Control-FREEC

Control-FREEC detects copy-number changes and allelic imbalances, including loss of heterozygosity (LOH), from next-generation sequencing (NGS) data to characterize genomic alterations.

Key Features:

• Input Data: Accepts aligned reads and constructs copy-number and B-allele frequency profiles from NGS data.
• Normalization and Segmentation: Performs normalization to account for sequencing depth and technical biases and applies segmentation algorithms to delineate genomic regions with consistent signals.
• Genotype Assignment: Assigns genotype status to each segmented region to report copy-number and allelic content.
• Somatic vs. Germline Discrimination: Uses a matched normal sample, when available, to distinguish somatic events from germline variations.
• Handling Complex Samples: Supports analysis of overdiploid tumor samples and samples contaminated with normal cells to detect somatic alterations in heterogeneous tumors.
• Exclusion of Low Mappability Regions: Allows exclusion of low-mappability regions using provided mappability tracks.

Scientific Applications:

• Cancer genomics: Detection of copy-number changes and LOH from NGS data to study tumor development and progression.
• Analysis of heterogeneous tumor samples: Characterization of somatic alterations in overdiploid and normal-contaminated tumor samples.

Methodology:

Uses aligned reads to build copy-number and B-allele frequency profiles, applies normalization for sequencing depth and technical biases, performs segmentation algorithms, assigns genotype status per segment, compares tumor to matched normal to call somatic versus germline events, and excludes low-mappability regions using mappability tracks.