Table 1.
Summary statistics and variable importance rankings of simulated causal effects on TG
| RF* | RF-RFE | ||||||
|---|---|---|---|---|---|---|---|
| r2 | −0.00203 | 0.19217a | |||||
| MSEOOB | 0.07378 | 0.05948a | |||||
| Chr | Causal SNP/CpG | MAF or Mean (SD) | Simulated h2† | Main Effects, β(SE), p value | Interaction Effects, β(SE), p value | Rank (percentile rank) | |
| 1 | rs9661059 | 0.12 | 0.125 | .14 (0.02), <0.0001 | −0.19 (0.07), 0.0109 | 1 (100.0) | 20 (100.0) |
| cg00000363 | 0.49 (0.33) | – | −0.05 (0.03), 0.0873 | 8680 (97.6) | 239,755 (32.7) | ||
| 6 | rs736004 | 0.09 | 0.075 | 0.09 (0.03), 0.0005 | −0.30 (0.08), 0.0001 | 13,480 (96.2) | 766 (99.8) |
| cg10480950 | 0.54 (0.33) | – | −0.04 (0.03), 0.1711 | 5332 (98.5) | 232,579 (34.7) | ||
| 8 | rs1012116 | 0.20 | 0.100 | 0.08 (0.02), <0.0001 | −0.21 (0.06), 0.0002 | 50,218 (85.9) | 333,504 (6.4) |
| cg18772399 | 0.56 (0.33) | – | −0.002 (0.03), 0.9466 | 339,475 (4.7) | 301,855 (15.3) | ||
| 10 | rs10828412 | 0.14 | 0.025 | 0.07 (0.02), 0.0007 | −0.07 (0.07), 0.2770 | 2984 (99.2) | 330,516 (7.3) |
| cg00045910 | 0.49 (0.34) | – | 0.01 (0.03), 0.7176 | 263,465 (26.1) | 231,315 (35.1) | ||
| 17 | rs4399565 | 0.41 | 0.050 | 0.04 (0.02), 0.0142 | −0.13 (0.05), 0.0038 | 11,078 (96.9) | 196,276 (44.9) |
| cg01242676 | 0.46 (0.32) | – | 0.01 (0.03), 0.8159 | 350,420 (1.9) | 350,420 (1.7) | ||
Bolded values are significant at a p<0.05
*RF is the first RF in RF-RFE
ar2 and MSEOOB are averaged over all 324 RFs in the RF-RFE column
†Simulated h2 was provided by GAW20 organizers and based on full 200 simulations; main and interaction effects are calculated within the data set used for this study, which uses the 84th simulation replicate. Effects are calculated with linear regression models using the residual of change in TG after adjusting for baseline TG as the outcome. Interaction effects include the main effects of the interaction terms being tested in the given model
Abbreviations: β Effect size, Chr Chromosome, h2 Heritability