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Table 3 Results from APOE filtering approach 1 versus 2 in the discovery: 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 – approach 1

14 / 237 (5.91 %)

19 / 1652 (1.15 %)

3.59 % - 0.64 %

0.10 (0.04, 0.24)

1.64E-07

  Discovery – approach 2

2 / 203 (0.99 %)

10 / 1577 (0.63 %)

0.49 % - 0.32 %

0.47 (0.07, 3.21)

0.44

 APOE*3/4 - WT vs HOM

  Discovery – approach 1

19 / 1401 (1.36 %)

14 / 2974 (0.47 %)

-

0.55 (0.38, 0.80)

1.58E-03

  Discovery – approach 2

4 / 1339 (0.29 %)

9 / 2914 (0.31 %)

-

1.09 (0.61, 1.94)

0.78

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