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Table 2 Results from APOE filtering approach 1: association findings for rs439401, when in-phase with APOE*4, with Alzheimer’s disease case-control status

From: Challenges at the APOE locus: a robust quality control approach for accurate APOE genotyping

 

Genotype distributions

AD Case-Control regression

Group/model

CN, carrier No. / Total No. (%)

AD, carrier No. / Total No. (%)

CN - AD, MAF (%)

OR (95% CI)

P-value

rs439401 - T allele tested

 APOE*4/4 - additive model

  Discovery

14 / 237 (5.91 %)

19 / 1652 (1.15 %)

3.59 % - 0.64 %

0.10 (0.04, 0.24)

1.64E-07

  Rotterdam

5 / 150 (3.33 %)

2 / 86 (2.33 %)

2.33 % - 1.16 %

0.43 (0.10, 1.80)

0.25

  EADI

1 / 62 (1.61 %)

2 / 205 (0.98 %)

0.80 % - 0.49 %

0.37 (0.01, 12.7)

0.58

  EADB

2 / 195 (1.03 %)

21 / 956 (2.20 %)

0.52 % - 1.20 %

1.61 (0.39, 6.77)

0.51

 APOE*3/4 - WT vs HOM

  Discovery

19 / 1401 (1.36 %)

14 / 2974 (0.47 %)

-

0.55 (0.38, 0.80)

1.58E-03

  Rotterdam

8 / 993 (0.81 %)

3 / 220 (1.36 %)

-

1.21 (0.31, 4.72)

0.78

  EADI

4 / 593 (0.67 %)

5 / 420 (1.19 %)

-

1.22 (0.60, 2.49)

0.58

  EADB

12 / 1343 (0.89 %)

21 / 2070 (1.01 %)

-

0.80 (0.55, 1.17)

0.25

  1. Abbreviations: CN cognitively normal, AD Alzheimer’s disease, OR odds ratio, CI confidence interval