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Table 5 Random Forest results of the analysis of ACTG data with HDL-c levels as trait and SNPs from ApoCIII, ApoE, EL and HL genes and race/ethnicity as predictors

From: Application of two machine learning algorithms to genetic association studies in the presence of covariates

  Include* Ignore* Residualize* White
(n = 317)
Stratify* Black
(n = 92)
Hispanic
(n = 103)
ApoC-III       
-482C/T (rs2854117) 12.68(0.63) 11.81(0.60) 13.07(0.66) 13.05(0.66) -2.04(0.96) 1.19(0.97)
-455T/C (rs2854116) 9.04(0.66) 9.69(0.66) 10.13(0.67) 8.90(0.69) -0.57(0.98) 1.27(0.98)
intron 1 (466)G/C (rs2070669) 4.70(0.93) 5.85(0.88) 5.91(0.90) 4.55(0.91) -2.78(0.94) -2.62(1.00)
Gly34Gly C/T (rs4520) 8.86(1.12) 5.51(1.03) 4.77(1.07) 2.99(1.02) 0.91(0.99) 11.87(0.91)
exon 4 SstI 4348(5) C/G(rs5128) 0.60(1.01) 2.12(1.04) 2.34(1.04) 2.91(1.03) -3.20(0.97) 2.95(1.00)
ApoE       
Arg112Cys T/C (rs429358) 4.87(1.08) 1.45(1.00) 2.29(1.06) 6.29(1.08) -5.22(0.96) 6.30(0.98)
Arg158Cys T/C (rs7412) 6.02(0.98) 7.49(1.00) 7.49(0.93) 5.08(0.92) -5.20(0.97) 2.69(0.98)
EL       
rs12970066, 3.94(1.03) 4.00(0.97) 5.54(0.97) 1.12(0.97) 8.57(0.91) -1.81(1.05)
Asn396Ser, 7.06(1.03) 8.30(1.05) 8.39(1.10) 2.27(1.04) 5.93(0.90) 2.09(0.97)
rs3829632 (-1309A/G) -1.10 (0.99) 1.24(0.98) 2.25(1.04) -1.64(0.98) 0.00(0.00) -2.25(0.96)
HL       
rs2070895 11.81(1.04) 7.86 (1.09) 5.54(0.99) 5.58(1.11) -1.73(0.95) 2.82(0.97)
rs12595191 -0.93(0.97) -1.77(1.00) -1.07(0.99) -3.62(1.00) -1.99(0.99) 0.07(0.99)
rs690 10.41(1.08) 1.28(0.99) 0.53(0.98) 3.93(1.05) -3.98(0.97) 9.61(0.96)
rs6084 7.42(1.01) 6.47(1.01) 6.27(1.06) -1.15(1.01) 9.31(0.86) 10.97(0.90)
Race/ethnicity 21.58(1.15) NA NA NA NA NA
  1. " * " indicates the approach to handling the race/ethnicity covariate;
  2. "NA" indicates that the predictor was not included in the analysis.
  3. The two highest importance scores from RF are in bold.