{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T15:28:20Z","timestamp":1784302100000,"version":"3.55.0"},"reference-count":39,"publisher":"SAGE Publications","license":[{"start":{"date-parts":[[2023,1,1]],"date-time":"2023-01-01T00:00:00Z","timestamp":1672531200000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":["journals.sagepub.com"],"crossmark-restriction":true},"short-container-title":["Cancer Control"],"published-print":{"date-parts":[[2023,1]]},"abstract":"<jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>Gene copy number variations have theranostic impact and require reliable methods for their identification. We aimed to evaluate the reliability of combined next-generation sequencing (NGS) and digital droplet PCR (ddPCR) method for gene amplification evaluation.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We conducted a retrospective multicentric observational study. MET\/ERBB2 amplifications were assessed in patients with lung or colorectal carcinoma (cohort A), from 2016 to 2020, by fluorescence in situ hybridization (FISH)\/immunohistochemistry (IHC), NGS and ddPCR. NGS-based script and ddPCR were then used to detect amplifications of 7 additional oncogenes ( EGFR, KRAS, BRAF, FGFR1, FGFR2, FGFR3, PIK3CA) in a cohort of patients (cohort B).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>55 patients (9 control, 25 ERBB2-amplified and 21 MET-amplified) out of 3779 patients tested were included in cohort A. Correlation coefficient between NGS-based script and FISH\/IHC results were .88 for MET (P &lt; .001) and .89 (P &lt; .001) for ERBB2. Using a threshold ratio of 1.56 with the NGS-based script, the sensitivity was 100% for both genes and the specificity 69% for MET and 90% for ERBB2, respectively . With an alternative 1.76 threshold, sensitivity was 94% for MET and 96% for ERBB2, while specificity was 85% for MET and 90% for ERBB2. Correlation coefficient between FISH and ddPCR ratio was .90 for MET and .88 for ERBB2. In both cohorts, NGS-based script and ddPCR results were significantly correlated regarding all genes (P &lt; .001).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>Combined NGS-based script and ddPCR method is reliable and easily feasible for the detection of gene amplifications, providing useful data for guided therapy in cancer.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1177\/10732748231167257","type":"journal-article","created":{"date-parts":[[2023,6,30]],"date-time":"2023-06-30T01:11:55Z","timestamp":1688087515000},"update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":3,"title":["Detection of Nine Oncogenes Amplification in Lung and Colorectal Cancer Formalin-Fixed Paraffin-Embedded Tissue Samples using Combined Next-Generation Sequencing-Based Script and Digital Droplet Polymerase Chain Reaction"],"prefix":"10.1177","volume":"30","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5446-6197","authenticated-orcid":false,"given":"Christophe","family":"Bontoux","sequence":"first","affiliation":[{"name":"Laboratory of Clinical and Experimental Pathology, Centre Hospitalier Universitaire de Nice, Universit\u00e9 C\u00f4te d'Azur, Hospital-Integrated Biobank, H\u00f4pital Pasteur, Nice, France"},{"name":"Department of Genetics, University Hospital Bichat-Claude Bernard, AP-HP, Paris University, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alice","family":"Guyard","sequence":"additional","affiliation":[{"name":"Department of Genetics, University Hospital Bichat-Claude Bernard, AP-HP, Paris University, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Audrey","family":"Lupo","sequence":"additional","affiliation":[{"name":"Department of Pathology, University Hospital Bichat-Claude Bernard, AP-HP, University Paris-Diderot, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karim","family":"Diallo","sequence":"additional","affiliation":[{"name":"Laboratory of Clinical and Experimental Pathology, Centre Hospitalier Universitaire de Nice, Universit\u00e9 C\u00f4te d'Azur, Hospital-Integrated Biobank, H\u00f4pital Pasteur, Nice, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Khedidja","family":"Rebah","sequence":"additional","affiliation":[{"name":"Laboratory of Clinical and Experimental Pathology, Centre Hospitalier Universitaire de Nice, Universit\u00e9 C\u00f4te d'Azur, Hospital-Integrated Biobank, H\u00f4pital Pasteur, Nice, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Agathe","family":"Hercent","sequence":"additional","affiliation":[{"name":"Laboratory of Clinical and Experimental Pathology, Centre Hospitalier Universitaire de Nice, Universit\u00e9 C\u00f4te d'Azur, Hospital-Integrated Biobank, H\u00f4pital Pasteur, Nice, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edouard","family":"Guenzi","sequence":"additional","affiliation":[{"name":"Laboratory of Clinical and Experimental Pathology, Centre Hospitalier Universitaire de Nice, Universit\u00e9 C\u00f4te d'Azur, Hospital-Integrated Biobank, H\u00f4pital Pasteur, Nice, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J\u00e9rome","family":"Cros","sequence":"additional","affiliation":[{"name":"Department of Pathology, H\u00f4pitaux Universitaire Paris Centre, H\u00f4pital Cochin, AP-HP, Universit\u00e9 de Paris, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J\u00e9rome","family":"Lamoril","sequence":"additional","affiliation":[{"name":"Laboratory of Clinical and Experimental Pathology, Centre Hospitalier Universitaire de Nice, Universit\u00e9 C\u00f4te d'Azur, Hospital-Integrated Biobank, H\u00f4pital Pasteur, Nice, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karen","family":"Leroy","sequence":"additional","affiliation":[{"name":"Department