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Table 4 Replication of previously reported heterogeneity by sex in PAGE

From: Investigation of gene-by-sex interactions for lipid traits in diverse populations from the population architecture using genomics and epidemiology study

   Prior study PAGE  
Gene Trait SNP CA CAF Beta (SE), male Beta (SE), female PAGE SNP §R2 CA CAF Required sample size@for 80% power to detect interaction Beta (SE), male Beta (SE), female Phet Sex with stronger absolute effect (prior, PAGE)
Significant heterogeneity in PAGE (phet < 0.05)
BUD13 TG rs11820589 A 0.05 0.131 (0.009) 0.091 (0.008) rs3135506 0.79 C 0.06 215,337 0.16 (0.02) 0.09 (0.01) 4.3E-4 MM
GCKR TG rs1260326 T 0.41 0.064 (0.005) 0.050 (0.004) rs1260326 - T 0.42 370,777 0.072 (0.009) 0.046 (0.006) 0.013 MM
LPL TG rs13702 T 0.70 0.070 (0.005) 0.047 (0.004) rs328 0.39 C 0.90 389,318 −0.110 (0.014) −0.069 (0.009) 0.013 MM
PLTP HDL rs6065904 A 0.22 −0.008 (0.003) −0.031 (0.004) rs7679 0.86 T 0.82 242,184 0.10 (0.30) 1.68 (0.37) 9.9E-4 FF
TRIB1 TG rs2954033 A 0.30 0.050 (0.005) 0.022 (0.004) rs2954029 0.36 A 0.54 137,339 −0.059 (0.010) −0.031 (0.006) 0.015 MM
No significant heterogeneity in PAGE (phet > 0.05)
APOB TG rs11902417 A 0.23 −0.038 (0.006) −0.024 (0.005) rs693 0.27 T 0.49 >1,000,000 −0.025 (0.009) −0.014 (0.007) 0.32 MM
APOB LDL rs531819 T 0.15 −0.092 (0.012) −0.128 (0.012) rs562338 0.70 T 0.19 126,763 −5.32 (0.73) −5.96 (0.66) 0.51 FF
CETP HDL rs7499892 T 0.17 −0.074 (0.004) −0.091 (0.005) rs1864163 0.57 A 0.24 525,658 −2.57 (1.55) −1.16 (2.68) 0.65 FM
CILP2 LDL rs10401969 T 0.07 0.15 (0.02) 0.03 (0.01) rs16996148 1.0 T 0.08 18,530 −3.44 (0.96) −2.11 (0.76) 0.28 MM
FADS1 HDL rs174548 C 0.70 0.015 (0.003) 0.024 (0.004) rs174547 0.80 T 0.66 986,476 0.82 (0.22) 0.60 (0.20) 0.47 FM
GALNT2 HDL rs2296065 A 0.85 0.015 (0.004) 0.030 (0.005) rs2144300 0.26 T 0.60 >1,000,000 0.21 (0.19) 0.63 (0.17) 0.091 FF
GALNT2 TG rs2296065 A 0.85 −0.015 (0.007) −0.027 (0.005) rs2144300 0.26 T 0.60 >1,000,000 0.015 (0.008) 0.019 (0.006) 0.73 FF
LIPC HDL rs2070895 A 0.22 0.033 (0.003) 0.051 (0.004) rs261332 0.91 A 0.20 375,405 1.77 (0.32) 1.72 (0.42) 0.96 FM
LIPG HDL rs2156552 A 0.16 −0.023 (0.004) −0.032 (0.005) rs2156552 - T 0.17 >1,000,000 −0.38 (0.24) −0.56 (0.24) 0.60 FF
LPL HDL rs10096633 A 0.40 0.014 (0.032) 0.079 (0.011) rs328 0.87 G 0.10 53,495 1.76 (0.31) 1.93 (0.28) 0.68 FF
LPL HDL rs12678919 A 0.12 −0.20 (0.01) −0.13 (0.01) rs328 1.0 G 0.10 40,123 1.76 (0.31) 1.93 (0.28) 0.68 MF
LPL HDL rs2083637 G 0.26 0.149 0.079 rs328 0.43 G 0.10 93,909 1.76 (0.31) 1.93 (0.28) 0.68 MF
PLTP TG rs6073952 A 0.19 0.009 (0.006) 0.030 (0.005) rs7679 1.0 T 0.82 247885 0.013 (0.013) 0.009 (0.011) 0.82 FM
TRIB1 LDL rs17321515 A 0.52 0.022 (0.008) 0.045 (0.009) rs2954029 0.97 A 0.54 63691 1.98 (0.67) 2.16 (0.49) 0.83 FF
  1. *Abbreviations: CA = coding allele; CAF = coding allele frequency; SE = standard error; Phet = heterogeneity by sex p-value.
  2. All prior SNPs shown are from Asselbergs et al. (2012), except for the three noted.
  3. Aulchenko, Ripatti et al., 2009. Standard errors were not reported for sex-specific effects.
  4. Teslovich, Musunuru, et al., 2010. Effect sizes were reported for standardized residuals and therefore are not directly comparable to the PAGE results.
  5. §LD was calculated using 1000 Genomes Pilot 1 data (CEU population).
  6. %Criteria for replication: phet < 0.05 in PAGE and consistent direction of interaction effect (e.g., stronger effects in females in both PAGE and prior study).
  7. @Sample size calculations for gene-environment interactions done on Quanto, assuming the CAF from PAGE and the difference in βfm from the prior study. Calculated sample sizes were then divided by R2 (the LD between the PAGE SNP and the prior SNP) to arrive at the final required sample size for 80% power, shown in the table.