We therefore assumed that most trans-eQTLs could be detected when removing approximately 25 PCs. We quantified this systematically, by removing increasing amounts of PCs from the expression data and conducting a full genome-wide trans-eQTL mapping. Indeed, in these analyses at most 244 significant trans-eQTLs could be detected (at FDR 0.05, with potential false-positives due to cross-hybridizations removed), when removing 25 PCs (Figure S9b). The overlap with the expression with no PCs removed was substantial: 62 of the 82 trans-eQTLs (77%), detected in the original analysis were detected as well in the analysis with 25 PCs removed (Figure S9c), all with identical allelic directions (Figure S9d).
