Transcriptomics in cancer diagnostics: developments in technology, clinical research and commercialization

Abstract

Transcriptomic technologies are evolving to diagnose cancer earlier and more accurately to provide greater predictive and prognostic utility to oncologists and patients. Digital techniques such as RNA sequencing are replacing still-imaging techniques to provide more detailed analysis of the transcriptome and aberrant expression that causes oncogenesis, while companion diagnostics are developing to determine the likely effectiveness of targeted treatments. This article examines recent advancements in molecular profiling research and technology as applied to cancer diagnosis, clinical applications and predictions for the future of personalized medicine in oncology.

KEYWORDS:

• Transcriptomics
• molecular diagnostics
• companion diagnostics
• personalized medicine
• cancer
• microarray
• serial analysis of gene expression (SAGE)
• RNA sequencing
• quantitative reverse transcription PCR (RT-qPCR)

Key issues

• RNA-Seq produces gene expression profiles comparable to DNA microarrays and is better suited for novel gene expression signature discovery, however, RNA-Seq is currently less prevalent due to cost and data storage issues.

• Gene expression profiles have been shown to be good predictors of response to and need for chemotherapy.

• Commercial gene expression signature diagnostic tests are available for many cancer types, including breast, colorectal, prostate and lung cancers.

• While some companies have successfully commercialized such tests, there are still many barriers to commercialization including biomarker selection, FDA regulation, cost and insurance coverage.

• Commercial companies have created diagnostic tests include Genomic Health’s Oncotype DX, Agendia’s MammaPrint Breat Cancer Recurrence Test, Sividon Diagnostics’ Endopredict and Nanostring Technologies’ Prosigna Breast Cancer Prognostic Gene Signature Assay.

• The success of gene expression profiles hinges on the assumption that more knowledge about the transcriptome can lead to earlier and more accurate diagnosis of disease subtypes as well as the development of targeted therapeutics.

• We predict that within 5 years most oncology patients will receive molecular diagnostic testing as clinical value, commercialization and physician adoption increase.

Financial & competing interests disclosure

The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.