
Matthew Hall ◽  
Oliver Ratmann ◽  
David Bonsall ◽  
Tanya Golubchik ◽  
...  

AbstractA central feature of pathogen genomics is that different infectious particles (virions, bacterial cells, etc.) within an infected individual may be genetically distinct, with patterns of relatedness amongst infectious particles being the result of both within-host evolution and transmission from one host to the next. Here we present a new software tool, phyloscanner, which analyses pathogen diversity from multiple infected hosts. phyloscanner provides unprecedented resolution into the transmission process, allowing inference of the direction of transmission from sequence data alone. Multiply infected individuals are also identified, as they harbour subpopulations of infectious particles that are not connected by within-host evolution, except where recombinant types emerge. Low-level contamination is flagged and removed. We illustrate phyloscanner on both viral and bacterial pathogens, namely HIV-1 sequenced on Illumina and Roche 454 platforms, HCV sequenced with the Oxford Nanopore MinION platform, and Streptococcus pneumoniae with sequences from multiple colonies per individual. phyloscanner is available from https://github.com/BDI-pathogens/phyloscanner.


2020 ◽  
Vol 89 (2) ◽  
pp. 252-256
Author(s):  
Е. Е. Куликов ◽  
А. К. Голомидова ◽  
В. В. Бабенко ◽  
А. В. Летаров
Keyword(s):  

Vaccines ◽  
2021 ◽  
Vol 9 (3) ◽  
pp. 282
Author(s):  
Juan David Ramírez ◽  
Marina Muñoz ◽  
Nathalia Ballesteros ◽  
Luz H. Patiño ◽  
Sergio Castañeda ◽  
...  

The continuing evolution of SARS-CoV-2 and the emergence of novel variants have raised concerns about possible reinfection events and potential changes in the coronavirus disease 2019 (COVID-19) transmission dynamics. Utilizing Oxford Nanopore technologies, we sequenced paired samples of three patients with positive RT-PCR results in a 1–2-month window period, and subsequent phylogenetics and genetic polymorphism analysis of these genomes was performed. Herein, we report, for the first time, genomic evidence of one case of reinfection in Colombia, exhibiting different SARS-CoV-2 lineage classifications between samples (B.1 and B.1.1.269). Furthermore, we report two cases of possible viral persistence, highlighting the importance of deepening our understanding on the evolutionary intra-host traits of this virus throughout different timeframes of disease progression. These results emphasize the relevance of genomic surveillance as a tool for understanding SARS-CoV-2 infection dynamics, and how this may translate effectively to future control and mitigations efforts, such as the national vaccination program.


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