CINdex

CINdex quantifies genome-wide DNA copy number alterations by computing the chromosome instability index (CIN) from experimental DNA copy number data (e.g., Affymetrix SNP 6.0 arrays).

Key Features:

• Automated Processing: Performs automated processing and interpretation of large-scale DNA copy number data from arrays and similar platforms.
• Chromosome Instability Index Calculation: Computes the chromosome instability index (CIN) to quantify overall genomic instability and separate gains and losses.
• Detailed Chromosomal and Cytoband Analysis: Characterizes copy number alterations at chromosome and cytoband levels to identify regions with significant variation.

Scientific Applications:

• Cancer Genomics: Quantifies DNA copy number alterations to characterize genomic instability in tumors.
• Biomarker and Therapeutic Target Discovery: Supports identification of candidate biomarkers or therapeutic targets by highlighting recurrent copy number changes.
• Clinical Correlation Studies: Enables studies correlating specific genomic copy number changes with clinical outcomes.

Methodology:

Implemented in R within the Bioconductor framework; it automates processing and interpretation of experimental DNA copy number data (e.g., Affymetrix SNP 6.0 arrays) and computes the chromosome instability index (CIN) with chromosome- and cytoband-level characterization of gains and losses.