PRISM: recovering cell-type-specific expression profiles from individual composite RNA-seq samples.

ABSTRACT:

Motivation

A major challenge in analyzing cancer patient transcriptomes is that the tumors are inherently heterogeneous and evolving. We analyzed 214 bulk RNA samples of a longitudinal, prospective ovarian cancer cohort and found that the sample composition changes systematically due to chemotherapy and between the anatomical sites, preventing direct comparison of treatment-naive and treated samples.

Results

To overcome this, we developed PRISM, a latent statistical framework to simultaneously extract the sample composition and cell-type-specific whole-transcriptome profiles adapted to each individual sample. Our results indicate that the PRISM-derived composition-free transcriptomic profiles and signatures derived from them predict the patient response better than the compo

SUBMITTER: Hakkinen A 

PROVIDER: S-EPMC8479664 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature