Robust gene expression and mutation analyses of RNA-sequencing of formalin-fixed diagnostic tumor samples

Abstract

Current genomic studies are limited by the availability of fresh tissue samples. Here, we show that Illumina RNA sequencing of formalin-fixed diagnostic tumor samples produces gene expression that is strongly correlated with matched frozen tumor samples (r > 0.89). In addition, sequence variations identified from FFPE RNA show 99.67% concordance with that from exome sequencing of matched frozen tumor samples. Because FFPE is a routine diagnostic sample preparation, the feasibility results reported here will facilitate the setup of large-scale research and clinical studies in medical genomics that are currently limited by the availability of fresh frozen samples.

Exome-capture RNA sequencing of decade-old breast cancers and matched decalcified bone metastases

“…This study reinforces and should encourage the use of capture-hybridization approaches to sequence RNA from retrospectively collected, low-yield, highly degraded, and decalcified archival specimens (Supplemental Table 14 and refs. [22][23][24]. Expanding sample sets and modalities for genomewide characterization, especially for rare specimen cohorts that may be impractical to obtain prospectively in large numbers, will accelerate translational discoveries.…”

“…In light of this, new capture-based methods of nucleic acid sequencing on aged FFPE specimens have shown efficacy in identifying DNA variants and even guiding care in academic centers (19)(20)(21). Exome-capture RNA sequencing (ecRNA-seq) is less well characterized in aged tumor samples, although recent studies on FFPE specimens have shown promising expression correlations with flash-frozen tissues (22)(23)(24).…”

Understanding the Effectiveness of Natural Compound Mixtures in Cancer through Their Molecular Mode of Action

“…Whole transcriptome sequencing comprehensively investigates messenger RNA (mRNA)-Seq and small/non-coding RNA-sequencing (RNA-Seq), analyzing tens of thousands of RNA transcripts to uncover their genetic functions. Transcriptomic results subjected to Gene Ontology (GO) clustering and annotation identify differentially expressed genes and can further identify candidate target pathways [16]. Here we highlight the efficacy of complex natural compound mixtures by using molecular approaches with specific emphasis on cancer apoptosis and chemosensitization.…”

Altered expression of major immune regulatory molecules in peripheral blood immune cells associated with breast cancer

“…Recently, biomarker analysis of immune cells was reported in the cancer microenvironment: TILs by immunohistochemistry, tumor digestion, and gene expression analysis of formalin-fixed and paraffin-embedded tissue samples, and flow cytometry analysis of immune checkpoint-related protein expression including inhibitory and activation molecules [13][14][15][16]. Additionally, PD-L1 expression by TILs rather than tumor cells was shown to be more predictive of the response to PD-1 pathway blockade [11,12].…”