infocalc

infocalc calculates statistics that quantify the ancestry informativeness of multiallelic genetic markers using information-theoretic principles to support population ancestry inference.

Key Features:

• Informativeness for assignment (I(n)): Calculates the I(n) metric to quantify how informative multiallelic markers are for ancestry assignment across any number of potential source populations.
• Applicability across populations: Applies the I(n) measure across diverse source populations to enable comparison of marker informativeness in global human genetic studies.
• Marker identification: Identifies and lists markers with the highest informativeness for regional ancestry inference and within-region population ancestry to inform marker selection for downstream analyses.
• Comparison of marker types: Compares informativeness between marker classes, including microsatellites (random dinucleotides) and single-nucleotide polymorphisms (SNPs), noting that dinucleotides are generally more informative than SNPs though some SNPs can exceed the median informativeness of dinucleotides.

Scientific Applications:

• Admixture mapping: Identifies genetic markers most informative for mapping ancestry within admixed populations.
• Structured-association mapping: Supports control and testing for the influence of ancestry in case-control genetic association studies.
• Ancestry studies: Provides lists of highly informative markers to guide selection of marker type and quantity for ancestry research.

Methodology:

Employs information-theoretic principles to derive the informativeness for assignment I(n) and performs empirical analyses on worldwide human microsatellite datasets to quantify marker informativeness.