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Cabello-Aguilar, Simon; Vendrell, Julie A.; Goethem, Charles van; Brousse, Mehdi; Goze, Catherine; Frantz, Laurent and Solassol, Jerome (2022): ifCNV: A novel isolation-forest-based package to detect copy-number variations from various targeted NGS datasets. In: Molecular Therapy - Nucleic Acids, Vol. 30: pp. 174-183

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Abstract

Copy-number variations (CNVs) are an essential component of genetic variation distributed across large parts of the human genome. CNV detection from next-generation sequencing data and artificial intelligence algorithms have progressed in recent years. However, only a few tools have taken advantage of machine-learning algorithms for CNV detection, and none propose using artificial intelligence to automatically detect probable CNV-positive samples. The most developed approach is to use a reference or normal dataset to compare with the sam-ples of interest, and it is well known that selecting appropriate normal samples represents a challenging task that dramatically influences the precision of results in all CNV-detecting tools. With careful consideration of these issues, we propose here ifCNV, a new software based on isolation forests that creates its own reference, available in R and python with customizable parameters. ifCNV combines artificial intelligence using two isolation forests and a comprehensive scoring method to faith-fully detect CNVs among various samples. It was validated us-ing targeted next-generation sequencing (NGS) datasets from diverse origins (capture and amplicon, germline and somatic), and it exhibits high sensitivity, specificity, and accuracy. ifCNV is a publicly available open-source software (https://github. com/SimCab-CHU/ifCNV) that allows the detection of CNVs in many clinical situations.

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