Gene Expression Analysis Platform Evaluation for FFPE Specimen Material-Based Studies

Email Principal Investigator
Assay Development

Mateusz Koptyra

Children’s Hospital of Philadelphia
Philadelphia, PA, USA

CBTN Specimen


CBTN Participants


CHOP Center for Data-Driven Discovery in Biomedicine

About this


Understanding pediatric brain cancers and developing new treatments requires constant innovation. In this project, researchers have developed a new technology for the analysis of tumor RNA, particularly mRNA, the strands of RNA that carry messages through a cell. This new method is called the HTG EdgeSeq technology pipeline for mRNA and/or miRNA profiling. HTG technology is able to detect the expression of 2568 genes from different sample types. HTG EdgeSeq is usable for small clinical specimens and according to the manufacturer it requires only a small amount of sliced tissue (formalin-fixed paraffin-embedded or FFPE) to obtain quality mRNA profiling. Researchers will analyze FFPE material from primitive neuroectodermal tumors, high grade gliomas, and medulloblastoma samples using HTG Oncology Biomarker Panel. To assess the HTG system’s ability to profile mRNA from FFPE, researchers are looking to analyze samples that have already undergone RNA sequencing. The Children’s Brain Tumor Network provides a unique resource of FFPE samples where RNAsequencing, an analysis of the RNA in a sample, was already completed. By comparing CBTN data with results from this work, researchers can validate their new RNA analysis platform appropriately. Potential implementation of such technology in the center may allow to obtain the quality data from highly degraded, and of very limited availability material specimens.

Ask The


Ask the scientists

What are the goals of this project?

Researchers will use CBTN samples to assess whether the HTG system can properly profile mRNA from FFPE.

What is the impact of this project?

This technology could allow for the extraction of high quality data from even highly degraded or limited specimen samples, advancing the field of cancer biology.

Why is the CBTN request important to this project?

The Children’s Brain Tumor Network already conducted RNA sequencing on samples provided to this project. Use of such samples will allow researchers to verify the usefulness of HTG technology for this purpose.

Specimen Data

The Children's Brain Tumor Network contributed to this project by providing slides for the generation of miRNAseq data.

Explore the data in these informatics portals