Sistema de Salut de Catalunya
Institut Català de la Salut
[Ruiz-Ciancio D] Instituto de Ciencias Biomédicas (ICBM), Facultad de Ciencias Médicas, Universidad Católica de Cuyo, Rivadavia, San Juan, Argentina. National Council of Scientific and Technical Research (CONICET), Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina. Cancer Genome Engineering Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain. [Veeramani S] Department of Internal Medicine, University of Iowa, Iowa City, IA, USA. Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA. [Singh R] Department of Computer Sciences, University of Iowa, Iowa City, IA, USA. [Embree E] Carver College of Medicine, University of Iowa, Iowa City, IA, USA. [Ortman C] Institute for Clinical and Translational Science, University of Iowa, Iowa City, IA, USA. [Thiel KW] Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA. Department of Obstetrics and Gynecology, University of Iowa, Iowa City, IA, USA
Vall d'Hebron Barcelona Hospital Campus
2024-12-19T10:42:20Z
2024-12-19T10:42:20Z
2024-12-10
Aptamer; Bioinformatics; Sequence analysis
Aptàmer; Bioinformàtica; Anàlisi de seqüència
Aptámero; Bioinformática; Análisis de secuencia
Aptamers are short single-stranded DNA or RNA molecules with high affinity and specificity for targets and are generated using the iterative systematic evolution of ligands by exponential enrichment (SELEX) process. Next-generation sequencing (NGS) revolutionized aptamer selections by allowing a more comprehensive analysis of SELEX-enriched aptamers as compared to Sanger sequencing. The current challenge with aptamer NGS datasets is identifying a diverse cohort of candidate aptamers with the highest likelihood of successful experimental validation. Here we present AptamerRunner, an aptamer sequence and/or structure clustering algorithm that synergistically integrates computational analysis with visualization and expertise-directed decision making. The visual integration of networked aptamers with ranking data, such as fold enrichment or scoring algorithm results, represents a significant advancement over existing clustering tools by providing a natural context to depict groups of aptamers from which ranked or scored candidates can be chosen for experimental validation. The inherent flexibility, user-friendly design, and prospects for future enhancements with AptamerRunner have broad-reaching implications for aptamer researchers across a wide range of disciplines.
This work was supported by an American Heart Association scientist development grant (14SDG18850071 to W.H.T.), the National Institutes of Health (R01HL139581 and R01HL157956 to W.H.T.; K22CA263783 to K.W.T.), the National Science Foundation (IIS-1817239 to R.S.), the Department of Defense (DOD CDMRP-PRCRP CA220729 to K.W.T.), the American Cancer Society (HCCC, IRG-18-165-43 to S.V.), the Bunge and Born Fund (FBB-20170609 to D.R.C.), and the Fulbright-Argentinean Ministry of Education (ME-FLB-2022-2023 to D.R.C.).
Article
Published version
English
Oligonucleòtids; Seqüència de nucleòtids; Biologia computacional; CHEMICALS AND DRUGS::Nucleic Acids, Nucleotides, and Nucleosides::Nucleotides::Polynucleotides::Oligonucleotides::Aptamers, Nucleotide; INFORMATION SCIENCE::Information Science::Informatics::Computational Biology; ANALYTICAL, DIAGNOSTIC AND THERAPEUTIC TECHNIQUES, AND EQUIPMENT::Investigative Techniques::Genetic Techniques::Sequence Analysis::High-Throughput Nucleotide Sequencing; COMPUESTOS QUÍMICOS Y DROGAS::nucleótidos y nucleósidos de ácidos nucleicos::nucleótidos::polinucleótidos::oligonucleótidos::aptámeros de nucleótidos; CIENCIA DE LA INFORMACIÓN::Ciencias de la información::informática::biología computacional; TÉCNICAS Y EQUIPOS ANALÍTICOS, DIAGNÓSTICOS Y TERAPÉUTICOS::técnicas de investigación::técnicas genéticas::análisis de secuencias::secuenciación de nucleótidos de alto rendimiento
Elsevier
Molecular Therapy - Nucleic Acids;35(4)
https://doi.org/10.1016/j.omtn.2024.102358
Attribution-NonCommercial-NoDerivatives 4.0 International
http://creativecommons.org/licenses/by-nc-nd/4.0/
