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. 2013 May 1;14:33. doi: 10.1186/1471-2156-14-33

Table 4.

Replication of previously reported heterogeneity by sex in PAGE

 
  
 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

*Abbreviations: CA = coding allele; CAF = coding allele frequency; SE = standard error; Phet = heterogeneity by sex p-value.

All prior SNPs shown are from Asselbergs et al. (2012), except for the three noted.

†Aulchenko, Ripatti et al., 2009. Standard errors were not reported for sex-specific effects.

‡Teslovich, Musunuru, et al., 2010. Effect sizes were reported for standardized residuals and therefore are not directly comparable to the PAGE results.

§LD was calculated using 1000 Genomes Pilot 1 data (CEU population).

%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).

@Sample size calculations for gene-environment interactions done on Quanto, assuming the CAF from PAGE and the difference in βf-βm 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.