Common CNVs detection by artificial intelligence methods

Wiktor Kuśmirek


Many organisms, in particular people, contain sections of the genome which could be present in various number of copies between individuals. This event is called copy number variations (CNVs) and in many cases is associated with genetic diseases. However, the accuracy of CNV detection in the human genome is still low. We propose the new algorithm for common CNVs detection based on artificial intelligence algorithms. We generalized a common CNVs detection task to classification problem. In this paper we showed some classification models and compare them in order to detect common CNVs. The algorithm contains three stages: counting depth of coverage in targets (whole exome sequencing), quality control of targets and training the models. Then, trained models are used to detetct CNVs in a new sample. The proposed approach was tested, the obtained CNVs calls showed the corecctness of our proposals. The results present, that our approach is designed to detect only common CNVs, the sensitivity and specificity of the approach are higher than for another algorithms. However, rare CNVs are not discovered, but we plan to extend presented approach in order to detect also rare CNVs (based on anomalies detection algorithms). The presented approach could improve the accuracy of detection common CNVs in the human genome. The described method could be useful in labolatories, where large volume of annotated common CNVs dataset exists. What is more, to our knowledge, this is the first paper which shows the usage of artificial intelligence methods in common CNVs detection problem.
Author Wiktor Kuśmirek (FEIT / IN)
Wiktor Kuśmirek,,
- The Institute of Computer Science
Publication size in sheets0.3
Book Romaniuk Ryszard, Linczuk Maciej Grzegorz (eds.): Proceedings of SPIE: Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2018, Proceedings of SPIE: The International Society for Optical Engineering, vol. 10808, 2018, SPIE - the International Society for Optics and Photonics, ISBN 9781510622036, 2086 p., DOI:10.1117/12.2504983
Keywords in Englishcopy number variant, artificial intelligence, classification, whole exome sequencing
projectSimultaneous analysis of single nucleotide and structural variants from whole exome or targeted sequencing. Project leader: Gambin Tomasz, , Phone: +48 22 234 6191, application date 26-10-2015, start date 21-10-2016, planned end date 21-10-2019, II/2016/IP/1, Implemented
WEiTI Projekty finansowane przez MNiSW
Languageen angielski
108083C_kusmirek.pdf 797.24 KB
Score (nominal)15
ScoreMinisterial score = 15.0, BookChapterSeriesAndMatConf
Ministerial score (2013-2016) = 15.0, BookChapterSeriesAndMatConf
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