Evaluating Diff-Quik cytology smears for large-panel mutation testing in lung cancer-Predicting DNA content and success with low-malignant-cellularity samples.

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Abstract

Cytology smears are commonly collected during endobronchial ultrasound-guided transbronchial needle aspiration (EBUS TBNA) procedures but are rarely used for molecular testing. Studies are needed to demonstrate their great potential, in particular for the prediction of malignant cell DNA content and for utility in molecular diagnostics using large gene panels.

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Recommendations for the use of next-generation sequencing (NGS) for patients with metastatic cancers: a report from the ESMO Precision Medicine Working Group

F. Mosele, J. Remon, J Mateo … (2020)

Next-generation sequencing (NGS) allows sequencing of a high number of nucleotides in a short time frame at an affordable cost. While this technology has been widely implemented, there are no recommendations from scientific societies about its use in oncology practice. The European Society for Medical Oncology (ESMO) is proposing three levels of recommendations for the use of NGS. Based on the current evidence, ESMO recommends routine use of NGS on tumour samples in advanced non-squamous non-small-cell lung cancer (NSCLC), prostate cancers, ovarian cancers and cholangiocarcinoma. In these tumours, large multigene panels could be used if they add acceptable extra cost compared with small panels. In colon cancers, NGS could be an alternative to PCR. In addition, based on the KN158 trial and considering that patients with endometrial and small-cell lung cancers should have broad access to anti-programmed cell death 1 (anti-PD1) antibodies, it is recommended to test tumour mutational burden (TMB) in cervical cancers, well- and moderately-differentiated neuroendocrine tumours, salivary cancers, thyroid cancers and vulvar cancers, as TMB-high predicted response to pembrolizumab in these cancers. Outside the indications of multigene panels, and considering that the use of large panels of genes could lead to few clinically meaningful responders, ESMO acknowledges that a patient and a doctor could decide together to order a large panel of genes, pending no extra cost for the public health care system and if the patient is informed about the low likelihood of benefit. ESMO recommends that the use of off-label drugs matched to genomics is done only if an access programme and a procedure of decision has been developed at the national or regional level. Finally, ESMO recommends that clinical research centres develop multigene sequencing as a tool to screen patients eligible for clinical trials and to accelerate drug development, and prospectively capture the data that could further inform how to optimise the use of this technology.

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Technical Aspects of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration: CHEST Guideline and Expert Panel Report.

Momen M Wahidi, Felix Herth, Kazuhiro Yasufuku … (2016)

Endobronchial ultrasound (EBUS) was introduced in the last decade, enabling real-time guidance of transbronchial needle aspiration (TBNA) of mediastinal and hilar structures and parabronchial lung masses. The many publications produced about EBUS-TBNA have led to a better understanding of the performance characteristics of this procedure. The goal of this document was to examine the current literature on the technical aspects of EBUS-TBNA as they relate to patient, technology, and proceduralist factors to provide evidence-based and expert guidance to clinicians.

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A high frequency of sequence alterations is due to formalin fixation of archival specimens.

C. Williams, F Ponten, C Moberg … (1999)

Genomic analysis of archival tissues fixed in formalin is of fundamental importance in biomedical research, and numerous studies have used such material. Although the possibility of polymerase chain reaction (PCR)-introduced artifacts is known, the use of direct sequencing has been thought to overcome such problems. Here we report the results from a controlled study, performed in parallel on frozen and formalin-fixed material, where a high frequency of nonreproducible sequence alterations was detected with the use of formalin-fixed tissues. Defined numbers of well-characterized tumor cells were amplified and analyzed by direct DNA sequencing. No nonreproducible sequence alterations were found in frozen tissues. In formalin-fixed material up to one mutation artifact per 500 bases was recorded. The chance of such artificial mutations in formalin-fixed material was inversely correlated with the number of cells used in the PCR-the fewer cells, the more artifacts. A total of 28 artificial mutations were recorded, of which 27 were C-T or G-A transitions. Through confirmational sequencing of independent amplification products artifacts can be distinguished from true mutations. However, because this problem was not acknowledged earlier, the presence of artifacts may have profoundly influenced previously reported mutations in formalin-fixed material, including those inserted into mutation databases.

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Author and article information

Journal

Journal ID (iso-abbrev): Cancer Cytopathol

Title: Cancer cytopathology

Publisher: Wiley

ISSN (Electronic): 1934-6638

ISSN (Print): 1934-662X

Publication date (Electronic): Jun 2023

Volume: 131

Issue: 6

Affiliations

[1 ] Department of Thoracic Medicine, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia.

[2 ] UQ Centre for Clinical Research, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia.

[3 ] Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia.

[4 ] QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.

[5 ] Department of Thoracic Medicine, Sunshine Coast University Hospital, Birtinya, Queensland, Australia.

[6 ] Department of Respiratory Medicine, Gold Coast University Hospital, Southport, Queensland, Australia.

[7 ] ACL Pathology, Bellavista, New South Wales, Australia.

[8 ] School of Biomedical Sciences, University of Queensland, St Lucia, Queensland, Australia.

Article

DOI: 10.1002/cncy.22690

PubMed ID: 36938641

SO-VID: 5d1ce32b-6b9f-46d7-b3bb-4af1bea8301a

History

Keywords: endobronchial ultrasound-guided transbronchial needle aspiration (EBUS TBNA),lung cancer,molecular diagnostics,TruSight Oncology 500 (TSO500),cytology

Data availability:

Keywords: endobronchial ultrasound-guided transbronchial needle aspiration (EBUS TBNA), lung cancer, molecular diagnostics, TruSight Oncology 500 (TSO500), cytology

Evaluating Diff-Quik cytology smears for large-panel mutation testing in lung cancer-Predicting DNA content and success with low-malignant-cellularity samples.

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European Journal of Microbiology and Immunology

Most cited references 32

Recommendations for the use of next-generation sequencing (NGS) for patients with metastatic cancers: a report from the ESMO Precision Medicine Working Group

Technical Aspects of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration: CHEST Guideline and Expert Panel Report.

A high frequency of sequence alterations is due to formalin fixation of archival specimens.

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