A robust workflow to benchmark deconvolution of multi-omic data

Abstract

Tumour heterogeneity significantly affects cancer progression and therapeutic response, yet quantifying it from bulk molecular data remains challenging. Deconvolution algorithms, which estimate cell-type proportions in bulk samples, offer a potential solution. However, there is no consensus on the optimal algorithm for transcriptomic or methylomic data. Here, we present an unbiased evaluation framework for the first comprehensive comparison of deconvolution algorithms across both omic types, including reference-based and -free approaches. Our evaluation covers raw performance, stability, and computational efficiency under varying conditions, such as missing or additional cell types and diverse sample compositions. We apply this framework across multiple benchmark datasets, including a novel multi-omics dataset generated specifically for this study. To ensure transparency and re-usability, we have designed a reproducible workflow using containerization and publicly available code. Our results highlight the strengths and limitations of various algorithms, and provides practical guidance for selecting the best method based on data type and analysis context. This benchmark sets a new standard for evaluating deconvolution methods and analysing tumour heterogeneity.