Ultra-Fast Amplicon-Based Next-Generation Sequencing in Non-Squamous Non-Small Cell Lung Cancer

Christophe Bontoux; Virginie Lespinet-Fabre; Olivier Bordone; Virginie Tanga; Maryline Allegra; Myriam Salah; Salom&#233; Lalv&#233;e; Samantha Goffinet; Jonathan Benzaquen; Charles-Hugo Marquette; Marius Ili&#233;; V&#233;ronique Hofman; Paul Hofman

doi:10.3791/65190

Sequenziamento ultraveloce di nuova generazione basato su ampliconi nel carcinoma polmonare non s...

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Ultra-Fast Amplicon-Based Next-Generation Sequencing in Non-Squamous Non-Small Cell Lung Cancer

Sequenziamento ultraveloce di nuova generazione basato su ampliconi nel carcinoma polmonare non squamoso non a piccole cellule

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07:59 min

September 8, 2023

DOI: 10.3791/65190-v

Christophe Bontoux^1,2,3,4,5, Virginie Lespinet-Fabre^1,2,3,4, Olivier Bordone^1,2,3,4, Virginie Tanga^1,2,3,4, Maryline Allegra^1,2,3,4, Myriam Salah^1,2,3,4, Salomé Lalvée^1,2,3,4, Samantha Goffinet^1,2,3,4, Jonathan Benzaquen^3,4,5,6, Charles-Hugo Marquette^3,4,5,6, Marius Ilié^1,2,3,4,5, Véronique Hofman^1,2,3,4,5, Paul Hofman^1,2,3,4,5

¹Laboratory of Clinical and Experimental Pathology, Centre Hospitalier Universitaire de Nice,Université Côte d’Azur, CHU de Nice, ²Hospital-Integrated Biobank (BB-0033-00025),Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, ³Institut Hospitalo-Universitaire (IHU), RespirERA,Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, ⁴FHU OncoAge,Université Côte d'Azur, ⁵Team 4, Institute of Research on Cancer and Aging (IRCAN), CNRS INSERM, Centre Antoine-Lacassagne,Université Côte d'Azur, ⁶Department of Pulmonary Medicine and Thoracic Oncology, Centre Hospitalier Universitaire de Nice,Université Côte d'Azur

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Overview

This study addresses the urgent need for rapid detection of genomic alterations in non-squamous non-small cell lung cancer (NS-NSCLC) to inform targeted therapies. An ultra-fast next-generation sequencing (NGS) workflow is presented as a solution for efficient analysis of small biopsy samples.

Key Study Components

Research Area

Oncology
Molecular diagnostics
Next-generation sequencing

Background

Targeted therapies for NS-NSCLC depend on timely detection of genomic alterations.
Traditional biopsy methods often yield small samples, complicating analysis.
A comprehensive approach for rapid testing is needed to enhance patient care.

Methods Used

Ultra-fast next-generation sequencing (NGS)
Analysis of formalin-fixed paraffin-embedded (FFPE) samples
Automated purification and sequencing processes

Main Results

The workflow identifies key genetic mutations and fusions in a time-efficient manner.
High sensitivity for detecting various genomic alterations was achieved.
Comprehensive molecular profiling was performed on 259 NS-NSCLC patients.

Conclusions

This study demonstrates a new standard for rapid genomic profiling in NS-NSCLC.
It provides critical insights for personalized treatment strategies in oncology.

Frequently Asked Questions

What are the advantages of the ultra-fast NGS workflow?

The ultra-fast NGS workflow allows for rapid detection of genetic mutations in small biopsy samples, minimizing the time to diagnosis and treatment.

How many patients were analyzed in this study?

A total of 259 patients with non-squamous non-small cell lung cancer were included in the analysis.

What sample types were used for this analysis?

The study utilized various biopsy types and surgical specimens, including formalin-fixed paraffin-embedded (FFPE) tissues.

What are the implications of this research for lung cancer treatment?

The findings support the development of rapid genomic profiling methods that can inform targeted therapy decisions, improving patient outcomes.

What methodologies are compared in this study?

The study compares traditional molecular testing methods, such as RT-PCR and fluorescence in situ hybridization, with the proposed NGS approach.

What is the primary goal of the proposed NGS workflow?

The primary goal is to enable timely and comprehensive genomic profiling for optimal therapy selection in NS-NSCLC patients.

L'aumento dei biomarcatori molecolari da testare per la gestione della cura del carcinoma polmonare non squamoso non a piccole cellule (NS-NSCLC) ha spinto lo sviluppo di metodi di rilevamento molecolare rapidi e affidabili. Descriviamo un flusso di lavoro per la valutazione dell'alterazione genomica per i pazienti NS-NSCLC utilizzando un approccio di sequenziamento di nuova generazione (NGS) ultraveloce.

Al giorno d'oggi, le terapie mirate per il carcinoma polmonare non a piccole cellule richiedono una rapida individuazione di molteplici alterazioni genomiche. Quindi è fondamentale per una cura ottimale, poiché le biopsie toraciche sono spesso piccole e contengono poche cellule tumorali. Presentiamo quindi un flusso di lavoro di sequenziamento di nuova generazione ultraveloce che viene implementato per la diagnosi di routine del carcinoma polmonare non a piccole cellule nel laboratorio di patologia.

L'NGS attualmente mirato che utilizza pannelli di diverse dimensioni, il test di sequenziamento genico con RT-PCR, la PCR digitale, l'ibridazione fluorescente in situ e l'immunoistochimica sono i diversi metodi utilizzati per rilevare le alterazioni molecolari. Tuttavia, la maggior parte di questi metodi può richiedere molto tempo e materiale tissutale, portando a una diagnosi ritardata e al rischio di sforzo tissutale. La sfida consiste nel rilevare in modo efficiente più alterazioni molecolari, risparmiando materiali e rispondendo a una diagnosi rapida.

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