Portuguese Consensus Recommendations for Next-Generation Sequencing of Lung Cancer, Rare Tumors, and Cancers of Unknown Primary Origin in Clinical Practice
Next-generation sequencing (NGS) has been implemented in clinical oncology for diagnosis, prognosis, and therapeutic guidance. Among the various NGS applications in molecular oncology, we focused on the following topics: laboratory standards for targeted gene panels (somatic mutations) and therapeu...
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| Format: | Article |
| Language: | English |
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Ordem dos Médicos
2022-09-01
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| Series: | Acta Médica Portuguesa |
| Subjects: | |
| Online Access: | https://actamedicaportuguesa.com/revista/index.php/amp/article/view/17680 |
| _version_ | 1811345310394351616 |
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| author | Manuel R. Teixeira Júlio Oliveira Paula Borralho Maria Gabriela O. Fernandes Teresa Almodovar Isabel Fernandes Daniela Macedo Ana Ferreira Ana Barroso Encarnação Teixeira José Carlos Machado |
| author_facet | Manuel R. Teixeira Júlio Oliveira Paula Borralho Maria Gabriela O. Fernandes Teresa Almodovar Isabel Fernandes Daniela Macedo Ana Ferreira Ana Barroso Encarnação Teixeira José Carlos Machado |
| author_sort | Manuel R. Teixeira |
| collection | DOAJ |
| description |
Next-generation sequencing (NGS) has been implemented in clinical oncology for diagnosis, prognosis, and therapeutic guidance. Among the various NGS applications in molecular oncology, we focused on the following topics: laboratory standards for targeted gene panels (somatic mutations) and therapeutic guidance based on NGS of lung cancer and rare cancers, namely sarcomas and cancers of unknown primary. Multiple quality control checkpoints should be addressed in the pre-analytical phase for good quality and interpretation of the NGS results. It includes tumor size and cellularity, tissue processing and decalcification, tumor fraction, tumor viability, fixatives, and staining. Communication between clinicians and laboratory support is also essential. In lung cancer, all patients with non-squamous non-small cell lung cancer should be tested with a NGS panel, and it should include not only genes with approved targeted therapies (ALK, BRAF, EGFR, MET, NTRK, RET, and ROS1) but also genes with potentially actionable genomic alterations (HER2 and KRAS). Since there is a lack of extensive knowledge regarding the use of NGS in rare tumors performing comprehensive genomic profiling, NGS panels to better manage the disease are recommended. Moreover, other patients with other incurable solid tumors may benefit from being included in biomarker-driven clinical trials. Multidisciplinary tumor boards with the participation of experts with the ability to integrate genomic profiling data are essential to tailor the best strategy for each patient. Considering that there are no national guidelines, this article aims to guide laboratory and clinical practice for the use of NGS in the context of lung cancer, rare tumors, and cancer of unknown primary in Portugal.
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| first_indexed | 2024-04-13T20:01:14Z |
| format | Article |
| id | doaj.art-6db7b99ec62f463f9c90b94b686aac13 |
| institution | Directory Open Access Journal |
| issn | 0870-399X 1646-0758 |
| language | English |
| last_indexed | 2024-04-13T20:01:14Z |
| publishDate | 2022-09-01 |
| publisher | Ordem dos Médicos |
| record_format | Article |
| series | Acta Médica Portuguesa |
| spelling | doaj.art-6db7b99ec62f463f9c90b94b686aac132022-12-22T02:32:12ZengOrdem dos MédicosActa Médica Portuguesa0870-399X1646-07582022-09-0135910.20344/amp.176805620Portuguese Consensus Recommendations for Next-Generation Sequencing of Lung Cancer, Rare Tumors, and Cancers of Unknown Primary Origin in Clinical PracticeManuel R. Teixeira0Júlio Oliveira1Paula Borralho2Maria Gabriela O. Fernandes3Teresa Almodovar4Isabel Fernandes5Daniela Macedo6Ana Ferreira7Ana Barroso8Encarnação Teixeira9José Carlos Machado10Serviço de Genética. Instituto Português de Oncologia do Porto Francisco Gentil. Porto. Instituto de Ciências Biomédicas Abel Salazar. Universidade do Porto. Porto.Serviço de Oncologia Médica. Instituto Português de Oncologia do Porto Francisco Gentil. Porto.Serviço de Anatomia Patológica. Hospital CUF Descobertas. Lisboa. Faculdade de Medicina. Universidade de Lisboa. Lisboa.Serviço de Pneumologia. Centro Hospitalar Universitário de São João. Porto. Departamento de Medicina. Faculdade de Medicina. Universidade do Porto. Porto. Institute of Molecular Pathology and Immunology. University of