PredictONCO: a web tool supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning.
Jan StouracSimeon BorkoRayyan T KhanPetra PokornaAdam DobiasJoan Planas-IglesiasStanislav MazurenkoGaspar PintoVeronika SzotkowskaJaroslav SterbaOndrej SlabyJiri DamborskyDavid BednářPublished in: Briefings in bioinformatics (2023)
PredictONCO 1.0 is a unique web server that analyzes effects of mutations on proteins frequently altered in various cancer types. The server can assess the impact of mutations on the protein sequential and structural properties and apply a virtual screening to identify potential inhibitors that could be used as a highly individualized therapeutic approach, possibly based on the drug repurposing. PredictONCO integrates predictive algorithms and state-of-the-art computational tools combined with information from established databases. The user interface was carefully designed for the target specialists in precision oncology, molecular pathology, clinical genetics and clinical sciences. The tool summarizes the effect of the mutation on protein stability and function and currently covers 44 common oncological targets. The binding affinities of Food and Drug Administration/ European Medicines Agency -approved drugs with the wild-type and mutant proteins are calculated to facilitate treatment decisions. The reliability of predictions was confirmed against 108 clinically validated mutations. The server provides a fast and compact output, ideal for the often time-sensitive decision-making process in oncology. Three use cases of missense mutations, (i) K22A in cyclin-dependent kinase 4 identified in melanoma, (ii) E1197K mutation in anaplastic lymphoma kinase 4 identified in lung carcinoma and (iii) V765A mutation in epidermal growth factor receptor in a patient with congenital mismatch repair deficiency highlight how the tool can increase levels of confidence regarding the pathogenicity of the variants and identify the most effective inhibitors. The server is available at https://loschmidt.chemi.muni.cz/predictonco.
Keyphrases
- protein protein
- drug administration
- epidermal growth factor receptor
- machine learning
- wild type
- tyrosine kinase
- palliative care
- decision making
- small molecule
- advanced non small cell lung cancer
- healthcare
- big data
- squamous cell carcinoma
- diffuse large b cell lymphoma
- case report
- artificial intelligence
- human health
- cell cycle
- papillary thyroid
- intellectual disability
- prostate cancer
- social media
- gene expression
- copy number
- rectal cancer
- dna methylation
- young adults
- squamous cell
- childhood cancer
- lymph node metastasis
- transcription factor
- electronic health record