TPES

TPES estimates tumor purity (TP) from single-nucleotide variants (SNVs) to infer the fraction of cancer cells in samples analyzed by next-generation sequencing (NGS).

Key Features:

• SNV-based estimation: Derives TP from single-nucleotide variants (SNVs) rather than relying on somatic copy-number alterations (SCNAs).
• Allelic fraction analysis: Infers tumor cell fraction by analyzing the allelic fraction distribution of SNVs.
• Applicability to euploid/SCNA-low tumors: Provides robust TP estimates for tumors with near-euploid genomes that lack identifiable SCNAs.
• Data compatibility: Operates on whole-exome sequencing (WES) data generated by NGS technologies.
• Validation: Demonstrated high concordance with existing TP estimation tools (Spearman's rho 0.68–0.82) across more than 7,800 TCGA WES tumor samples.

Scientific Applications:

• Pan-cancer studies: Enables consistent TP assessment across diverse cancer types for comparative analyses.
• Mutation burden estimation: Improves accuracy of somatic mutation burden calculations by accounting for tumor cell fraction.
• Clonal evolution studies: Supports interpretation of variant allele frequencies in analyses of clonal architecture and evolutionary dynamics.
• Driver mutation identification: Aids identification and interpretation of driver mutations by correcting for tumor purity effects.

Methodology:

Derives tumor purity from the allelic fraction distribution of SNVs in whole-exome sequencing data and validated estimates against existing methods using Spearman's correlation (0.68–0.82) across >7,800 TCGA WES samples.