SNPscan

SNPscan analyzes high-density single nucleotide polymorphism (SNP) array data to detect chromosomal copy-number changes, microdeletions, microduplications, and regions of loss of heterozygosity, including uniparental isodisomy.

Key Features:

• Quality Assessment: Compares SNP data against a benchmark dataset derived from a control population for visual and quantitative quality assessment.
• Visualization of Chromosomal Anomalies: Displays SNP intensity and allelic call data to enable detection of chromosomal copy-number anomalies such as duplications and deletions.
• Detection of Uniparental Isodisomy (UPD): Identifies uniparental isodisomy by analyzing loss of heterozygosity (LOH) across genomic regions.
• Paired Sample Comparison: Compares paired samples (e.g., tumor and normal tissue) to identify genetic differences between samples.
• Integration with Genome Browsers: Generates files compatible with the University of California, Santa Cruz (UCSC) Human Genome Browser for genomic-context visualization.

Scientific Applications:

• Chromosomal Abnormality Detection: Characterizes aneuploidies, microdeletions, and microduplications in clinical and research samples.
• UPD and LOH Analysis: Maps regions of loss of heterozygosity to detect uniparental isodisomy and other LOH-associated events.
• Somatic Variation Analysis: Assesses genetic differences between paired samples such as tumor versus normal to identify somatic copy-number changes.
• Genome-Context Interpretation: Produces UCSC Genome Browser-compatible files to facilitate interpretation of SNP-derived copy-number and LOH data in a genomic context.

Methodology:

Processes data exported from the Affymetrix Copy Number Analysis Tool; analyzes SNP intensity and allelic calls to detect copy-number anomalies and loss of heterozygosity; performs paired-sample comparisons; and outputs files compatible with the University of California, Santa Cruz (UCSC) Human Genome Browser.