the models to correct for the Braak stages and observed a significant association for the relative proportion of neurons with the APOE ε4 allele in the Knight-ADRC dataset (β = − 0.06; p = 3.66 × 10−02; Table 4) and a significant association for the relative proportion of astrocytes in the MSBB (β = 0.04; p = 4.89 × 10−02; Table 4). Furthermore, we performed a meta-analysis to combine the evidence of both studies and observed a significant association of the relative neuronal proportion with APOE ε4 allele (p = 1.86 × 10−02) and marginally significant association for the relative astrocytic relative proportion (p = 0.09).Table 4Gene-specific cellular proportion analysis for Knight-ADRC and Mount Sinai Brain Bank studiesVariant carriersSample sizeNeuronAstrocyteOligodendrocyteMicroglia n Effectp valueEffectp valueEffectp valueEffectp valueKnight-ADRC PLD3 vs Control49− 0.11.6 × 10−040.132.84 × 10−03− 0.036.17 × 10−027.05 × 10−047.89 × 10− 01 TREM2 vs Control36− 0.077.93 × 10−020.111.05 × 10−02− 0.034.9 × 10−021.65 × 10−035.84 × 10− 01 Sporadic AD vs Control45− 0.115.45 × 10−030.132.95 × 10−04− 0.024.55 × 10−01− 3.48 × 10−031.13 × 10−01 APOEε4+ vs APOEε4- LOAD cases & controls100− 0.062.11 × 10−020.055.35 × 10−020.013.72 × 10−01− 8.09 × 10−046.31 × 10−01 APOEε4+ vs APOEε4- LOAD cases only84−
