Marker preparation and analytical implementation for imputation were performed as follows: genetic markers were excluded which demonstrated high missingness (> 0.05), failed Hardy-Weinberg equilibrium (P < 0.0005), or had exceedingly rare alternative alleles (minor allele frequency < 0.005).
Poor quality SNP markers were excluded from the analysis by removing any markers where there was statistical evidence that plates varied in the amount of heterozygosity detected.
Therefore, these two markers were excluded from further analysis.
Therefore, RAPD markers were excluded to improve the quality of the maps.
X chromosome markers were excluded because these markers are best analyzed using gender stratification and our sample size is too small for this analysis.
Following quality control checks, 846 of the 54,001markers were excluded because of low (<95%) call rate, 6511 markers were excluded because of low minor allele frequency (MAF) <0.002 and 294 markers were excluded because they were out of Hardy-Weinberg equilibrium in controls at a false discovery rate (FDR <0.2).
The results with or without the EuroAIMs with predicted function were largely similar, albeit the distinction of Northwest Africans from Southern European populations was not as apparent when these markers were excluded from the analyses (not shown).
Seventy markers were excluded from the following analysis, as they showed highly significant departure from Hardy Weinberg equilibrium (P<10−5), obtaining 5,192 markers for the following analysis.
Approximately 90% of the SWAT and MWAT samples included high levels of lymphocyte markers, and to obtain within-depot uniformity, SWAT and MWAT samples with no expression of lymphocyte markers were excluded.
Outlier markers were excluded.
Unstable markers were excluded from the analysis.