Porto. Porto.Serviço de Pneumologia. Instituto Português de Oncologia de Lisboa Francisco Gentil. Lisboa.Faculdade de Medicina. Universidade de Lisboa. Lisboa. Serviço de Oncologia Médica. Centro Hospitalar Universitário de Lisboa Norte. Lisboa. Instituto de Medicina Molecular João Lobo Antunes. Faculdade de Medicina. Universidade de Lisboa. Lisboa.Centro de Oncologia. Hospital Lusíadas Lisboa. Lisboa.Serviço de Oncologia Médica. Instituto Português de Oncologia do Porto Francisco Gentil. Porto.Unidade Multidisciplinar de Tumores Torácicos. Serviço de Pneumologia. Centro Hospitalar de Vila Nova de Gaia/Espinho. Vila Nova de Gaia.Serviço de Pneumologia. Centro Hospitalar Universitário de Lisboa Norte. Lisboa. Serviço de Pneumologia. Hospital CUF Descobertas. Lisboa. Serviço de Pneumologia. Hospital CUF Tejo. Lisboa.Institute of Molecular Pathology and Immunology. University of Porto. Porto. Departamento de Patologia. Faculdade de Medicina. Universidade do Porto. Porto. Next-generation sequencing (NGS) has been implemented in clinical oncology for diagnosis, prognosis, and therapeutic guidance. Among the various NGS applications in molecular oncology, we focused on the following topics: laboratory standards for targeted gene panels (somatic mutations) and therapeutic guidance based on NGS of lung cancer and rare cancers, namely sarcomas and cancers of unknown primary. Multiple quality control checkpoints should be addressed in the pre-analytical phase for good quality and interpretation of the NGS results. It includes tumor size and cellularity, tissue processing and decalcification, tumor fraction, tumor viability, fixatives, and staining. Communication between clinicians and laboratory support is also essential. In lung cancer, all patients with non-squamous non-small cell lung cancer should be tested with a NGS panel, and it should include not only genes with approved targeted therapies (ALK, BRAF, EGFR, MET, NTRK, RET, and ROS1) but also genes with potentially actionable genomic alterations (HER2 and KRAS). Since there is a lack of extensive knowledge regarding the use of NGS in rare tumors performing comprehensive genomic profiling, NGS panels to better manage the disease are recommended. Moreover, other patients with other incurable solid tumors may benefit from being included in biomarker-driven clinical trials. Multidisciplinary tumor boards with the participation of experts with the ability to integrate genomic profiling data are essential to tailor the best strategy for each patient. Considering that there are no national guidelines, this article aims to guide laboratory and clinical practice for the use of NGS in the context of lung cancer, rare tumors, and cancer of unknown primary in Portugal. https://actamedicaportuguesa.com/revista/index.php/amp/article/view/17680High-Throughput Nucleotide SequencingLung Neoplasms/geneticsNeoplasmsUnknown Primary/geneticsSarcoma/genetics |
| spellingShingle | Manuel R. Teixeira Júlio Oliveira Paula Borralho Maria Gabriela O. Fernandes Teresa Almodovar Isabel Fernandes Daniela Macedo Ana Ferreira Ana Barroso Encarnação Teixeira José Carlos Machado Portuguese Consensus Recommendations for Next-Generation Sequencing of Lung Cancer, Rare Tumors, and Cancers of Unknown Primary Origin in Clinical Practice Acta Médica Portuguesa High-Throughput Nucleotide Sequencing Lung Neoplasms/genetics Neoplasms Unknown Primary/genetics Sarcoma/genetics |
| title | Portuguese Consensus Recommendations for Next-Generation Sequencing of Lung Cancer, Rare Tumors, and Cancers of Unknown Primary Origin in Clinical Practice |
| title_full | Portuguese Consensus Recommendations for Next-Generation Sequencing of Lung Cancer, Rare Tumors, and Cancers of Unknown Primary Origin in Clinical Practice |
| title_fullStr | Portuguese Consensus Recommendations for Next-Generation Sequencing of Lung Cancer, Rare Tumors, and Cancers of Unknown Primary Origin in Clinical Practice |
| title_full_unstemmed | Portuguese Consensus Recommendations for Next-Generation Sequencing of Lung Cancer, Rare Tumors, and Cancers of Unknown Primary Origin in Clinical Practice |
| title_short | Portuguese Consensus Recommendations for Next-Generation Sequencing of Lung Cancer, Rare Tumors, and Cancers of Unknown Primary Origin in Clinical Practice |
| title_sort | portuguese consensus recommendations for next generation sequencing of lung cancer rare tumors and cancers of unknown primary origin in clinical practice |
| topic | High-Throughput Nucleotide Sequencing Lung Neoplasms/genetics Neoplasms Unknown Primary/genetics Sarcoma/genetics |
| url | https://actamedicaportuguesa.com/revista/index.php/amp/article/view/17680 |
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