Multiplexed transcriptome analysis to detect ALK, ROS1 and RET rearrangements in lung cancer

Toni-Maree Rogers,Andrew P Fellowes,Yvette Emmanuel,Stephen Huang,Georgina L Ryland,Omar D Perez,Stephen B Fox,Gisela Mir Arnau,Maruja E Lira,Stephen Q Wong,Darryl Irwin

doi:10.1038/srep42259

Toni-Maree Rogers, Andrew P Fellowes + Show 9 more

Open Access

https://doi.org/10.1038/srep42259

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Abstract

ALK, ROS1 and RET gene fusions are important predictive biomarkers for tyrosine kinase inhibitors in lung cancer. Currently, the gold standard method for gene fusion detection is Fluorescence In Situ Hybridization (FISH) and while highly sensitive and specific, it is also labour intensive, subjective in analysis, and unable to screen a large numbers of gene fusions. Recent developments in high-throughput transcriptome-based methods may provide a suitable alternative to FISH as they are compatible with multiplexing and diagnostic workflows. However, the concordance between these different methods compared with FISH has not been evaluated. In this study we compared the results from three transcriptome-based platforms (Nanostring Elements, Agena LungFusion panel and ThermoFisher NGS fusion panel) to those obtained from ALK, ROS1 and RET FISH on 51 clinical specimens. Overall agreement of results ranged from 86–96% depending on the platform used. While all platforms were highly sensitive, both the Agena panel and Thermo Fisher NGS fusion panel reported minor fusions that were not detectable by FISH. Our proof–of–principle study illustrates that transcriptome-based analyses are sensitive and robust methods for detecting actionable gene fusions in lung cancer and could provide a robust alternative to FISH testing in the diagnostic setting.

Highlights

Lung cancer remains one of the major causes of cancer mortality in both men and women worldwide[1]
Subsequent studies have reported anaplastic lymphoma kinase (ALK) rearrangements occurring in 3–5% of non-small cell lung cancer (NSCLC), where they are associated with younger patients who have a light or no smoking history[9]
All samples were tested by Fluorescence In Situ Hybridization (FISH) (Table 1) for ALK, ROS1 and RET as part of routine diagnostic testing at the Peter MacCallum Cancer Centre Pathology Department

Summary

Introduction

Lung cancer remains one of the major causes of cancer mortality in both men and women worldwide[1]. Structural genomic rearrangements involving the anaplastic lymphoma kinase (ALK) gene have been identified in NSCLCs. The most common rearrangement, occurring between ALK and echinoderm microtubule-associated protein-like 4 (EML4), is an inversion event resulting in the fusion of the 5′end of EML4 to the 3′end of ALK, leading to constitutive kinase activity and malignant growth[4]. Occurs after a negative FISH result can waste time and valuable material This is pertinent in limited lung cancer clinical specimens where the starting material is often limited to a core needle biopsy. Other techniques such as immunohistochemistry (IHC) and reverse transcription-polymerase chain reaction (RT-PCR) exist, are used with varying frequencies for ALK, RET and ROS1 fusion detection depending on the laboratory’s acceptance of the analytical performance of the test[15,16]

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