Using Fisher's exact test, there was significant association of both ABI3_rs616338-T (OR = 1.41, p = 0.044) and PLCG2_rs72824905-G (OR = 0.56, p = 0.008) with AD.
We observed three new genome-wide significant nonsynonymous variants associated with Alzheimer's disease: a protective variant in PLCG2 (rs72824905: p.Pro522Arg, P = 5.38 × 10<sup>-10</sup>, odds ratio (OR) = 0.68, minor allele frequency (MAF)<sub>cases</sub> = 0.0059, MAF<sub>controls</sub> = 0.0093), a risk variant in ABI3 (rs616338: p.Ser209Phe, P = 4.56 × 10<sup>-10</sup>, OR = 1.43, MAF<sub>cases</sub> = 0.011, MAF<sub>controls</sub> = 0.008), and a new genome-wide significant variant in TREM2 (rs143332484: p.Arg62His, P = 1.55 × 10<sup>-14</sup>, OR = 1.67, MAF<sub>cases</sub> = 0.0143, MAF<sub>controls</sub> = 0.0089), a known susceptibility gene for Alzheimer's disease.
We found that, in the progressive mild cognitive impairment group, rs5978930 was associated with total tau levels and rs16947151 was associated with cognitive function scores at baseline and over time, suggesting that ABI3 variants may be associated with cognitive decline and may influence AD onset through tau pathology.