of Pathology, University Hospital Beaujon, AP-HP, University Paris-Diderot, Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nathalie","family":"Theou-Anton","sequence":"additional","affiliation":[{"name":"Laboratory of Clinical and Experimental Pathology, Centre Hospitalier Universitaire de Nice, Universit\u00e9 C\u00f4te d'Azur, Hospital-Integrated Biobank, H\u00f4pital Pasteur, Nice, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"179","published-online":{"date-parts":[[2023,6,29]]},"reference":[{"key":"bibr1-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1053\/j.gastro.2015.05.061"},{"key":"bibr2-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1016\/j.humpath.2015.06.007"},{"key":"bibr3-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1200\/JCO.19.00033"},{"issue":"1","key":"bibr4-10732748231167257","first-page":"63","volume":"13","author":"Pauletti G","year":"1996","journal-title":"Oncogene"},{"key":"bibr5-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(16)32417-5"},{"key":"bibr6-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1093\/annonc\/mdy100"},{"key":"bibr7-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0171280"},{"key":"bibr8-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1186\/s13045-019-0759-9"},{"key":"bibr9-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1002\/path.2267"},{"key":"bibr10-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1186\/bcr1262"},{"key":"bibr11-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1002\/path.2601"},{"key":"bibr12-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1200\/JCO.2012.43.0454"},{"key":"bibr13-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1158\/0008-5472.CAN-06-0191"},{"key":"bibr14-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1038\/s41379-020-0560-x"},{"key":"bibr15-10732748231167257","doi-asserted-by":"publisher","DOI":"10.3390\/cancers11081197"},{"key":"bibr16-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1158\/2159-8290.CD-14-1518"},{"key":"bibr17-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1038\/s41571-018-0115-y"},{"key":"bibr18-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1200\/JCO.2018.77.8738"},{"key":"bibr19-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1038\/modpathol.2015.98"},{"key":"bibr20-10732748231167257","doi-asserted-by":"publisher","DOI":"10.5858\/arpa.2016-0331-CP"},{"key":"bibr21-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1038\/gim.2015.156"},{"key":"bibr22-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1016\/j.yexmp.2018.04.004"},{"key":"bibr23-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2014.170"},{"key":"bibr24-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-02217-x"},{"key":"bibr25-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1007\/s12032-018-1210-8"},{"key":"bibr26-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1016\/j.csbj.2019.09.003"},{"key":"bibr27-10732748231167257","doi-asserted-by":"publisher","DOI":"10.7326\/0003-4819-147-8-200710160-00010"},{"key":"bibr28-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0181968"},{"key":"bibr29-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1186\/s40164-021-00245-y"},{"key":"bibr30-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1093\/annonc\/mdz407"},{"key":"bibr31-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1007\/s11523-021-00811-8"},{"key":"bibr32-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1016\/S1470-2045(19)30785-5"},{"key":"bibr33-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa2002787"},{"key":"bibr34-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1158\/2159-8290.CD-12-0095"},{"key":"bibr35-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1126\/scisignal.2004088"},{"key":"bibr36-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1080\/14737140.2019.1643239"},{"key":"bibr37-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1158\/0008-5472.CAN-16-2359"},{"key":"bibr38-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1200\/JCO.18.00177"},{"key":"bibr39-10732748231167257","doi-asserted-by":"publisher","DOI":"10.1158\/1078-0432.CCR-19-2035"}],"container-title":["Cancer Control"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.1177\/10732748231167257","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/full-xml\/10.1177\/10732748231167257","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.1177\/10732748231167257","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,28]],"date-time":"2026-04-28T14:23:28Z","timestamp":1777386208000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.sagepub.com\/doi\/10.1177\/10732748231167257"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,1]]},"references-count":39,"alternative-id":["10.1177\/10732748231167257"],"URL":"https:\/\/doi.org\/10.1177\/10732748231167257","relation":{"has-review":[{"id-type":"doi","id":"10.1177\/10732748231167257\/v1\/decision1","asserted-by":"object"},{"id-type":"doi","id":"10.1177\/10732748231167257\/v2\/review2","asserted-by":"object"},{"id-type":"doi","id":"10.1177\/10732748231167257\/v2\/decision1","asserted-by":"object"},{"id-type":"doi","id":"10.1177\/10732748231167257\/v1\/review2","asserted-by":"object"},{"id-type":"doi","id":"10.1177\/10732748231167257\/v1\/review1","asserted-by":"object"},{"id-type":"doi","id":"10.1177\/10732748231167257\/v2\/review1","asserted-by":"object"}]},"ISSN":["1073-2748","1526-2359"],"issn-type":[{"value":"1073-2748","type":"print"},{"value":"1526-2359","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,1]]},"article-number":"10732748231167257"}}