Journal Article

Translating RNA sequencing into clinical diagnostics: opportunities and challenges

Carpten, John D., Byron, Sara A., Van Keuren-Jensen, Kendall R., Engelthaler, David M., Craig, David W.

2016

Overview

Key Points RNA-based measurements have the potential for application across diverse areas of human health, including disease diagnosis, prognosis and therapeutic selection. Current clinical applications include infectious diseases, cancer, transplant medicine and fetal monitoring. RNA sequencing (RNA-seq) allows for the detection of a wide variety of RNA species, including mRNA, non-coding RNA, pathogen RNA, chimeric gene fusions, transcript isoforms and splice variants, and provides the capability to quantify known, pre-defined RNA species and rare RNA transcript variants within a sample. In addition to differential expression and detection of novel transcripts, RNA-seq also supports the detection of mutations and germline variation for hundreds to thousands of expressed genetic variants, facilitating assessment of allele-specific expression of these variants. Circulating RNAs and small regulatory RNAs, such as microRNAs, are very stable. These RNA species are vigorously being tested for their potential as biomarkers. However, there are currently few agreed upon methods for isolation or quantitative measurements and a current lack of quality controls that can be used to test platform accuracy and sample preparation quality. Analytical, bioinformatic and regulatory challenges exist, and ongoing efforts toward the establishment of benchmark standards, assay optimization for clinical conditions and demonstration of assay reproducibility are required to expand the clinical utility of RNA-seq. RNA sequencing (RNA-seq) is a powerful approach for comprehensive analyses of transcriptomes. This Review describes the widespread potential applications of RNA-seq in clinical medicine, such as detecting disease-associated mutations and gene expression disruptions, as well as characteristic non-coding RNAs, circulating extracellular RNAs or pathogen RNAs. The authors also highlight the challenges in adopting RNA-seq routinely into clinical practice. With the emergence of RNA sequencing (RNA-seq) technologies, RNA-based biomolecules hold expanded promise for their diagnostic, prognostic and therapeutic applicability in various diseases, including cancers and infectious diseases. Detection of gene fusions and differential expression of known disease-causing transcripts by RNA-seq represent some of the most immediate opportunities. However, it is the diversity of RNA species detected through RNA-seq that holds new promise for the multi-faceted clinical applicability of RNA-based measures, including the potential of extracellular RNAs as non-invasive diagnostic indicators of disease. Ongoing efforts towards the establishment of benchmark standards, assay optimization for clinical conditions and demonstration of assay reproducibility are required to expand the clinical utility of RNA-seq.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 631/1647/2217/2218 / 631/1647/514/2254 / 631/208/191/2018 / 631/208/212/2019 / 631/208/2489/144/68 / 631/208/514/1949 / 631/326/421 / 631/337/384 / 692/308/53/2421 / Agriculture / Alternative splicing / Animal Genetics and Genomics / Biomedicine / Cancer Research / Computational Biology - methods / Diagnostic Tests, Routine - methods / Disease - genetics / Fetal monitoring / Fetuses / Gene expression / Gene Expression Profiling / Gene Function / Genetic diversity / High-Throughput Nucleotide Sequencing - methods / Human Genetics / Humans / Infectious diseases / Isoforms / Methods / miRNA / Molecular diagnostic techniques / Mutation / Non-coding RNA / Pathogens / Rare species / review-article / RNA - genetics / RNA sequencing / Sequence Analysis, RNA - methods / Transcriptomes