ASPEX

ASPEX performs multipoint exclusion mapping using affected sibling pair genotype data to analyze allele sharing and linkage for discrete traits.

Key Features:

• sib_ibd (Identity-by-Descent): Calculates the probability that affected siblings share alleles identical by descent at genetic loci.
• sib_phase: Determines the phase of alleles shared between siblings to inform mapping and interpretation.
• sib_map: Performs linkage analysis to identify chromosomal regions associated with the trait under investigation.
• sib_tdt (Transmission Disequilibrium Test): Evaluates transmission patterns of alleles from parents to affected offspring to assess family-based association while accounting for linkage.
• sib_kin: Computes kinship coefficients and related familial relationship metrics used in genetic analyses.
• Multipoint LOD scores: Computes multipoint logarithm of odds (lod) scores across multiple loci to assess likelihoods of linkage.
• Allele sharing analysis: Evaluates allele sharing patterns among affected siblings to identify potential genetic markers associated with the trait.

Scientific Applications:

• Complex trait linkage mapping: Mapping discrete and multifactorial disease loci using affected sibling pair data and multipoint exclusion methods.
• Family-based association testing: Detecting transmission distortion and association via sib_tdt and sibling-based allele-sharing analyses.
• Applied genetic studies: Used in research contexts such as the Collaborative Study on the Genetics of Alcoholism to analyze concordant and discordant sibling pairs.

Methodology:

Input affected sibling pair genotype data; programs compute IBD probabilities, determine allele phase, perform linkage mapping and TDT, calculate kinship coefficients, and produce multipoint LOD scores and allele sharing patterns as outputs.