Cross-sectional analysis of circulating tumor DNA in primary colorectal cancer at surgery and during post-surgery follow-up by liquid biopsy
Abstract Background Liquid biopsy (LB) in early-stage, non-metastatic colorectal cancer (CRC) must be sensitive enough to detect extremely low circulating tumor DNA (ctDNA) levels. This challenge has been seldom and non-systematically investigated. Methods Next generation sequencing (NGS) and digita...
| Main Authors: | , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2020-04-01
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| Series: | Journal of Experimental & Clinical Cancer Research |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13046-020-01569-z |
| _version_ | 1818274926462763008 |
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| author | Matteo Allegretti Giuliano Cottone Fabio Carboni Ettore Cotroneo Beatrice Casini Elena Giordani Carla Azzurra Amoreo Simonetta Buglioni Maria Diodoro Edoardo Pescarmona Settimio Zazza Orietta Federici Massimo Zeuli Laura Conti Giovanni Cigliana Francesco Fiorentino Mario Valle Patrizio Giacomini Francesca Spinella |
| author_facet | Matteo Allegretti Giuliano Cottone Fabio Carboni Ettore Cotroneo Beatrice Casini Elena Giordani Carla Azzurra Amoreo Simonetta Buglioni Maria Diodoro Edoardo Pescarmona Settimio Zazza Orietta Federici Massimo Zeuli Laura Conti Giovanni Cigliana Francesco Fiorentino Mario Valle Patrizio Giacomini Francesca Spinella |
| author_sort | Matteo Allegretti |
| collection | DOAJ |
| description | Abstract Background Liquid biopsy (LB) in early-stage, non-metastatic colorectal cancer (CRC) must be sensitive enough to detect extremely low circulating tumor DNA (ctDNA) levels. This challenge has been seldom and non-systematically investigated. Methods Next generation sequencing (NGS) and digital PCR (dPCR) were combined to test tumor DNAs (tDNAs) and paired ctDNAs collected at surgery from 39 patients, 12 of whom were also monitored during the immediate post-surgery follow up. Patients treated for metastatic disease (n = 14) were included as controls. Results NGS and dPCR concordantly (100% agreement) called at least one single nucleotide variant (SNV) in 34 tDNAs, estimated differences in allelic frequencies being negligible (±1.4%). However, despite dPCR testing, SNVs were only detectable in 15/34 (44.1%) ctDNAs from patients at surgery, as opposed to 14/14 (100%) metastatic patients. This was likely due to striking differences (average 10 times, up to 500) in ctDNA levels between groups. NGS revealed blood-only SNVs, suggesting spatial heterogeneity since pre-surgery disease stages, and raising the combined NGS/dPCR sensitivity to 58.8%. ctDNA levels at surgery correlated with neither tumor size, stage, grade, or nodal status, nor with variant abundance in paired tDNA. LB sensitivity reached 63.6% when ctDNA was combined with CEA. Finally, persistence and absence of ctDNA on the first conventional (month 3) post-surgery follow-up were associated with fast relapse and a disease-free status in 3 and 7 patients, respectively. Conclusions A simple clinical NGS/dPCR/CEA combination effectively addresses the LB challenge in a fraction of non-metastatic CRC patients. |
| first_indexed | 2024-12-12T22:21:37Z |
| format | Article |
| id | doaj.art-d6505d17803540319382cf1574effd62 |
| institution | Directory Open Access Journal |
| issn | 1756-9966 |
| language | English |
| last_indexed | 2024-12-12T22:21:37Z |
| publishDate | 2020-04-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Experimental & Clinical Cancer Research |
| spelling | doaj.art-d6505d17803540319382cf1574effd622022-12-22T00:09:54ZengBMCJournal of Experimental & Clinical Cancer Research1756-99662020-04-0139111210.1186/s13046-020-01569-zCross-sectional analysis of circulating tumor DNA in primary colorectal cancer at surgery and during post-surgery follow-up by liquid biopsyMatteo Allegretti0Giuliano Cottone1Fabio Carboni2Ettore Cotroneo3Beatrice Casini4Elena Giordani5Carla Azzurra Amoreo6Simonetta Buglioni7Maria Diodoro8Edoardo Pescarmona9Settimio Zazza10Orietta Federici11Massimo Zeuli12Laura Conti13Giovanni Cigliana14Francesco Fiorentino15Mario Valle16Patrizio Giacomini17Francesca Spinella18Oncogenomics and Epigenetics, IRCSS Regina Elena National Cancer InstituteOncogenomics Division, Eurofins Genoma GroupDigestive Surgery, IRCSS Regina Elena National Cancer InstituteOncogenomics Division, Eurofins Genoma GroupPathology, IRCSS Regina Elena National