Following alignment and quantification of RNA-Seq reads, LeafCutter20 was applied to estimate “percent spliced in” values (PSI) for local alternative splicing events (Fig. 1). We identified 53,251 alternatively spliced intronic excision clusters in 16,557 genes. We report more alternatively spliced intron clusters in the cortex than any other tissues or brain regions previously analyzed21. To identify aberrant splicing events, we analyzed the association between the PSI of each intron excision event and a pathologic diagnosis of Alzheimer’s disease or quantitative measures of neuropathology including neuritic plaques (NP), neurofibrillary tangles (NFT), and amyloid-β burden, while accounting for confounding factors. At a False Discovery Rate (FDR) < 0.05, we identified a total of 82 differentially spliced introns in 67 genes associated with different neuropathologies including 5 with NP, 20 with amyloid, and 48 with NFT (Supplementary Table 2). A heat map of the top differentially spliced introns associated with NFT is shown in Fig. 2a. On average, these differentially excised introns explain ~2–13% of total variation in neuropathologic burden after accounting for biological and technical covariates (Fig. 2b; Supplementary Fig. 1).
