J Cancer 2018; 9(13):2249-2265. doi:10.7150/jca.24744

Review

Gene Expression Detection Assay for Cancer Clinical Use

Shavira Narrandes1,2, Wayne Xu1,2,3✉

1. Departments of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada;
2. Research Institute of Oncology and Hematology, CancerCare Manitoba, Winnipeg, Canada;
3. College of Pharmacy, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada.

Abstract

Cancer is a genetic disease where genetic variations cause abnormally functioning genes that appear to alter expression. Proteins, the final products of gene expression, determine the phenotypes and biological processes. Therefore, detecting gene expression levels can be used for cancer diagnosis, prognosis, and treatment prediction in a clinical setting. In this review, we investigated six gene expression assay systems (qRT-PCR, DNA microarray, nCounter, RNA-Seq, FISH, and tissue microarray) that are currently being used in clinical cancer studies. Some of these methods are also commonly used in a modified way; for example, detection of DNA content or protein expression. Herein, we discuss their principles, sample preparation, design, quantification and sensitivity, data analysis, time for sample preparation and processing, and cost. We also compared these methods according to their sample selection, particularly for the feasibility of using formalin-fixed paraffin-embedded (FFPE) samples, which are routinely archived for clinical cancer studies. We intend to provide a guideline for choosing an assay method with respect to its oncological applications in a clinical setting.

Keywords: gene expression, assay, cancer, clinical use, qRT-PCR, DNA microarray, nCounter, RNA-Seq, FISH, tissue microarray

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How to cite this article:
Narrandes S, Xu W. Gene Expression Detection Assay for Cancer Clinical Use. J Cancer 2018; 9(13):2249-2265. doi:10.7150/jca.24744. Available from http://www.jcancer.org/v09p2249.htm