CEQer

CEQer analyzes copy number alterations (CNA) and allelic imbalance (AI) from matched whole-exome sequencing data to generate exon-level CNA profiles and detect loss of heterozygosity (LOH) across the exome.

Key Features:

• Comparative Digital Exonic Quantification: Utilizes case-control matched exome data to perform comparative digital quantification at the exon level, producing high-resolution CNA calls.
• Exome-wide LOH and Allelic Imbalance Detection: Integrates CNA data with detection of LOH and AI across the entire exome.
• Statistical/Heuristic Modeling: Employs mixed statistical and heuristic models to identify CNA and AI events.

Scientific Applications:

• Cancer genomics (leukemias and solid tumors): Identifies CNAs and LOH/AI that may contribute to oncogenesis and tumor progression.
• Whole-exome sequencing analysis: Generates accurate exon-level CNA and allelic imbalance profiles from whole-exome sequencing data for downstream genetic variation studies.

Methodology:

Performs comparative digital quantification using matched case-control exome data to generate CNA profiles, integrates CNA calls with LOH and AI detection across the exome, and applies mixed statistical and heuristic models to identify events.