Given that APOE is one of the most important genetic risk factors for Alzheimer’s disease, we leveraged publicly available RNA-sequencing data from the Religious Orders Study and Memory and Aging Project (ROSMAP) studies to quantify the usage of the intron-3 retaining transcript of APOE in post-mortem dorsolateral prefrontal cortex brain tissue derived from individuals with Alzheimer’s disease (n = 222) and mild cognitive impairment (MCI) (n = 158) compared to control individuals (defined as the final clinical diagnosis blinded to pathological findings, n = 202). This evidence concerns the gene APOE and early-onset autosomal dominant Alzheimer disease.