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Related Experiment Video

Updated: May 22, 2025

Single-cell RNA Sequencing and Analysis of Human Pancreatic Islets

Single-cell RNA Sequencing and Analysis of Human Pancreatic Islets

Published on: July 18, 2019

Variation in bulk RNA-seq and estimated cell type proportion using deconvolution when comparing pancreatic cancer

Rick J Jansen¹, Sarah A Munro², Samuel O Antwi³

¹Masonic Cancer Center, University of Minnesota, Minneapolis, MN.

Medrxiv : the Preprint Server for Health Sciences

|May 19, 2025

Summary

Tumor gene expression analysis may vary between patient samples, impacting personalized cancer treatment. Multiple tumor biopsies might be necessary for accurate genomic interpretation and effective treatment planning.

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Last Updated: May 22, 2025

Single-cell RNA Sequencing and Analysis of Human Pancreatic Islets

Single-cell RNA Sequencing and Analysis of Human Pancreatic Islets

Published on: July 18, 2019

Pancreatic Tissue Dissection to Isolate Viable Single Cells

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Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

Area of Science:

Oncology
Genomics
Bioinformatics

Background:

Genomic data holds promise for personalized cancer treatment.
Intratumor genetic heterogeneity necessitates understanding variations within a tumor.
Assessing gene expression across multiple tumor samples is crucial for treatment strategy.

Purpose of the Study:

To investigate if tumor gene expression analysis interpretation varies between two specimens from the same patient.
To compare cell type proportions and gene expression reliability across paired tumor samples.

Main Methods:

Bulk RNA-sequencing was performed on FFPE samples from 16 patients.
Three deconvolution methods were used to compare cell type proportions.
Transcripts per million normalization and batch effect adjustment were applied for gene expression comparison.

Main Results:

Significant variations in average cell type proportions were observed for NK cells and macrophages between samples.
No significant differences in average expression were found for selected key pancreatic cancer genes.
Concordance in gene expression measurements varied, with substantial agreement only for JUN.

Conclusions:

Findings suggest that multiple tumor samples may be required for effective cancer treatment planning.
Differences in observed expression values could be attributed to varying cell type proportions.
Further studies are needed to confirm interpretations due to small sample size and different sequencing technologies.