Efﬁcient Lung Cancer Molecular Diagnostics by Combining Next Generation Sequencing with Reﬂex Idylla Genefusion Assay Testing

Q: What diagnostic strategy does the study evaluate for lung cancer testing?

It evaluates combining DNA-only small-gene next-generation sequencing (<50 genes) with ultra-rapid reflex testing for common fusion transcripts using the Idylla Genefusion assay.

Q: How does the proposed approach affect upfront ALK/ROS1 fusion testing by FISH?

The study demonstrates that the combined workflow can largely negate the need for upfront ALK and ROS1 fusion testing by FISH for most cases.

Q: When is additional reflex testing recommended?

Additional reflex testing capability is needed for a small subset of specimens with rarer genetic aberrations, including rare single-nucleotide variants, indels, fusion transcripts, and secondary post-treatment resistance mutations.

Sep 24, 2026

Uploaded by Bintang

Molecular diagnostics for lung cancer is a well-established standard of care, yet selecting the most cost-effective use of available diagnostic tools remains unresolved. This study shows that DNA-only, small gene next-generation sequencing (sNGS) panels (<50 genes) combined with ultra-rapid reflex testing for common fusion transcripts using the Idylla Genefusion assay can provide a cost-effective and comprehensive testing approach for most lung cancer cases. It also outlines when additional reflex testing is needed for rarer variants, indels, fusion transcripts, and post-treatment resistance mutations, and suggests an adaptable workflow for other solid tumors with extensive profiles.

LanguageEnglish

CategoryHealthcare

FormatPDF

Pages10

Reading Time25 min

AccessFree to download

Abstract

Introduction

University of Rochester workflow and diagnostic modalities

Materials and Methods

Clinical specimens

Idylla gene fusion assay validation sample collection

Article Efﬁcient Lung Cancer Molecular Diagnostics by Combining Next Generation Sequencing with Reﬂex Idylla Genefusion Assay Testing Dingani Nkosi , Giby V. George, Huijie Liu, Meghan Buldo, Moises J. Velez and Zolt¡n N. Oltvai * Citation: Nkosi, D.; George, G.V.; Liu, H.; Buldo, M.; Velez, M.J.; Oltvai, Z.N. Efﬁcient Lung Cancer Molecular Diagnostics by Combining Next Generation Sequencing with Reﬂex Idylla Genefusion Assay Testing. Genes 2023, 14, 1551. [https://](https://)[ ](https://)[doi.org/10.3390/genes14081551](doi.org/10.3390/genes14081551) Academic Editors: Pawel Mroz, Bryan L. Betz and Charles Billington Received: 6 July 2023 Revised: 25 July 2023 Accepted: 27 July 2023 Published: 28 July 2023 Copyright: © 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ([https://](https://)[ ](https://)[creativecommons.org/licenses/by/](creativecommons.org/licenses/by/)[ ](creativecommons.org/licenses/by/)[4.0/](4.0/)) . Department of Pathology and Laboratory Medicine, School of Medicine & Dentistry, University of Rochester, Rochester, NY 14642, USA * Correspondence: [zoltan_oltvai@urmc.rochester.edu](zoltan_oltvai@urmc.rochester.edu); Tel.: +1-(585)-275-1883 Abstract: Molecular diagnostics for lung cancer is a well-established standard of care, but how to use the available diagnostic tools for optimal and cost-effective patient care remains unresolved. Here, we show that DNA-only, small gene next-generation sequencing (sNGS) panels (<50 genes) combined with ultra-rapid reﬂex testing for common fusion transcripts using the Idylla Genefusion assay provide a cost-effective and sufﬁciently comprehensive testing modality for the majority of lung cancer cases. We also demonstrate the need for additional reﬂex testing capability on larger DNA and fusion panels for a small subset of lung cancers bearing rare single-nucleotide variants, indels and fusion transcripts and secondary, post-treatment resistance mutations. A similar testing workﬂow could be adopted for other solid tumor types for which extensive gene/fusion variant proﬁles are available both in the treatment-naïve and post-therapy settings. Keywords: lung cancer; molecular diagnostics; next-generation sequencing; Idylla platform 1. Introduction More than 65% of patients diagnosed with advanced non-small cell lung cancer harbor actionable gene mutations, gene ampliﬁcations, or oncogenic fusion transcripts [1,2] . Consequentially, NGS-based tumor molecular proﬁling is now the standard of care for patients with advanced non-small cell lung cancer (NSCLC) [3–6] . Multiple genetic alterations have been identiﬁed as therapeutic targets in lung adenocarcinoma, including mutations in EGFR, ERBB2, BRAF, KRAS, and MET and rearrangements ofALK, RET, and ROS1 [4,5,7,8] . Moreover, several other oncogenes with potential prognostic roles in lung adenocarcinoma, including MET and PIK3CA, have also been described [7–9] . Currently, various diagnostic tools and platforms are being used in both academic and commercial pathology laboratory settings to proﬁle lung tumors. The modalities being used include ﬂuorescence in situ hybridization (FISH), immunohistochemistry (IHC), and next-generation sequencing (NGS) . However, the optimal combination(s) of the different diagnostic modalities to enhance timely yet cost effective patient care remains to be determined. Currently, as is the case in most academic laboratories, the University of Rochester Medical Center (URMC) molecular genetic pathology (MGP) unit (molecular diagnosticsand cytogenetics laboratories) utilizes both FISH and NGS to proﬁle actionable genomic mutations and rearrangements in lung cancer. In the present URMC workﬂow, parallel testing for ALK and ROS1 rearrangements is evaluated through FISH and the search for gene mutations and ampliﬁcations is conducted using

FAQs

What diagnostic strategy does the study evaluate for lung cancer testing?

It evaluates combining DNA-only small-gene next-generation sequencing (<50 genes) with ultra-rapid reflex testing for common fusion transcripts using the Idylla Genefusion assay.

How does the proposed approach affect upfront ALK/ROS1 fusion testing by FISH?

The study demonstrates that the combined workflow can largely negate the need for upfront ALK and ROS1 fusion testing by FISH for most cases.

When is additional reflex testing recommended?

Additional reflex testing capability is needed for a small subset of specimens with rarer genetic aberrations, including rare single-nucleotide variants, indels, fusion transcripts, and secondary post-treatment resistance mutations.

Sep 24, 2026

Uploaded by Bintang