Use of a rapid automated PCR assay to rescue failed RNA next generation sequencing for detection of gene fusion events in non-squamous, non-small cell neuroendocrine carcinoma (NSCLC) of the lung: a clinical, retrospective pilot verification study

ucjournals March 2, 2024

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Presented in Emirates Pathology, Digital Pathology & Cancer Conference Holiday Inn Dubai, UAE & Virtual
Speaker Name: Dr. Alison Finall (UAE)
Global Journal of Pathology & Laboratory Medicine
Unified Citation Journals, Pathology 2024, ISSN 2754-0952
Research interest: Molecular Pathology

Biography:
Dr Alison Finall is Head of the Department of Pathology and Deputy Clinical Director of Laboratory Services at Burjeel Medical City in Abu Dhabi, UAE. She is an expert in reporting anatomical pathology for thoracic and gynecological subspecialties as well as having in experience in molecular pathology. She submitted her MD thesis this year regarding rapid molecular techniques to suit urgent clinical oncological settings. She has written more than 35 publications to her name

Alison Finall1 , Charles Hall1 , Rehana Sikander2, Kate Hurlow2, Annemarie Moul2 Gareth Leopold1, Kate Mur-phy2, Tawfik Elazzabi1.
1. Morriston Hospital, Swansea Bay University Health Board, Heol Maes Eglwys, Swansea SA6 6NL
2. Singleton Hospital, Swansea Bay University Health Board, Sketty Lane, Swansea SA2 8AA
Introduction:
Lung cancer is the most common cause of death from cancer worldwide.1 Improvements in survival might be made by detec-tion of actionable molecular fusion events at an earlier point in lung can-cer diagnostic pathways.2,3

Methods:
A retrospective sample of failed RNA sequencing tests were selected from a prior audit and retested using a rapid fully automated PCR assay. The GeneFusion assay on Idylla (Biocartis, Belgium) plat-form was used to assess for structural rearrangements in ALK1, ROS1, NTRK 1,2 ,3 MET (Exon14 skipping) and RET.
Tissue samples were used after sections for both DNA and RNA sequencing panels had been submitted. Limited tissue was remaining in this cohort of 19 patients See figure 1.

Figure 1: Specimen residual assessment by H&E.
The photograph illustrates the small nature of tissue biopsy samples in each glass slide.

The Idylla gene fusion assay gave a valid result in all but two samples that had previously failed RNA sequencing results. See figure 2. The failure rate of the rapid PCR method in our cohort of 19 patients was 9%. We detected one mesenchymal-epithelial transition factor (MET) exon 14 skipping lesion that was missed by NGS due to assay failure.

Figure 2: Photomicrographs of pleural cytology cases that failed to produce a valid Gene Fusion assay result. A] TNC 10%, B] TNC 2% Both H&E, x400 magnification. TNC: tumour nucler content.

Results and Discussion:
We found an RNA NGS failure rate of 32% in 75 patients undergoing standard of care testing for non-small cell lung cancer. This study ascertains whether the Idylla Gene Fusion rapid PCR assay could be used as a salvage test for those cases that fail RNA sequencing.

References:
[1] Arnold M, Rutherford MJ, et al Lancet Oncol. 2019.
[2] Davidson MR, Gazdar AF, Clarke BE. J Thorac Dis. 2013;5 Suppl 5:S463-78.
[3] Finall A, Davies G, Jones T, Emlyn G, Huey P, Mullard A. J Clin Pathol. 2022.[4] Depoilly T, Garinet S, et al J Mol Diagn. 2022;24(9):1021-30.[5] Finall A. J Mol Pathol. 2022;3:307-18.

Tags:
Immunodeficiency States, Immunophenotyping, Molecular Diagnostics & Proteomics, Evolutionary Medicine, Functional Identification & Biomarkers, Hematopoietic & other Malignancies, Anatomical Pathology, Clinical Pathology, Dermato Pathology, Forensic Pathology, Hemato Pathology, Histopathology, Molecular Pathology, Surgical Pathology, Histopathology, Chemical Pathology, Hematopathology, Histopathology, Cytopathology, Forensic Pathology, Dermatopathology, Clinical Biochemistry, Infection Control, Cytokines, Enzymology, Endocrinology, Cellular Lineage, Virology, Rheology, Toxicology, Neuropathology, Diagnostic Pathology, Mesothelial Proliferations, Transfusion medicine, Clinical microbiology, Cytogenetics, Molecular Genetics Pathology, Immunopathology, Veterinary Pathology, Anatomical Pathology, General Pathology