pediSNP

pediSNP performs reverse pedigree analysis to infer inheritance patterns and localize meiotic crossover sites from high-density SNP array genotypes.

Key Features:

• Reverse Pedigree Analysis: Contrasts genotypes of two siblings with those of their parents to infer inheritance patterns and identify crossover locations on parental gametes, including X chromosome crossovers inferred from two sons and their father.
• High-Resolution Crossover Identification: Employs high-density SNP array technologies and informative markers with a segmentation algorithm to localize meiotic crossovers with reported specificity of 92% and sensitivity of 89%.
• Visualization Capabilities: Produces visualizations of inheritance differences among siblings and maps of inferred crossover locations.
• Application in Disease Studies: Identifies haplotypes shared by probands within pedigrees to investigate recombination patterns in disease, demonstrated on genotypes from eight multiplex autism families with analysis of maternal-to-paternal recombination ratios and affected versus unaffected comparisons.
• Complementary Methodology: Offers an alternative approach that leverages unique sets of genotype markers within pedigree data to complement existing crossover-identification methods.

Scientific Applications:

• Genetic Diversity Studies: Enables study of meiotic recombination as a mechanism generating genetic diversity.
• Disease Association Research: Supports investigation of genetic factors contributing to disease by locating crossovers and shared haplotypes in pedigrees, including autism studies.
• Recombination Analysis: Provides detailed information on crossover events for research into meiotic recombination processes.

Methodology:

Contrasts genotypes of two siblings with parental genotypes using high-density SNP array data and informative markers; applies a segmentation algorithm to infer crossover sites and inheritance patterns; validated on synthetic data sets and genotypes from multiplex autism families.