focalCall

focalCall identifies somatic focal copy number aberrations (CNAs) and distinguishes them from germ-line copy number variations (CNVs) to enable accurate analysis of focal genomic alterations in cancer using high-resolution array and sequencing data.

Key Features:

• User-defined size cutoffs: Allows specification of size thresholds to define focal aberrations for detection.
• Integration with established algorithms: Builds upon array comparative genomic hybridization segmentation and calling algorithms for segmentation and calling.
• Reference utilization: Uses matched patient normal signals as references and a list of known population CNVs when matched normals are unavailable.
• Differentiation capabilities: Distinguishes homozygous and heterozygous deletions, gains, and amplifications.
• Applicability to high-resolution data: Operates on high-resolution array and sequencing data for detailed focal CNA analysis.

Scientific Applications:

• Cancer genomics: Detection and classification of somatic focal CNAs for tumor genomic characterization.
• Tumor biology studies: Identification of focal deletions, gains, and amplifications to investigate genetic drivers of cancer.
• Targeted therapy research: Characterization of focal amplifications and deletions that may inform therapeutic target selection.
• Personalized medicine and translational studies: Differentiation of somatic CNAs from germ-line CNVs to support individualized genomic analyses.

Methodology:

Implements array comparative genomic hybridization segmentation and calling algorithms, applies user-defined size cutoffs, and uses matched patient normal signals or population CNV lists as references to differentiate somatic CNAs from germ-line CNVs.