SNPitty

SNPitty analyzes next-generation sequencing (NGS) variant data to detect copy number variation, loss of heterozygosity, allelic imbalance, and somatic mutations for clinical genomics applications.

Key Features:

• VCF and variant-metric integration: Examines variant call format (VCF) files using B-allele frequencies, coverage metrics, and copy number analysis results for inspection of single-nucleotide polymorphisms (SNPs), single-nucleotide variants (SVs), and somatic mutations.
• Genome-wide heterozygous marker analysis: Uses genome-wide heterozygous markers to support detection and interpretation of copy number variation and allelic states.
• Loss-of-heterozygosity and allelic imbalance detection: Identifies and displays LOH, allelic imbalance, chromosomal and gene amplifications, and homozygous or heterozygous deletions.
• Dynamic heuristic filtering and multi-region visualization: Applies dynamic heuristic filtering and simultaneous visualization across multiple regions of interest to prioritize and inspect genetic events.
• Disease-specific reporting: Generates predefined reports that summarize and highlight disease-specific genetic targets of interest for diagnostic interpretation.

Scientific Applications:

• Diagnostic interpretation of somatic events: Validated for diagnostic interpretation of somatic events, including assessment with a serial dilution series of glioma tissue.
• Clinical sequencing analyses: Applied to whole-exome sequencing data from peripheral blood samples, including analyses relevant to conditions such as Down syndrome.
• Molecular relationship and clonal analysis: Distinguishes molecular relationships between multiple tumors from a single patient to assess clonal evolution and tumor heterogeneity.

Methodology:

Processes VCF files by leveraging B-allele frequencies, coverage metrics, copy number analysis results, genome-wide heterozygous markers, and dynamic heuristic filtering to detect copy number variations, LOH, chromosomal/gene amplifications, deletions, and somatic mutations.