Cell-type-specific subtyping of epigenomes improves prognostic stratification of cancer.

ABSTRACT:

Background

Most molecular classifications of cancer are based on bulk-tissue profiles that measure an average over many distinct cell types. As such, cancer subtypes inferred from transcriptomic or epigenetic data are strongly influenced by cell-type composition and do not necessarily reflect subtypes defined by cell-type-specific cancer-associated alterations, which could lead to suboptimal cancer classifications.

Methods

To address this problem, we here propose the novel concept of cell-type-specific combinatorial clustering (CELTYC), which aims to group cancer samples by the molecular alterations they display in specific cell types. We illustrate this concept in the context of DNA methylation data of liver and kidney cancer, deriving in each case novel cancer subtypes and

SUBMITTER: Luo Q 

PROVIDER: S-EPMC11967111 | biostudies-literature | 2025 Apr

REPOSITORIES: biostudies-literature