Table 2. Risk-weighted burden analysis results for APOE and 9 LOAD Candidate Genes.

Beta coefficients (β), 95% Confidence Intervals, and P-values are from four logistic regression models examining weighted scores for the peak SNP associations in APOE and 9 LOAD candidate genes. Scores are the product of the log-transformed odds ratio for each SNP association multiplied by minor allele dosage from imputed genotype probabilities.

	Model 1: Adjustment for PCs & Site		Model 2: Adjustment for Model 1 + APOE		Model 3: Adjustment for Model 1 + 9 LOAD Genes		Model 4: Adjustment for Model 1 + APOE + 9 LOAD Genes
	β (95% CI)	P	β (95% CI)	P	β (95% CI)	P	β (95% CI)	P
(Intercept)	74.2 (73.5, 75.0)	<10-32	70.6 (69.8, 71.4)	<10−32	72.9 (71.6, 74.1)	<10−32	69.1 (67.9, 70.4)	<10−32
CR1 Score	--	--	--	--	1.01 (0.59, 1.43)	2.66×10−6	1.01 (0.60, 1.43)	1.51×10−6
BIN1 Score	--	--	--	--	−0.97 (−1.45, −0.50)	5.27×10−5	−1.04 (−1.51, −0.58)	9.99×10−6
CD2AP Score	--	--	--	--	−0.51 (−1.00, −0.03)	0.0381	−0.43 (−0.90, 0.05)	0.0764
EPHA1 Score	--	--	--	--	−0.73 (−1.49, 0.03)	0.0586	−0.67 (−1.41, 0.07)	0.0778
CLU Score	--	--	--	--	0.83 (0.36, 1.29)	4.63×10−4	0.89 (0.44, 1.35)	1.11×10−4
MS4A4A Score	--	--	--	--	0.87 (0.34, 1.40)	0.00120	0.91 (0.39, 1.43)	5.58×10−4
PICALM Score	--	--	--	--	1.11 (0.63, 1.59)	6.78x10−6	1.03 (0.56, 1.51)	1.83×10−5
ABCA7 Score	--	--	--	--	0.92 (0.35, 1.50)	0.00164	0.97 (0.41, 1.53)	7.35×10−4
CD33 Score	--	--	--	--	−0.84 (−1.41, −0.28)	0.00315	−0.81 (−1.36, −0.26)	0.00405
APOE Score	--	--	−0.77 (−0.85, −0.70)	1.03×10−79	--	--	-0.78 (−0.86, −0.70)	5.48×10−81
ACT	9.67 (8.62, 10.7)	3.31×10−72	10.3 (9.30, 11.4)	1.10×10−84	11.15 (9.64, 12.66)	8.89×10−47	11.9 (10.42, 13.39)	6.69×10−55
ADC1	−1.76 (−2.60, −0.93)	3.66x10−5	0.54 (−0.32, 1.39)	0.219	−1.74 (−2.81, −0.67)	0.00139	0.62 (−0.45, 1.70)	0.256
ADC2	−i.03 (−1.96, −0.10)	0.0294	−1.47 (−2.38, −0.56)	0.00157	0.33 (−1.20, 1.87)	0.671	−0.09 (−1.59, 1.42)	0.909
ADC3	0.19 (−0.74, 1.13)	0.684	0.40 (−0.52, 1.32)	0.393	1.17 (−0.68, 3.02)	0.215	1.31 (−0.50, 3.13)	0.155
ADNI	−1.20 (−2.57, 0.18)	0.0882	−0.91 (−2.26, 0.44)	0.187	−0.26 (−1.90, 1.39)	0.758	0.22 (−1.39, 1.84)	0.787
GenADA	0.36 (−0.57, 1.28)	0.449	−1.42 (−2.34, −0.50)	0.00258	2.46 (1.19, 3.72)	1.39×10−4	0.79 (−0.46, 2.04)	0.216
LOAD	−0.67 (−1.49, 0.15)	0.111	0.42 (−0.40, 1.23)	0.316	−0.37 (−1.55, 0.80)	0.533	0.77 (−0.38, 1.93)	0.190
MIRAGE	−3.08 (−4.04, −2.11)	4.66×10−10	0.37 (−0.64, 1.38)	0.472	−2.17 (−3.51, −0.83)	0.00146	1.36 (0, 2.72)	0.0504
OHSU	11.9 (10.5, 13.3)	2.06×10−59	12.5 (11.1, 13.9)	5.29×10−68	13.55 (11.72, 15.39)	5.32×10−47	14.4 (12.6, 16.2)	1.16×10−54
ROSMAP	11.4 (10.3, 12.5)	6.52×10−90	9.21 (8.11, 10.3)	4.63×10−60	13.26 (11.57, 14.95)	1.34×10−52	11.22 (9.55, 12.9)	3.11×10−39
TGEN2	0.55 (−1.03, 2.13)	0.494	0.69 (−0.86, 2.24)	0.385	1.47 (−3.09, 6.03)	0.528	1.55 (−2.92, 6.03)	0.497
UM/VU/MSSM	−0.33 (−1.20, 0.53)	0.449	−0.6 (−1.45, 0.25)	0.165	1.18 (−0.10, 2.46)	0.0704	0.92 (−0.33, 2.18)	0.149
UPITT	−1.33 (−2.18, −0.47)	0.0233	−0.61 (−1.45, 0.23)	0.155	0.7 (−0.54, 1.94)	0.267	1.38 (0.16, 2.59)	0.0261
PC1	6.76 (3.09, 10.4)	3.10×10−4	6.16 (2.56, 9.76)	8.01×10−4	7.04 (3.38, 10.7)	1.61×10−4	6.44 (2.85, 10.02)	4.32×10−4
PC2	1.12 (−2.60, 4.84)	0.554	1.99 (−1.66, 5.64)	0.285	0.81 (−2.90, 4.51)	0.670	1.65 (−1.98, 5.28)	0.372
PC3	−0.89 (−4.54, 2.77)	0.634	−0.34 (−3.93, 3.24)	0.852	−1.07 (−4.71, 2.57)	0.564	−0.5 (−4.07, 3.06)	0.782
F (df1, df2)	164.2 (13, 9114)		184.8 (14, 9113)		103.3 (22, 9105)		119.1 (23, 9104)
P	<10−100		<10−100		<10−100		<10−100
Multiple R2	0.1898		0.2211		0.1998		0.2313
Adjusted R2	0.1886		0.2199		0.1979		0.2294