Background
The three main alleles of the
APOE
gene (ε4, ε3 and ε2) carry differential risks for conditions including Alzheimer's disease (AD) and cardiovascular disease. Due to their clinical significance, we explored disease associations of the
APOE
genotypes using a hypothesis-free, data-driven, phenome-wide association study (PheWAS) approach.
Methods
We used data from the UK Biobank to screen for associations between
APOE
genotypes and over 950 disease outcomes using genotype ε3ε3 as a reference. Data was restricted to 337,484 white British participants (aged 37–73 years).
Findings
After correction for multiple testing, PheWAS analyses identified associations with 37 outcomes, representing 18 distinct diseases. As expected, ε3ε4 and ε4ε4 genotypes associated with increased odds of AD (p ≤ 7.6 × 10
−46
), hypercholesterolaemia (p ≤ 7.1 × 10
−17
) and ischaemic heart disease (p ≤ 2.3 × 10
−4
), while ε2ε3 provided protection for the latter two conditions (p ≤ 3.7 × 10
−10
) compared to ε3ε3. In contrast, ε4-associated disease protection was seen against obesity, chronic airway obstruction, type 2 diabetes, gallbladder disease, and liver disease (all p ≤ 5.2 × 10
−4
) while ε2ε2 homozygosity increased risks of peripheral vascular disease, thromboembolism, arterial aneurysm, peptic ulcer, cervical disorders, and
hallux valgus
(all p ≤ 6.1 × 10
−4
). Sensitivity analyses using brain neuroimaging, blood biochemistry, anthropometric, and spirometric biomarkers supported the PheWAS findings on
APOE
associations with respective disease outcomes.
Interpretation
PheWAS confirms strong associations between
APOE
and AD, hypercholesterolaemia, and ischaemic heart disease, and suggests potential ε4-associated disease protection and harmful effects of the ε2ε2 genotype, for several conditions.
Funding
National Health and Medical Research Council of Australia.