FACETS

FACETS performs allele-specific copy number analysis from next-generation sequencing (NGS) data, producing integer copy number calls adjusted for tumor purity, ploidy, and clonal heterogeneity.

Key Features:

• Allele-specific copy number analysis: Resolves allele-specific copy number changes from NGS data (ASCN).
• Deletion and LOH detection: Detects homozygous and heterozygous deletions and copy-neutral loss-of-heterozygosity (LOH).
• Allele-specific gains and amplifications: Identifies allele-specific gains and amplifications.
• Integer copy number calls: Generates integer copy number calls corrected for tumor purity, ploidy, and clonal heterogeneity.
• BAM file post-processing: Performs sequencing BAM file post-processing.
• Joint segmentation: Conducts joint segmentation of total- and allele-specific read counts.
• Integrated visualization: Produces comprehensive output with integrated visualization capabilities.
• Supported sequencing platforms: Applicable to whole-genome, whole-exome, and targeted panel sequencing data.

Scientific Applications:

• Clinical cancer sequencing: Interprets copy number alterations and actionable mutations from clinical sequencing to inform treatment decisions.
• TCGA whole-exome analysis: Applied to The Cancer Genome Atlas (TCGA) whole-exome sequencing data from lung adenocarcinoma samples.
• Targeted gene panels: Used on targeted clinical sequencing panels to detect copy number changes in cancer genes.

Methodology:

Performs sequencing BAM file post-processing, joint segmentation of total- and allele-specific read counts, and integer copy number calling with corrections for tumor purity, ploidy, and clonal heterogeneity.