Detail publikace

Analysis of mutations in precision oncology using the automated, accurate, and user-friendly web tool PredictONCO

KHAN, R. POKORNÁ, P. ŠTOURAČ, J. BORKO, S. DOBIÁŠ, A. PLANAS-IGLESIAS, J. MAZURENKO, S. AREFIEV, I. PINTO, G. SZOTKOWSKÁ, V. ŠTĚRBA, J. DAMBORSKÝ, J. SLABÝ, O. BEDNÁŘ, D.

Originální název

Analysis of mutations in precision oncology using the automated, accurate, and user-friendly web tool PredictONCO

Typ

článek v časopise ve Web of Science, Jimp

Jazyk

angličtina

Originální abstrakt

Next-generation sequencing technology has created many new opportunities for clinical diagnostics, but it faces the challenge of functional annotation of identified mutations. Various algorithms have been developed to predict the impact of missense variants that influence oncogenic drivers. However, computational pipelines that handle biological data must integrate multiple software tools, which can add complexity and hinder nonspecialist users from accessing the pipeline. Here, we have developed an online user-friendly web server tool PredictONCO that is fully automated and has a low barrier to access. The tool models the structure of the mutant protein in the first step. Next, it calculates the protein stability change, pocket level information, evolutionary conservation, and changes in ionisation of catalytic amino acid residues, and uses them as the features in the machine-learning predictor. The XGBoost-based predictor was validated on an independent subset of held-out data, demonstrating areas under the receiver operating characteristic curve (ROC) of 0.97 and 0.94, and the average precision from the precision-recall curve of 0.99 and 0.94 for structure-based and sequence-based predictions, respectively. Finally, PredictONCO calculates the docking results of small molecules approved by regulatory authorities. We demonstrate the applicability of the tool by presenting its usage for variants in two cancer-associated proteins, cellular tumour antigen p53 and fibroblast growth factor receptor FGFR1. Our free web tool will assist with the interpretation of data from next-generation sequencing and navigate treatment strategies in clinical oncology: https://loschmidt.chemi.muni.cz/predictonco/.

Klíčová slova

Precision oncology; Webserver; Mutation; Prediction; Treatment; Next-generation sequencing; Virtual screening; Oncogenicity; Automation; Machine learning

Autoři

KHAN, R.; POKORNÁ, P.; ŠTOURAČ, J.; BORKO, S.; DOBIÁŠ, A.; PLANAS-IGLESIAS, J.; MAZURENKO, S.; AREFIEV, I.; PINTO, G.; SZOTKOWSKÁ, V.; ŠTĚRBA, J.; DAMBORSKÝ, J.; SLABÝ, O.; BEDNÁŘ, D.

Vydáno

1. 12. 2024

Nakladatel

ELSEVIER

Místo

AMSTERDAM

ISSN

2001-0370

Periodikum

Computational and Structural Biotechnology Journal

Ročník

24

Číslo

1

Stát

Švédské království

Strany od

734

Strany do

738

Strany počet

5

URL

https://pdf.sciencedirectassets.com/311228/1-s2.0-S2001037023X00038/1-s2.0-S2001037024003982/main.pdf?X-Amz-Security-Token=IQoJb3JpZ2luX2VjEJf%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaCXVzLWVhc3QtMSJHMEUCIDrbD45VakUk3X6NUr5GGZD9isB0FAlD5cQ1HxEfov7RAiEA0BXxZPBaFp7QqmYr5PcJnghZbJPLwfJIW2GcqZPc%2FlgqvAUI%2F%2F%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FARAFGgwwNTkwMDM1NDY4NjUiDBziFBGFHDXfGQj83iqQBeI9vb0CM%2F6x0tX0oTz11Of68Yp%2FA1w%2BtqnSsrhXbah7fkFYpCrxOwMdUXiloKXOkQ3WE8iSFH%2B3D6gRbneby2cDLZAIHaTClB9%2Fy6Zy8UorCpnmirKzD4dMlZfjU5KKU

BibTex

@article{BUT197612,
  author="Rayyan {Khan} and Petra {Pokorná} and Jan {Štourač} and Simeon {Borko} and Adam {Dobiáš} and Joan {Planas-Iglesias} and Stanislav {Mazurenko} and Ihor {Arefiev} and Gaspar P. {Pinto} and Veronika {Szotkowská} and Jaroslav {Štěrba} and Jiří {Damborský} and Ondřej {Slabý} and David {Bednář}",
  title="Analysis of mutations in precision oncology using the automated, accurate, and user-friendly web tool PredictONCO",
  journal="Computational and Structural Biotechnology Journal",
  year="2024",
  volume="24",
  number="1",
  pages="734--738",
  doi="10.1016/j.csbj.2024.11.026",
  issn="2001-0370",
  url="https://pdf.sciencedirectassets.com/311228/1-s2.0-S2001037023X00038/1-s2.0-S2001037024003982/main.pdf?X-Amz-Security-Token=IQoJb3JpZ2luX2VjEJf%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEaCXVzLWVhc3QtMSJHMEUCIDrbD45VakUk3X6NUr5GGZD9isB0FAlD5cQ1HxEfov7RAiEA0BXxZPBaFp7QqmYr5PcJnghZbJPLwfJIW2GcqZPc%2FlgqvAUI%2F%2F%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FARAFGgwwNTkwMDM1NDY4NjUiDBziFBGFHDXfGQj83iqQBeI9vb0CM%2F6x0tX0oTz11Of68Yp%2FA1w%2BtqnSsrhXbah7fkFYpCrxOwMdUXiloKXOkQ3WE8iSFH%2B3D6gRbneby2cDLZAIHaTClB9%2Fy6Zy8UorCpnmirKzD4dMlZfjU5KKU"
}

Odpovědnost: Ing. Marek Strakoš