Standard genome-wide association studies (GWAS) scan for relationships between each of
p molecular markers and a continuously distributed target trait. Typically, a marker-based
matrix of genomic similarities among individuals (G) is constructed, to account more properly
for the covariance structure in the linear regression model used. We show that the
generalized least-squares estimator of the regression of phenotype on one or on m markers
is invariant with respect to whether or not the marker (s) tested is (are) used for building G …