CAnD

CAnD implements the Chromosomal Ancestry Differences (CAnD) test to detect heterogeneity in population structure across the genome by comparing ancestry proportions across chromosomes in admixed populations such as Hispanics and African-Americans.

Key Features:

• Chromosomal-Specific Analysis: Evaluates ancestry proportions for each chromosome or chromosomal segment rather than aggregating measures across autosomal chromosomes, enabling identification of regions with significant deviations from expected ancestry contributions.
• P-value Calculation: Calculates p-values for each chromosome and an overall genome-wide analysis to assess the significance of observed heterogeneity in ancestry.
• Plotting Functions: Provides plotting functions to visualize chromosome-specific and genome-wide ancestry heterogeneity.

Scientific Applications:

• Admixed Population Studies: Examines populations with complex ancestral backgrounds, including Mexican-Americans (MXL) and African-Americans (ASW), to detect chromosome-specific ancestry differences.
• Genomic Research: Identifies chromosomes or regions with significant ancestry deviations to investigate evolutionary forces such as selection pressures and nonrandom mating.
• Population Genetics: Aids in understanding how historical admixture events influence current population structure.
• HapMap Sample Analysis: Applied to HapMap Project Phase III samples to reveal elevated Native American and reduced European ancestry on the X chromosome of Mexican-Americans and predominant African-derived ancestry across chromosomes in African-Americans with no detected heterogeneity.

Methodology:

The CAnD test leverages SNP genotype data to infer local or chromosome-wide ancestry, computes p-values per chromosome and genome-wide, and has been validated through simulation studies using real genotype data from the HapMap Project Phase III.