SNPduo

SNPduo analyzes genetic relatedness between two individuals using Single Nucleotide Polymorphism (SNP) data by calculating identity by state (IBS) to characterize relationships and shared genomic regions.

Key Features:

• Identity-by-State (IBS) calculations: Uses IBS calculations that do not require allele frequency estimates or pedigree information for relationship inference.
• Data compatibility: Processes SNP data exported from Affymetrix CNAT 4.0, Illumina Beadstudio, and HapMap downloads, and accepts correctly formatted SNP datasets.
• UCSC track generation: Produces UCSC Genome Browser–viewable tracks representing shared genomic regions.
• Command-line implementation: Provides a portable C++ command-line implementation optimized for large datasets and able to accept pedigree information for compatibility with existing software.
• Analytical capabilities: Detects shared genomic segments to define relatedness, analyze meiotic crossovers, and identify chromosomal anomalies such as hemizygous deletions and uniparental disomy.
• Performance and compatibility: Performs favorably in benchmarking studies and is compatible with tools such as PLINK.

Scientific Applications:

• Relatedness inference: Identification of unexpected relationships and consanguinity among nominally unrelated individuals.
• Meiotic crossover analysis: Mapping and analysis of meiotic crossovers between paired samples.
• Chromosomal anomaly detection: Detection of hemizygous deletions, uniparental disomy, mosaic chromosomal loss, and other genetic irregularities.
• Population sample quality control: Identification of undeclared related individuals in population datasets such as HapMap.
• Family-based genetic studies: Application to multiplex autism families to detect related parents, mosaic loss of chromosome 18, maternal heterodisomy of chromosome 16, and unexplained replicate samples.

Methodology:

Performs identity-by-state (IBS) calculations on SNP datasets (Affymetrix CNAT 4.0, Illumina Beadstudio, HapMap formats), generates UCSC viewable tracks, and includes a portable C++ command-line implementation that can accept pedigree input for compatibility.