ASTWAS: modeling alternative polyadenylation and SNP effects in kernel-driven TWAS reveal novel genetic associations for complex traits

Alternative polyadenylation (APA) of $3^{\prime}$untranslated regions ($3^{\prime}$UTRs) is a pervasive mechanism that regulates mRNA stability, localization, and translational efficiency by generating isoforms with distinct $3^{\prime}$UTR lengths and regulatory element composition. Despite its critical role in fine-tuning gene expression, APA has been largely overlooked in transcriptome-wide association studies (TWAS), which traditionally rely on linear models of SNP effects. To bridge this gap, we developed ASTWAS, a two-stage framework that first trains APA usage prediction models (BLUP, Elastic Net, LASSO, and TOP1) to quantify SNP impacts on distal poly(A) site choice via the percentage of distal poly(A) site usage index, and then aggregates weighted SNP effects within a kernel method to capture both linear and nonlinear genetic interactions. In extensive simulations spanning additive, epistatic, heterogeneous, compensatory, and single-variant architectures under both pleiotropy and causality scenarios, ASTWAS shows higher statistical power than linear APA-TWAS ($3^{\prime}$aTWAS), especially at low heritability and in the presence of SNP interactions. Applied to WTCCC type 1 diabetes and rheumatoid arthritis cohorts, ASTWAS not only rediscovers known susceptibility genes but also suggests novel candidates (e.g. GABBR1, RGL2) that form coherent interaction modules and enrich immune-related pathways, underscoring the biological significance of our algorithm in complex trait genetics. ASTWAS is implemented in Python and freely available at https://github.com/wl-Simplecss/ASTWAS.