teff: estimation of Treatment EFFects on transcriptomic data using causal random forest

Abstract

Motivation: Causal inference on high-dimensional feature data can be used to find a profile of patients who will benefit the most from treatment rather than no treatment. However, there is a need for usable implementations for transcriptomic data. We developed teff that applies random causal forest on gene expression data to target individuals with high expected treatment effects. Results: We extracted a profile of high benefit of treating psoriasis with brodalumab and observed that it was associated with higher T cell abundance in non-lesional skin at baseline and a lower response for etanercept in an independent study. Individual patient targeting with causal inference profiling can inform patients on choosing between treatments before the intervention begins. Availability and implementation: teff is an R package available at https://teff-package.github.io. The data underlying this article are available in GEO, at https://www.ncbi.nlm.nih.gov/geo/.