Table 5

Scenarios that could occur across the genome with the optimal method of selection.

Structured Phenotype

(K1 ≠ K2)

Non-Structured Phenotype

(K1 = K2)


Structured Genotype

(p1≠ p2)

Any method of selection except no PC adjustment

Selecting a fixed number of PCs or PCs associated with the SNP


Non-Structured Genotype

(p1 = p2)

Selecting PCs associated with the SNP (α = 0.01), 10% Rule, no PC adjustment

Any method of selection


p1 and p2 are the allele frequencies in population 1 and 2, respectively. K1 and K2 are the frequency of disease in population 1 and 2, respectively.

Peloso and Lunetta BMC Genetics 2011 12:64   doi:10.1186/1471-2156-12-64

Open Data