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. 2021 Dec 2;52(2):92–107. doi: 10.1007/s10519-021-10094-4

Table 1.

Results of the polygenic score (PGS) analyses in the NTR and NEMESIS-2 sample with lifetime smoking as outcome

Lifetime smoking NTR (N = 12,584–14,618)a Lifetime smoking NEMESIS-2 (N = 3090)
b SE OR p b SE OR p
0
 Age 0.706 0.021 2.03 1.46E − 252  − 0.125 0.083 0.883 0.133
 Sexb  − 0.291 0.036 0.748 9.46E − 16  − 0.158 0.042 0.854 2.07E − 4
R2 = 11.7% R2 = 1.9%
1a
 PGSallsmok 0.389 0.019 1.476  < 1E − 320 0.354 0.042 1.424  < 1E − 320
 Age 0.652 0.022 1.919  < 1E − 320  − 0.165 0.043 0.848 1.38E − 04
 Sex  − 0.273 0.037 1.314 1.41E − 13  − 0.141 0.084 0.869 0.095
R2 = 16.3% (Δ = 4.6%) R2 = 5.4% (Δ = 3.5%)
1b
 PGSEA  − 0.223 0.020 0.800  < 1E − 320  − 0.462 0.059 0.630 5.33E − 15
 PGSsmok-noEA 0.347 0.019 1.415  < 1E − 320 0.335 0.058 1.398 8.36E − 09
 Age 0.663 0.022 1.941  < 1E − 320  − 0.169 0.043 0.845 9.49E − 05
 Sex  − 0.272 0.037 1.313 1.84E − 13  − 0.138 0.084 0.871 0.100
R2 = 16.8% (Δ = 5.1%) R2 = 4.9% (Δ = 3.0%)
2a
 PGSallsmok 0.396 0.022 1.486  < 1E − 320 0.354 0.042 1.425  < 1E − 320
 Neighborhood  − 0.158 0.023 0.854 1.77E − 11 0.071 0.042 1.073 0.091
Age 0.798 0.028 2.222  < 1E − 320  − 0.167 0.043 0.846 1.19E − 04
 Sex  − 0.273 0.043 1.314 1.89E − 10  − 0.148 0.084 0.863 0.080
R2 = 18.2% (Δ = 6.5%) R2 = 5.6% (Δ = 3.7%)
2b
 PGSEA  − 0.196 0.022 0.822  < 1E − 320  − 0.461 0.059 0.631 6.44E − 15
 PGSsmok-noEA 0.359 0.022 1.432  < 1E − 320 0.336 0.058 1.399 7.91E − 9
 Neighborhood  − 0.145 0.023 0.865 5.32E − 10 0.064 0.042 1.067 0.123
 Age 0.804 0.028 2.235  < 1E − 320  − 0.171 0.043 0.843 8.40E − 05
 Sex  − 0.272 0.043 1.312 2.56E − 10  − 0.145 0.084 0.865 0.086
R2 = 18.4% (Δ = 6.7%) R2 = 5.2% (Δ = 3.3%)
3a
 PGSallsmok 0.398 0.022 1.489  < 1E320 0.361 0.043 1.435  < 1E320
 Neighborhood  − 0.171 0.024 0.843  < 1E320 0.027 0.054 1.028 0.616
 PGSallsmok × neigh  − 0.046 0.022 0.955 0.034  − 0.028 0.050 0.972 0.571
 Age 0.801 0.028 2.228  < 1E320  − 0.171 0.044 0.843  < 1E320
 Sex 0.278 0.043 1.320  < 1E320  − 0.135 0.087 0.874 0.122
R2 = 18.5% (Δ = 6.8%) R2 = 6.5% (Δ = 4.6%)
3b
 PGSEA  − 0.190 0.023 0.827  < 1E320  − 0.257 0.044 0.774  < 1E320
 PGSsmok-noEA 0.360 0.022 1.433  < 1E320 0.289 0.043 1.335  < 1E320
 Neighborhood  − 0.163 0.024 0.850  < 1E320 0.037 0.056 1.038 0.504
 PGSEA × neigh 0.053 0.022 1.054 0.014 0.009 0.049 1.009 0.852
 PGSsmok-noEA × neigh  − 0.031 0.021 0.969 0.141  − 0.024 0.050 0.976 0.629
 Age 0.809 0.028 2.246  < 1E320  − 0.174 0.044 0.840  < 1E320
 Sex 0.277 0.043 1.319  < 1E320  − 0.145 0.088 0.865 0.098
R2 = 18.9% (Δ = 7.2%) R2 = 8.1% (Δ = 6.2%)

Models include the effects of the PGS based on EA and the PGS based on smoking-without-EA, main effects of neighborhood environment (income in NTR; quality in NEMESIS-2), and interaction between PGSs and neighborhood. Covariates in all models 0-3b included age, sex, and the first 10 principal components (PCs) for genetic ancestry; in models 3a-b we also added the interaction terms between the PGSs, PCs, and neighborhood (parameters estimates for all predictors can be found in Supplementary Tables S9a and S10a). Effects with p < 0.006 (corrected for 8 independent tests) are bold-faced. Explained variance (R2 of the total model is given, with the difference to the null model (Δ)

PGS polygenic score, allsmok all smoking, EA educational attainment, smok-noEA effects on smoking independent from EA, Neighborhood (neigh) neighborhood characteristics, in NTR neighborhood-level income, in NEMESIS-2 neighborhood quality

aDue to missingness in the neighborhood measure, model 2 and 3 had a sample size of N = 12,584

bSex was coded 1 = male, 2 = female