Evaluation of a Targeted Next-Generation Sequencing Panel for the Non-Invasive Detection of Variants in Circulating DNA of Colorectal Cancer
Molecular profiling of circulating cell-free DNA (cfDNA) has shown utility for the management of colorectal cancer (CRC). TruSight Tumor 170 (TST170) is a next-generation sequencing (NGS) panel that covers 170 cancer-related genes, including <i>KRAS</i>, which is a key driver gene in CRC...
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| Format: | Article |
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MDPI AG
2021-09-01
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| Series: | Journal of Clinical Medicine |
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| Online Access: | https://www.mdpi.com/2077-0383/10/19/4487 |
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| author | Aitor Rodríguez-Casanova Aida Bao-Caamano Ramón M. Lago-Lestón Elena Brozos-Vázquez Nicolás Costa-Fraga Isabel Ferreirós-Vidal Ihab Abdulkader Yolanda Vidal-Insua Francisca Vázquez Rivera Sonia Candamio Folgar Rafael López-López Laura Muinelo-Romay Angel Diaz-Lagares |
| author_facet | Aitor Rodríguez-Casanova Aida Bao-Caamano Ramón M. Lago-Lestón Elena Brozos-Vázquez Nicolás Costa-Fraga Isabel Ferreirós-Vidal Ihab Abdulkader Yolanda Vidal-Insua Francisca Vázquez Rivera Sonia Candamio Folgar Rafael López-López Laura Muinelo-Romay Angel Diaz-Lagares |
| author_sort | Aitor Rodríguez-Casanova |
| collection | DOAJ |
| description | Molecular profiling of circulating cell-free DNA (cfDNA) has shown utility for the management of colorectal cancer (CRC). TruSight Tumor 170 (TST170) is a next-generation sequencing (NGS) panel that covers 170 cancer-related genes, including <i>KRAS</i>, which is a key driver gene in CRC. We evaluated the capacity of TST170 to detect gene variants in cfDNA from a retrospective cohort of 20 metastatic CRC patients with known <i>KRAS</i> variants in tumor tissue and in cfDNA previously analyzed by pyrosequencing and BEAMing, respectively. The cfDNA of most of the patients (95%) was successfully sequenced. We frequently detected variants with clinical significance in <i>KRAS</i> (79%, 15/19) and <i>PIK3CA</i> (26%, 5/19) genes. Variants with potential clinical significance were also identified in another 27 cancer genes, such as <i>APC</i>. The type of <i>KRAS</i> variant detected in cfDNA by TST170 showed high concordance with those detected in tumor tissue (77%), and very high concordance with cfDNA analyzed by BEAMing (94%). The variant allele fractions for <i>KRAS</i> obtained in cfDNA by TST170 and BEAMing correlated strongly. This proof-of-principle study indicates that targeted NGS analysis of cfDNA with TST170 could be useful for non-invasive detection of gene variants in metastatic CRC patients, providing an assay that could be easily implemented for detecting somatic alterations in the clinic. |
| first_indexed | 2024-03-10T06:58:29Z |
| format | Article |
| id | doaj.art-fd2de473015f4bb59e8e3c2b963a7f9d |
| institution | Directory Open Access Journal |
| issn | 2077-0383 |
| language | English |
| last_indexed | 2024-03-10T06:58:29Z |
| publishDate | 2021-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Journal of Clinical Medicine |
| spelling | doaj.art-fd2de473015f4bb59e8e3c2b963a7f9d2023-11-22T16:20:18ZengMDPI AGJournal of Clinical Medicine2077-03832021-09-011019448710.3390/jcm10194487Evaluation of a Targeted Next-Generation Sequencing Panel for the Non-Invasive Detection of Variants in Circulating DNA of Colorectal CancerAitor Rodríguez-Casanova0Aida Bao-Caamano1Ramón M. Lago-Lestón2Elena Brozos-Vázquez3Nicolás Costa-Fraga4Isabel Ferreirós-Vidal5Ihab Abdulkader6Yolanda Vidal-Insua7Francisca Vázquez Rivera8Sonia Candamio Folgar9Rafael López-López10Laura Muinelo-Romay11Angel Diaz-Lagares12Cancer Epigenomics, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, SpainCancer Epigenomics, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, SpainTranslational Medical Oncology Group (Oncomet), Liquid Biopsy Analysis Unit, Health Research Institute of Santiago (IDIS), 15706 Santiago de Compostela, SpainTranslational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, SpainCancer