This article proposes the development of a novel tool for analyzing the structure and characteristics of recombinant adeno-associated virus (rAAV) vectors during vector production and quality assessment. The tool utilizes dotplots, a graphical method for comparing sequences, and a deep learning-based image classification approach. The focus is on the inverted terminal repeats (ITRs) sequences, which play a critical role in identifying and differentiating AAV types. The tool aims to infer the ITR origin, and improve vector analysis and quality control. The dataset creation process involves generating dotplots of wild-type AAV ITRs and introducing small mutations to simulate biological noise. Future work includes addressing the impact of mutations on vector characteristics to detect major structural anomalies, as well as further analyzing pair-dotplots for vector characterization.
Alignment-free characterization of Inverted Terminal Repeats (ITR) in wild-type and recombinant AAV genomes / Ostellino, Sofia; Fronza, Raffaele; Benso, Alfredo. - (2023), pp. 116-121. (Intervento presentato al convegno ICET 2023: International Conference on Emerging Technologies 2023 tenutosi a Peshawar (Pakistan) nel 6-7 November 2023) [10.1109/ICET59753.2023.10374991].
Alignment-free characterization of Inverted Terminal Repeats (ITR) in wild-type and recombinant AAV genomes
Sofia Ostellino;Alfredo Benso
2023
Abstract
This article proposes the development of a novel tool for analyzing the structure and characteristics of recombinant adeno-associated virus (rAAV) vectors during vector production and quality assessment. The tool utilizes dotplots, a graphical method for comparing sequences, and a deep learning-based image classification approach. The focus is on the inverted terminal repeats (ITRs) sequences, which play a critical role in identifying and differentiating AAV types. The tool aims to infer the ITR origin, and improve vector analysis and quality control. The dataset creation process involves generating dotplots of wild-type AAV ITRs and introducing small mutations to simulate biological noise. Future work includes addressing the impact of mutations on vector characteristics to detect major structural anomalies, as well as further analyzing pair-dotplots for vector characterization.File | Dimensione | Formato | |
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https://hdl.handle.net/11583/2984863