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

Email Principal Investigator

Mateusz Koptyra

Children’s Hospital of Philadelphia
Philadelphia, PA, USA

CBTN Participants

CBTN Data Used


CHOP Center for Data-Driven Discovery in Biomedicine

About this


This project aims to validate a novel RNA analysis platform. FFPE tissue material will be processed by the HTG EdgeSeq technology pipeline for mRNA and/or miRNA profiling.

The HTG EgdeSeq system is an automated chemistry and workflow solution based on the HTG Molecular Diagnostics’ (HTG) extraction-free sample preparation technology and quantitative nuclease protection chemistry. HTG technology does not require RNA extraction for the samples tested and is able to detect expression of 2568 genes from different sample types. HTG EdgeSeq is amenable to small clinical specimens and according to the manufacturer it requires only few square millimeters of 5µm sliced tissue (FFPE) to obtain quality mRNA profiling

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What are the goals of this project?

Analyze FFPE material from PNET/HGG and medulloblastoma samples using HTG Oncology Biomarker Panel. To analyze capability of HTG system to profile mRNA from FFPE, we choose to analyze samples for which RNA-Seq data is available in the CBTN. Material obtained from FFPE samples will be processed with HTG pipeline for mRNA profiling using Oncology Biomarker Panel consisting of more than 2500 genes.

What is the impact of this project?

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.

Why the CBTN request is important to this project?

CBTN provides a unique resource of FFPE samples where RNAseq was already completed on RNA extracted from flash frozen tissue. This will allow for an evaluation of this resource.

Specimen Data

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

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