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Table 6 Height association results with methods for selecting PCs.

From: Choice of population structure informative principal components for adjustment in a case-control study

   beta (p-value) of SNP
   sSNP* nSNP** Positive Control SNPs
Method for selecting PCs Selected PCs rs2322659 rs2290305 rs1042725 rs6060369
No PC Adjustment NA -0.406 (< 0.001) -0.086 (0.338) -0.251 (0.002) 0.221 (0.007)
Top 2 PCs PC1, PC2 -0.043 (0.646) -0.064 (0.491) -0.149 (0.073) 0.336 (< 0.001)
Top 10 PCs PC1 - PC10 -0.057 (0.563) -0.054 (0.571) -0.132 (0.121) 0.322 (< 0.001)
Tracy-Widom statistic PC1 - PC81 -0.062 (0.566) -0.057 (0.581) -0.174 (0.061) 0.318 (0.001)
Associated with the outcome at α = 0.05 PC1, PC2, PC4, PC8, PC21, PC25, PC28, PC39, PC47, PC49, PC56, PC64, PC77 -0.03 (0.762) -0.049 (0.617) -0.164 (0.059) 0.313 (0.001)
Associated with the outcome at α = 0.01 PC1, PC4, PC21, PC25, PC28, PC49, PC77 -0.015 (0.875) -0.053 (0.578) -0.162 (0.059) 0.322 (< 0.001)
Associated with the outcome at α = 0.001 PC1, PC4, PC28 0.014 (0.884) -0.047 (0.619) -0.163 (0.055) 0.322 (< 0.001)
Associated with the SNP at α = 0.05 varied by SNP -0.041 (0.677) -0.092 (0.312) -0.148 (0.075) 0.333 (< 0.001)
Associated with the SNP at α = 0.01 varied by SNP -.038 (0.703) -0.086 (0.338) -0.164 (0.170) 0.313 (< 0.001)
10% Rule PC1# -0.037 (0.692) -0.086 (0.338) -0.148 (0.075) 0.333 (< 0.001)
PC-Finder [21] NA -0.406 (< 0.001) -0.086 (0.338) -0.251 (0.002) 0.221 (0.007)
  1. Regression estimate (p-value) of the association between outcome and SNP adjusting for the selected PCs are displayed in the table. *sSNP is a structured SNP. This SNP is in the lactase gene, and varies in frequency across Europe; ** nSNP is a non-structured SNP. This SNP does not vary among subgroups in the FHS sample; # PC1 was selected except for the nSNP (rs2290305), in which case, no PCs were selected by the 10% rule.