A second way to estimate heritability is to consider the additive effect of all SNPs considered simultaneously using GCTA. GCTA has become increasingly used to provide an estimate of the heritability in a trait due to measured SNPs (Yang, Lee, et al., 2011; Yang, Manolio, et al., 2011). The method evaluates the joint effect of all SNPs considered simultaneously as a random effect, and estimates the variance in the phenotype attributable to this random effect. In practice, the method computes the genetic relatedness based on SNPs between all pairs of individuals in the sample. This genetic relatedness matrix (GRM) is then used as input in the random effects model, and the similarity among individuals in genetic relatedness predicts the similarity in phenotypic relatedness. In a sample of unrelated subjects the method produces the variance in the trait accounted for by the SNPs, because the relationships between genetically unrelated subjects are not influenced by shared environment or non-SNP genetic variance. In a sample of related subjects, such as the families used in the present study, phenotypic relatedness and genetic relatedness are
