CScape

CScape predicts the oncogenic status of somatic point mutations across coding and non-coding regions of the genome.

Key Features:

• Comprehensive Mutation Analysis: Evaluates somatic point mutations across both coding and non-coding genomic regions.
• Integrative Classifier: Integrates multiple data sources and analytical techniques to assess the likelihood that specific mutations are cancer drivers.
• High Predictive Accuracy: Reports balanced accuracy of 91% in coding regions and 70% in non-coding regions.
• Threshold-Based High-Confidence Predictions: Applies score thresholds to isolate high-confidence predicted oncogenic mutations.
• Statistical Enrichment Analysis: Identifies genomic regions enriched for high-confidence predicted disease-driver mutations using statistical methods.
• Input Formats: Accepts mutation records in standardized format (chromosome, position, reference, mutant) or VCF files with columns (chromosome, position, id, reference, mutant).

Scientific Applications:

• Genomic Research: Characterizing the mutational landscape associated with different cancers by classifying somatic point mutations.
• Targeted Therapies: Highlighting candidate oncogenic drivers that may serve as potential therapeutic targets.
• Personalized Medicine: Informing interpretation of tumor-specific somatic mutations to guide individualized treatment considerations.

Methodology:

Integrates multiple data sources and analytical techniques and processes mutation records (chromosome, position, reference, mutant) or VCF files (chromosome, position, id, reference, mutant) to generate predictions of oncogenic likelihood.