Epigenomics, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, SpainTranslational Medical Oncology Group (Oncomet), Liquid Biopsy Analysis Unit, Health Research Institute of Santiago (IDIS), 15706 Santiago de Compostela, SpainDepartment of Pathology, University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, SpainTranslational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, SpainTranslational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, SpainTranslational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, SpainTranslational Medical Oncology Group (Oncomet), Roche-Chus Joint Unit, Health Research Institute of Santiago (IDIS), 15706 Santiago de Compostela, SpainTranslational Medical Oncology Group (Oncomet), Liquid Biopsy Analysis Unit, Health Research Institute of Santiago (IDIS), 15706 Santiago de Compostela, SpainCancer Epigenomics, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, SpainMolecular profiling of circulating cell-free DNA (cfDNA) has shown utility for the management of colorectal cancer (CRC). TruSight Tumor 170 (TST170) is a next-generation sequencing (NGS) panel that covers 170 cancer-related genes, including <i>KRAS</i>, which is a key driver gene in CRC. We evaluated the capacity of TST170 to detect gene variants in cfDNA from a retrospective cohort of 20 metastatic CRC patients with known <i>KRAS</i> variants in tumor tissue and in cfDNA previously analyzed by pyrosequencing and BEAMing, respectively. The cfDNA of most of the patients (95%) was successfully sequenced. We frequently detected variants with clinical significance in <i>KRAS</i> (79%, 15/19) and <i>PIK3CA</i> (26%, 5/19) genes. Variants with potential clinical significance were also identified in another 27 cancer genes, such as <i>APC</i>. The type of <i>KRAS</i> variant detected in cfDNA by TST170 showed high concordance with those detected in tumor tissue (77%), and very high concordance with cfDNA analyzed by BEAMing (94%). The variant allele fractions for <i>KRAS</i> obtained in cfDNA by TST170 and BEAMing correlated strongly. This proof-of-principle study indicates that targeted NGS analysis of cfDNA with TST170 could be useful for non-invasive detection of gene variants in metastatic CRC patients, providing an assay that could be easily implemented for detecting somatic alterations in the clinic.https://www.mdpi.com/2077-0383/10/19/4487colorectal cancerTruSight Tumor 170NGSBEAMingliquid biopsytumor biomarkers |
| spellingShingle | Aitor Rodríguez-Casanova Aida Bao-Caamano Ramón M. Lago-Lestón Elena Brozos-Vázquez Nicolás Costa-Fraga Isabel Ferreirós-Vidal Ihab Abdulkader Yolanda Vidal-Insua Francisca Vázquez Rivera Sonia Candamio Folgar Rafael López-López Laura Muinelo-Romay Angel Diaz-Lagares Evaluation of a Targeted Next-Generation Sequencing Panel for the Non-Invasive Detection of Variants in Circulating DNA of Colorectal Cancer Journal of Clinical Medicine colorectal cancer TruSight Tumor 170 NGS BEAMing liquid biopsy tumor biomarkers |
| title | Evaluation of a Targeted Next-Generation Sequencing Panel for the Non-Invasive Detection of Variants in Circulating DNA of Colorectal Cancer |
| title_full | Evaluation of a Targeted Next-Generation Sequencing Panel for the Non-Invasive Detection of Variants in Circulating DNA of Colorectal Cancer |
| title_fullStr | Evaluation of a Targeted Next-Generation Sequencing Panel for the Non-Invasive Detection of Variants in Circulating DNA of Colorectal Cancer |
| title_full_unstemmed | Evaluation of a Targeted Next-Generation Sequencing Panel for the Non-Invasive Detection of Variants in Circulating DNA of Colorectal Cancer |
| title_short | Evaluation of a Targeted Next-Generation Sequencing Panel for the Non-Invasive Detection of Variants in Circulating DNA of Colorectal Cancer |
| title_sort | evaluation of a targeted next generation sequencing panel for the non invasive detection of variants in circulating dna of colorectal cancer |
| topic | colorectal cancer TruSight Tumor 170 NGS BEAMing liquid biopsy tumor biomarkers |
| url | https://www.mdpi.com/2077-0383/10/19/4487 |
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