Next Generation Sequencing for Gene Fusion Analysis in Lung Cancer: A Literature Review
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 mor...
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-07-01
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| Series: | Diagnostics |
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| Online Access: | https://www.mdpi.com/2075-4418/10/8/521 |
| _version_ | 1827712330274701312 |
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| author | Rossella Bruno Gabriella Fontanini |
| author_facet | Rossella Bruno Gabriella Fontanini |
| author_sort | Rossella Bruno |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T18:12:30Z |
| format | Article |
| id | doaj.art-d939d743d345447b80d8856fc6528544 |
| institution | Directory Open Access Journal |
| issn | 2075-4418 |
| language | English |
| last_indexed | 2024-03-10T18:12:30Z |
| publishDate | 2020-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Diagnostics |
| spelling | doaj.art-d939d743d345447b80d8856fc65285442023-11-20T08:03:21ZengMDPI AGDiagnostics2075-44182020-07-0110852110.3390/diagnostics10080521Next Generation Sequencing for Gene Fusion Analysis in Lung Cancer: A Literature ReviewRossella Bruno0Gabriella Fontanini1Unit of Pathological Anatomy, University Hospital of Pisa, Via Roma 67, 56126 Pisa, ItalyDepartment of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Via Savi 10, 56126 Pisa, ItalyGene 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.https://www.mdpi.com/2075-4418/10/8/521next generation sequencinggene fusionslung cancersolid and liquid biopsy |
| spellingShingle | Rossella Bruno Gabriella Fontanini Next Generation Sequencing for Gene Fusion Analysis in Lung Cancer: A Literature Review Diagnostics next generation sequencing gene fusions lung cancer solid and liquid biopsy |
| title | Next Generation Sequencing for Gene Fusion Analysis in Lung Cancer: A Literature Review |
| title_full | Next Generation Sequencing for Gene Fusion Analysis in Lung Cancer: A Literature Review |
| title_fullStr | Next Generation Sequencing for Gene Fusion Analysis in Lung Cancer: A Literature Review |
| title_full_unstemmed | Next Generation Sequencing for Gene Fusion Analysis in Lung Cancer: A Literature Review |
| title_short | Next Generation Sequencing for Gene Fusion Analysis in Lung Cancer: A Literature Review |
| title_sort | next generation sequencing for gene fusion analysis in lung cancer a literature review |
| topic | next generation sequencing gene fusions lung cancer solid and liquid biopsy |
| url | https://www.mdpi.com/2075-4418/10/8/521 |
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