SCANSTAT

SCANSTAT identifies contiguous single nucleotide polymorphisms (SNPs) that are jointly associated with disease susceptibility by applying scan statistics across adjacent genetic markers.

Key Features:

• Integration of Multiple Markers: Combines contiguous SNPs to enhance power to detect associations that single-marker analyses may miss.
• Application to Genome Screens: Applicable to genome-wide screens for identification of susceptibility loci for complex diseases.
• Dichotomous Outcome Handling: Focuses on dichotomous outcomes such as case-control status and affected-affected versus affected-unaffected sibling pairs.

Scientific Applications:

• Autism family genome screens: Applied to autism family data to identify a susceptibility region reaching genome-wide significance (P = 0.038) that was not detected by conventional methods.

Methodology:

Uses single-marker statistics to evaluate candidate regions; employs Monte Carlo permutation tests to assess significance of scan statistics for specified scan lengths; compares P values across varying scan lengths and selects the smallest observed P value as the primary statistic, determining the overall significance for that statistic.