CalMaTe

CalMaTe calibrates allele-specific copy number estimates (ASCNs) from DNA microarray data by correcting SNP-specific allelic crosstalk to improve accuracy for downstream segmentation and copy-neutral loss of heterozygosity (CN-LOH) detection.

Key Features:

• Calibration of preprocessed ASCNs: Adjusts raw allele-specific copy number estimates to reduce SNP-specific biases prior to downstream analysis.
• SNP-specific allelic crosstalk correction: Models and controls allelic crosstalk effects at individual SNPs to improve allelic balance measures.
• Segmentation support: Enhances the accuracy of segmentation methods for detecting transitions between copy number states.
• CN-LOH enhancement: Improves detection sensitivity for copy-neutral loss of heterozygosity events.
• Microarray platform compatibility: Applies to data from Affymetrix and Illumina microarray technologies.
• R package implementation: Provided as an R package for computational integration into analysis workflows.
• Aroma Project add-on: Includes an add-on for the Aroma Project framework for integration with Aroma-based analyses.

Scientific Applications:

• Tumor copy number analysis: Improves detection of copy number alterations and CN-LOH in cancer genomics studies.
• Segmentation-based pipelines: Increases reliability of segmentation results used to map copy number state changes.
• Allele-specific copy number studies: Refines allelic balance estimates for studies of copy number variation and allelic imbalance.

Methodology:

Calibration of preprocessed ASCNs through adjustment of raw ASCN data to control SNP-specific allelic crosstalk.