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RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

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Updated: May 12, 2025

Detection of a Circulating MicroRNA Custom Panel in Patients with Metastatic Colorectal Cancer

Detection of a Circulating MicroRNA Custom Panel in Patients with Metastatic Colorectal Cancer

Published on: March 14, 2019

Detection of Circulating mRNA Variants in Hepatocellular Carcinoma Patients Using Targeted RNAseq.

Daniel Zezulinski¹, Maarouf A Hoteit², David E Kaplan^2,3

¹Baruch S. Blumberg Institute, Doylestown, PA, USA.

|May 7, 2025

Summary

Circulating tumor mRNA variants show promise for early hepatocellular carcinoma (HCC) detection. A panel of 36 specific variants accurately identified all HCC patients in a new study, highlighting their clinical potential.

Keywords:

Circulating RNA variants Early- and late-stage hepatocellular carcinoma Indel and bidirectional fusion variants SNP Targeted RNAseq

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A Blood-based Test for the Detection of ROS1 and RET Fusion Transcripts from Circulating Ribonucleic Acid Using Digital Polymerase Chain Reaction

A Blood-based Test for the Detection of ROS1 and RET Fusion Transcripts from Circulating Ribonucleic Acid Using Digital Polymerase Chain Reaction

Published on: April 5, 2018

Area of Science:

Oncology
Molecular Biology
Biomarker Discovery

Background:

Circulating nucleic acids are explored as biomarkers for hepatocellular carcinoma (HCC) detection.
Circulating tumor mRNA and its mutants (ctmutRNA) are less understood compared to DNA and microRNA.
Previous work identified 288 potential HCC-selective ctmutRNA variants.

Purpose of the Study:

To validate the specificity and sensitivity of previously identified HCC-selective ctmutRNA variants.
To assess these variants in an independent cohort of patients with liver cirrhosis (LC).

Main Methods:

Targeted RNA sequencing was employed to analyze plasma samples from HCC and LC patients.
RNA was isolated from small extracellular vesicles, and specific primers were used for 288 ctmutRNA candidates.
Variant calling and annotation were performed using GATK HaplotypeCaller and snpEff.

Main Results:

75 of the original 288 ctmutRNA candidates were detected in the new cohort.
388 additional variants were found in HCC but not LC plasma samples.
A subset of 36 HCC-selective variants successfully identified all HCC patients, with Indels and SNPs being most common. Novel mRNA fusions were also identified.

Conclusions:

Circulating RNA is a robust analyte for noninvasive early detection of HCC.
Circulating RNA panels offer powerful tools for the clinical management of HCC.