Evaluating cell type deconvolution in FFPE breast tissue: application to benign breast disease.

ABSTRACT: Transcriptome profiling using RNA sequencing (RNA-seq) of bulk formalin-fixed paraffin-embedded (FFPE) tissue blocks is a standard method in biomedical research. However, when used on tissues with diverse cell type compositions, it yields averaged gene expression profiles, complicating biomarker identification due to variations in cell proportions. To address the need for optimized strategies for defining individual cell type compositions from bulk FFPE samples, we constructed single-cell RNA-seq reference data for breast tissue and tested cell type deconvolution methods. Initial simulation experiments showed similar performances across multiple commonly used deconvolution methods. However, the introduction of FFPE artifacts significantly impacted their performances, with a root mean squar

SUBMITTER: Liu Y 

PROVIDER: S-EPMC11952925 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature