Next Generation Sequencing for Gene Fusion Analysis in Lung Cancer: A Literature Review.

Next Generation Sequencing for Gene Fusion Analysis in Lung Cancer: A Literature Review.

Publication date: Jul 27, 2020

Gene fusions have a pivotal role in non-small cell lung cancer (NSCLC) precision medicine. Several techniques can be used, from fluorescence in situ hybridization and immunohistochemistry to next generation sequencing (NGS). Although several NGS panels are available, gene fusion testing presents more technical challenges than other variants. This is a PubMed-based narrative review aiming to summarize NGS approaches for gene fusion analysis and their performance on NSCLC clinical samples. The analysis can be performed at DNA or RNA levels, using different target enrichment (hybrid-capture or amplicon-based) and sequencing chemistries, with both custom and commercially available panels. DNA sequencing evaluates different alteration types simultaneously, but large introns and repetitive sequences can impact on the performance and it does not discriminate between expressed and unexpressed gene fusions. RNA-based targeted approach analyses and quantifies directly fusion transcripts and is more accurate than DNA panels on tumor tissue, but it can be limited by RNA quality and quantity. On liquid biopsy, satisfying data have been published on circulating tumor DNA hybrid-capture panels. There is not a perfect method for gene fusion analysis, but NGS approaches, though still needing a complete standardization and optimization, present several advantages for the clinical practice.

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Concepts Keywords
Amplicon Tumor
Basel NSCLC
Fluorescence Lung Cancer
Hybrid Clinical medicine
Hybridization Branches of biology
Immunohistochemistry Lung cancer
Introns DNA
Lung Biopsy
Optimization Cancer screening
Precision Medicine Liquid biopsy
PubMed Non-small-cell lung carcinoma
RNA Hybridization
Tumor

Semantics

Type Source Name
disease MESH Lung Cancer
disease MESH non-small cell lung cancer
pathway KEGG Non-small cell lung cancer
disease MESH tumor
disease MESH biopsy
drug DRUGBANK Methionine
drug DRUGBANK L-Tyrosine
drug DRUGBANK Entrectinib
drug DRUGBANK Crizotinib
drug DRUGBANK Larotrectinib
drug DRUGBANK Cabozantinib
drug DRUGBANK Vandetanib
drug DRUGBANK Gold
drug DRUGBANK Formaldehyde
drug DRUGBANK Mecasermin
drug DRUGBANK Nitrogen trichloride
disease MESH bas
drug DRUGBANK Spinosad
drug DRUGBANK Aspartame
disease MESH microsatellite instability
drug DRUGBANK Cefadroxil
pathway KEGG Apoptosis
drug DRUGBANK Osimertinib
disease MESH point mutations
drug DRUGBANK Serine
drug DRUGBANK L-Threonine
drug DRUGBANK Edetic Acid
drug DRUGBANK Nonoxynol-9
disease MESH separation
disease MESH smokers
disease MESH Infections
disease MESH Inflammations
disease MESH lung adenocarcinoma
drug DRUGBANK Polyethylene glycol
disease MESH adenocarcinoma
drug DRUGBANK PPI-1019
disease MESH Diagnosis
disease MESH small cell lung cancer
pathway KEGG Small cell lung cancer
disease MESH malignant pleural effusion
drug DRUGBANK Pentaerythritol tetranitrate
drug DRUGBANK Gefitinib
disease MESH lymphoma

Original Article

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