Cancer InstituteOncogenomics and Epigenetics, IRCSS Regina Elena National Cancer InstitutePathology, IRCSS Regina Elena National Cancer InstitutePathology, IRCSS Regina Elena National Cancer InstitutePathology, IRCSS Regina Elena National Cancer InstitutePathology, IRCSS Regina Elena National Cancer InstituteDigestive Surgery, IRCSS Regina Elena National Cancer InstituteDigestive Surgery, IRCSS Regina Elena National Cancer InstituteMedical Oncology 1, IRCSS Regina Elena National Cancer InstituteClinical Pathology, IRCSS Regina Elena National Cancer InstituteClinical Pathology, IRCSS Regina Elena National Cancer InstituteOncogenomics Division, Eurofins Genoma GroupDigestive Surgery, IRCSS Regina Elena National Cancer InstituteOncogenomics and Epigenetics, IRCSS Regina Elena National Cancer InstituteOncogenomics Division, Eurofins Genoma GroupAbstract Background Liquid biopsy (LB) in early-stage, non-metastatic colorectal cancer (CRC) must be sensitive enough to detect extremely low circulating tumor DNA (ctDNA) levels. This challenge has been seldom and non-systematically investigated. Methods Next generation sequencing (NGS) and digital PCR (dPCR) were combined to test tumor DNAs (tDNAs) and paired ctDNAs collected at surgery from 39 patients, 12 of whom were also monitored during the immediate post-surgery follow up. Patients treated for metastatic disease (n = 14) were included as controls. Results NGS and dPCR concordantly (100% agreement) called at least one single nucleotide variant (SNV) in 34 tDNAs, estimated differences in allelic frequencies being negligible (±1.4%). However, despite dPCR testing, SNVs were only detectable in 15/34 (44.1%) ctDNAs from patients at surgery, as opposed to 14/14 (100%) metastatic patients. This was likely due to striking differences (average 10 times, up to 500) in ctDNA levels between groups. NGS revealed blood-only SNVs, suggesting spatial heterogeneity since pre-surgery disease stages, and raising the combined NGS/dPCR sensitivity to 58.8%. ctDNA levels at surgery correlated with neither tumor size, stage, grade, or nodal status, nor with variant abundance in paired tDNA. LB sensitivity reached 63.6% when ctDNA was combined with CEA. Finally, persistence and absence of ctDNA on the first conventional (month 3) post-surgery follow-up were associated with fast relapse and a disease-free status in 3 and 7 patients, respectively. Conclusions A simple clinical NGS/dPCR/CEA combination effectively addresses the LB challenge in a fraction of non-metastatic CRC patients.http://link.springer.com/article/10.1186/s13046-020-01569-zColorectal carcinomaLiquid biopsyCirculating tumor DNANext generation sequencingDigital PCR |
| spellingShingle | Matteo Allegretti Giuliano Cottone Fabio Carboni Ettore Cotroneo Beatrice Casini Elena Giordani Carla Azzurra Amoreo Simonetta Buglioni Maria Diodoro Edoardo Pescarmona Settimio Zazza Orietta Federici Massimo Zeuli Laura Conti Giovanni Cigliana Francesco Fiorentino Mario Valle Patrizio Giacomini Francesca Spinella Cross-sectional analysis of circulating tumor DNA in primary colorectal cancer at surgery and during post-surgery follow-up by liquid biopsy Journal of Experimental & Clinical Cancer Research Colorectal carcinoma Liquid biopsy Circulating tumor DNA Next generation sequencing Digital PCR |
| title | Cross-sectional analysis of circulating tumor DNA in primary colorectal cancer at surgery and during post-surgery follow-up by liquid biopsy |
| title_full | Cross-sectional analysis of circulating tumor DNA in primary colorectal cancer at surgery and during post-surgery follow-up by liquid biopsy |
| title_fullStr | Cross-sectional analysis of circulating tumor DNA in primary colorectal cancer at surgery and during post-surgery follow-up by liquid biopsy |
| title_full_unstemmed | Cross-sectional analysis of circulating tumor DNA in primary colorectal cancer at surgery and during post-surgery follow-up by liquid biopsy |
| title_short | Cross-sectional analysis of circulating tumor DNA in primary colorectal cancer at surgery and during post-surgery follow-up by liquid biopsy |
| title_sort | cross sectional analysis of circulating tumor dna in primary colorectal cancer at surgery and during post surgery follow up by liquid biopsy |
| topic | Colorectal carcinoma Liquid biopsy Circulating tumor DNA Next generation sequencing Digital PCR |
| url | http://link.springer.com/article/10.1186/s13046-020-01569-z |
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