Table 1.

Comparison of haplotype-based and diplotype-based association analyses

	Haplotype-based association analysis	Diplotype-based association analysis
Composition	A haplotype is a subset of all alleles on specific chromosomes in the population.	A diplotype is a subset of all genotypes on homologous chromosome pairs in the population. A specific diplotype is one variant of all possible combinations of the haplotypes that exist in the population.
Feature	Both alleles and haplotypes reflect the components of chromosomes in individuals and in the population.	Both genotypes and diplotypes reflect the components of chromosome pairs in individuals and in the population.
n independent single-nucleotide polymorphisms (SNPs)	At most 2n haplotypes	At most 2n(2n+1)/2 diplotypes.
Degrees of freedom in analysis	2n-1	[2n(2n+1)/2]-1
Markers not in Hardy-Weinberg Equilibrium (HWE)	Less powerful predictor of disease status	More powerful predictor of disease status
Recessive genetic model	Less powerful predictor of disease status	More powerful predictor of disease status
With interaction	Less powerful predictor of disease status	More powerful predictor of disease status
Without interaction	Less powerful predictor of disease status	More powerful predictor of disease status
Sample size (n individuals)	2n	n
Frequency of rare categories	Less common	More common (decrease power)