Custom Targeted RNA Sequencing of FFPE Biopsy Specimens | GenomeWeb
September 15, 2016
Sponsored by
Agilent Technologies

Custom Targeted RNA Sequencing of FFPE Biopsy Specimens


Associate Professor of Pathology & Laboratory Medicine and Biomedical Informatics, Emory University

This webinar discussed a customized protocol for RNA sequencing that was developed enable focused RNAseq analysis of formalin-fixed paraffin-embedded biopsies for biomarker discovery in prostate cancer.

Our speaker, Carlos Moreno, Associate Professor of Pathology & Laboratory Medicine and Biomedical Informatics at Emory University, provided an overview of a custom RNA-seq panel his team developed using the Agilent SureSelect capture system.

In previous work, Dr. Moreno and colleagues used FFPE-derived radical prostatectomy RNA samples to identify a set of 24 mRNAs that could be used to discriminate between prostate cancer with and without biochemical recurrence (BCR) using whole transcriptome RNA-seq analysis. However, a more relevant point to assay for biomarkers is at the point of positive biopsy to ascertain whether active surveillance is needed.

To enable focused RNA-seq analysis of FFPE biopsies, Dr. Moreno and his team developed a customized protocol using the Agilent SureSelect capture system. So far, they have successfully sequenced a panel of 295 genes using FFPE RNA from 102 biopsies and 24 matching prostatectomies. Analysis of biopsy and prostatectomy-derived RNAseq data indicates that the data from both sources are strongly correlated. Analysis of multiple biopsies from the same source was able to detect a change in RNA signal due to tumor heterogeneity. The 256 gene panel also detected differences between African-American and Caucasian prostate cancer samples.

Dr. Moreno outlined the details of this work, which indicated that targeted RNA-seq of FFPE biopsies is feasible, increasing the available tissue resources for biomarker discovery.

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