RNA Sequencing of Cancer Biopsy Specimens: new research demonstrates robustness for use in a clinical decision-making setting

A recent study published in Nature’s Scientific Reports has shown that progress continues to advance in precision medicine, this time at the intersection of tumor biopsy tissue and RNA sequencing.

Two of the often-cited obstacles to practical applications of precision medicine are the availability of patient tumor tissue after biopsy, and the methods of preserving that tissue for genomic analysis — in particular transcriptome profiling, also known as  RNA sequencing

Formalin‑Fixed Paraffin‑Embedded (FFPE) is one of the most routine ways to store biopsy specimens: the tissue is fixed in formalin and embedded in blocks of paraffin. While extracting RNA from FFPE tissue samples is known to be difficult as the RNA can degrade, several FDA-approved assays, such as Mammaprint and Oncotype DX do so successfully.

In the study which was prepared via a collaboration between NantHealth, NantOmics, and ImmunityBio, researchers have compared different methodologies to extract RNA from FFPE clinical samples (e.g. Poly-A, and ribo-depletion), and how much it may influence gene expression levels of clinically relevant genes. By comparing it with data from fresh/frozen samples (FF), they concluded that, despite the fact that the extraction methods may lead to differences in gene expression levels of histone transcripts, exome coverage was highly concordant in direct FFPE and FF replicates, with 98% agreement in coding exon coverage and a median correlation of whole transcriptome profiles of 0.95.

These results are in agreement with another recent study published in the JCO Precision Oncology, which also concluded that FFPE samples can be used to generate high quality RNA-seq data, especially if ribo-depletion protocols are employed, and the downstream analysis has a heavy focus on protein-coding genes.

Therefore, both of these studies seem to support the notion that FFPE-derived RNA sequencing is reproducible, robust, and consistent with whole transcriptome profiling from FF, and could be used in a clinical decision-making setting.

Finally, according to NantHealth

“The study also demonstrates that RNA sequencing is not only clinically viable but valuable and can provide a more thorough understanding of what genes are driving each individual patient’s tumor to better inform personalized treatment decisions.”


As evidenced in the WINTHER trial (Nature Med, April 2019), RNA analysis surfaces actionable data and gives patients and their oncologists the tools to make better treatment decisions about advanced cancers whose biomarkers are hiding in plain sight. 

RNA sequencing in the clinical setting is becoming a valuable asset, providing oncologists and their patients with sharper tools to improve efforts at identifying the origin of those cancers known as “of unknown primary,” as well as determine optimal, personalized treatment protocols.

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