Bulk RNA-seq deconvolution heterogeneity across paired pancreatic cancer human samples.

ABSTRACT:

Introduction

There is great promise in using genomic data to inform individual cancer treatment plans. Assessing intratumor genetic heterogeneity, studies have shown it may be possible to target biopsies to tumor subclones driving disease progression or treatment resistance. Here, we explore if the interpretation of tumor gene expression analysis varies across two specimens from the same patient.

Material and methods

We performed bulk RNA-seq using FFPE samples from 16 patients who also had a previous separate bulk RNA-seq performed and deposited in TCGA. We used three different deconvolution methods to compare cell type proportions for these paired data. We normalized study-specific gene expression values per gene by calculating transcripts per million and adjusted for batc

SUBMITTER: Jansen RJ 

PROVIDER: S-EPMC12702501 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature