Table 6

Height association results with methods for selecting PCs.

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)


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.

Peloso and Lunetta BMC Genetics 2011 12:64   doi:10.1186/1471-2156-12-64

Open Data