RNA-based NGS – the best way to identify NTRK gene fusion

Date：2020-09-02

How to identify NTRK gene fusions?

IHC testing vs FISH testing vs RT-PCR testing vs NGS testing

NTRK gene fusions can serve as biomarkers for pan-cancer TRK inhibitors. Using biomarker-driven companion diagnostics, clinicians are able to predict the effects of targeted agents against those rare genetic mutations that are potentially tumorigenic across pan-cancer. Immunohistochemistry (IHC), Fluorescence in situ hybridization (FISH), Reverse Transcription Polymerase Chain Reaction (RT-PCR), and Next-generation Sequencing (NGS) testing are commonly used to identify NTRK gene fusions.

The IHC method visualizes the expression of cancer-related protein in cancer tissue. The FISH method uses multi-coloured fluorescent probes to detect break points in a gene. The RT-PCR method amplifies known RNA fusion transcripts for subsequent detection. The NGS technology is a massively parallel method that can sequence both known and novel gene fusions.

Here is a comparison summary table for different methods:

	Detection	Pros	Cons
IHC method	TRK protein expression, which is potentially driven by NTRK gene fusions	Rapid results Low costs	TRK proteins are also expressed in rapid-growing tissues without the presence of NTRK gene fusions Cannot determine fusion partners and breakpoints
FISH method	Translocations, amplifications, or deletions on chromosomes	Rapid results Low costs	Cannot determine fusion partners and breakpoints Requires extra works from experienced and qualified pathologists to carefully interpret the test results
RT-PCR method	Fusion transcripts with specific NTRK gene fusion combinations	A relatively sensitive test Available in most molecular genetic laboratories	Cannot detect novel fusion partners Difficult to amplify across large introns
NGS testing	Fusions partners and positions among any NTRK genes	Comprehensive and high throughput Potential for multiplexed testing	Relatively expensive

Why we should consider RNA-based NGS to identify NTRK gene fusions?

Both RNA-based and DNA-based NGS are capable of multiplexed assessment for different fusion targets. However, RNA-based NGS is preferred for identifying NTRK gene fusions, due to its capability to detect expressed fusion transcripts directly, with more accurate breakpoint readout. RNA-based NGS avoids the difficulties of sequencing larger intronic regions associated with NTRK gene fusions. It also has a faster sequencing process compare to DNA-based NGS. Its detection accuracy can vary depending on the choice of library preparation methods, for example, hybridization-based capture or amplicon-based approach.

Why choose Codex for NGS testing?

Codex provides comprehensive cancer screening using next-generation sequencing (NGS) technology, which helps identify genetic mutations associated with 523 cancer-related genes and 9 types of cancer. The CoGenesis® Bioinformatics platforms allow comprehensive and accurate profiling for data analysis. It provides AI-assisted matching of genomic variants. The platform is fully scalable with shortened computation time. It improves the query performance of complex biological queries.

Codex’s laboratory is using the latest sequencer – Illumina NextSeq 2000, for next-generation sequencing (NGS). It simplifies sequencing workflows and minimizes the need for additional resources. Therefore, sequencing turnaround time is reduced.

Codex Genetics applies a DNA and RNA hybridization-based approach for detecting a broad range of NTRK gene fusions. This approach allows us to detect a larger number of genes and genomic regions, while offering a high level of sensitivity for detecting fusions with novel fusion partners.

#NTRK #NGS #pan-cancer