FREEC

FREEC detects copy number alterations (CNAs) and allelic imbalances (including loss of heterozygosity) from deep-sequencing data, supporting analyses without matched normal controls and enabling absolute copy-number assignment when ploidy is provided.

Key Features:

• Control-free analysis: Detects CNAs without requiring a matched normal sample.
• Normalization using control or GC content: Normalizes copy number profiles (CNPs) using provided control data or GC-content-based correction and performs CNP smoothing.
• Segmentation and CNA calling: Automatically segments normalized profiles and calls copy number alterations from segmented data.
• Absolute copy-number assignment: Assigns absolute copy numbers to CNAs when sample ploidy is known.
• Allelic imbalance and LOH detection: Identifies allelic imbalance events, including loss of heterozygosity.
• Sequencing-technology compatibility: Works with Illumina single-end, mate-pair, and paired-end sequencing data.

Scientific Applications:

• CNA profiling in cancer genomics: Characterizes somatic copy number alterations and allelic imbalances relevant to tumor biology and progression.
• Analysis of samples without matched normals: Enables CNA and LOH analysis in rare tumors or cases where obtaining a matched normal sample is impractical.

Methodology:

Normalization of raw CNPs using control data or GC content, automatic segmentation of normalized profiles, CNA calling from segmented data, and optional assignment of absolute copy numbers when ploidy information is available.