iSubGen: Integrative Subtype Generation by Pairwise Similarity Assessment

Abstract

There are myriad types of biomedical data- genetics, transcriptomics, clinical, imaging, wearable devices and many more. When a group of patients with the same underlying disease exhibit similarities across multiple types of data, this is called a subtype. Disease subtypes can reflect etiology and sometimes predict clinical behaviour. Existing subtyping approaches struggle to simultaneously handle multiple diverse data types, particularly when there is missing information, as is common in most real-world clinical datasets. To improve subtype discovery, we exploited changes in the correlation-structure between different data types to create iSubGen, an algorithm for integrative subtype generation. iSubGen can combine arbitrary data types for subtype discovery, such as merging molecular, mutational signature, pathway and micro-environmental data. iSubGen recapitulates known subtypes across multiple diseases, even in the face of substantial missing data. It identifies groups of patients with divergent clinical outcomes, and can combine arbitrary data types for subtype discovery, such as merging molecular, mutational signature, pathway and micro-environmental data. iSubGen can accommodate any feature that can be compared with a similarity-metric, and provides a versatile approach for creating subtypes. It is available at https://CRAN.R-project.org/package=iSubGen.