Methodological Considerations in Estimation of Phenotype ...
Several authors have raised concerns about the behavior of the LMM applied to GWAS data in the presence of population structure either due to gross population stratification or more subtle relatedness [5, 6].We undertook a more thorough analysis of the issue of the effect of small amounts of residual relatedness in GWAS data on heritability estimation using the LMM than has been described before.