{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,23]],"date-time":"2026-03-23T10:07:57Z","timestamp":1774260477338,"version":"3.50.1"},"reference-count":38,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2025,9,9]],"date-time":"2025-09-09T00:00:00Z","timestamp":1757376000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Lomonosov Moscow State University"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Cell-free DNA (cfDNA) analysis-based liquid biopsy is a rapidly emerging diagnostic and prognostic tool in pancreatic ductal adenocarcinoma (PDAC). KRAS point mutations are the main biomarkers used for the detection of tumor cfDNA. However, there is another less studied yet frequent genetic alteration in this gene, namely copy number gain (CNG). The aim of this study was to evaluate the diagnostic and prognostic potential of KRAS CNG analysis in plasma and bile of patients with PDAC using ddPCR. This study included healthy volunteers (n = 69), patients with PDAC (n = 94), and other pancreatic neoplasms (OPN) (n = 17). The sensitivity and specificity of KRAS CNG compared to the control group were 16% and 100% (AUC-ROC\u20140.580), and compared to the OPN group, 16% and 94% (AUC-ROC\u20140.554), respectively. Addition of KRAS point mutations to the analysis increased the sensitivity to 65% (AUC-ROC\u20140.824 and 0.801, respectively). Bile exhibited an equal KRAS CNG detection rate compared to plasma (20% vs. 16%). KRAS CNG was not associated with clinical parameters, except prognosis. The probability of survival was worse in patients with KRAS CNG (HR\u20143.54; 95% CI: 1.55\u20138.12; p = 0.001). KRAS CNG in cfDNA might be a promising biomarker for both diagnostic and prognostic purposes in PDAC.<\/jats:p>","DOI":"10.3390\/ijms26188763","type":"journal-article","created":{"date-parts":[[2025,9,10]],"date-time":"2025-09-10T10:27:12Z","timestamp":1757500032000},"page":"8763","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["KRAS Copy Number Gain in Cell-Free DNA Analysis-Based Liquid Biopsy of Plasma and Bile in Patients with Various Pancreatic Neoplasms"],"prefix":"10.3390","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6594-8113","authenticated-orcid":false,"given":"Mark","family":"Jain","sequence":"first","affiliation":[{"name":"University Clinic, Lomonosov Moscow State University, 119992 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Atayan","sequence":"additional","affiliation":[{"name":"Joint Stock Company \u201cIlyinsky Hospital\u201d, 143421 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4601-3478","authenticated-orcid":false,"given":"Tagir","family":"Rakhmatullin","sequence":"additional","affiliation":[{"name":"University Clinic, Lomonosov Moscow State University, 119992 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tatiana","family":"Dakhtler","sequence":"additional","affiliation":[{"name":"Joint Stock Company \u201cIlyinsky Hospital\u201d, 143421 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-5388-4356","authenticated-orcid":false,"given":"Victoria","family":"Inokenteva","sequence":"additional","affiliation":[{"name":"University Clinic, Lomonosov Moscow State University, 119992 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pavel","family":"Popov","sequence":"additional","affiliation":[{"name":"Joint Stock Company \u201cIlyinsky Hospital\u201d, 143421 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aleksandr","family":"Farmanov","sequence":"additional","affiliation":[{"name":"Joint Stock Company \u201cIlyinsky Hospital\u201d, 143421 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6551-8810","authenticated-orcid":false,"given":"Mikhail","family":"Viborniy","sequence":"additional","affiliation":[{"name":"Joint Stock Company \u201cIlyinsky Hospital\u201d, 143421 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4900-8997","authenticated-orcid":false,"given":"Iuliia","family":"Gontareva","sequence":"additional","affiliation":[{"name":"Joint Stock Company \u201cIlyinsky Hospital\u201d, 143421 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Larisa","family":"Samokhodskaya","sequence":"additional","affiliation":[{"name":"University Clinic, Lomonosov Moscow State University, 119992 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vyacheslav","family":"Egorov","sequence":"additional","affiliation":[{"name":"Joint Stock Company \u201cIlyinsky Hospital\u201d, 143421 Moscow, Russia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,9,9]]},"reference":[{"key":"ref_1","first-page":"229","article-title":"Global Cancer Statistics 2022: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries","volume":"74","author":"Bray","year":"2024","journal-title":"CA Cancer J. Clin."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"2913","DOI":"10.1158\/0008-5472.CAN-14-0155","article-title":"Projecting Cancer Incidence and Deaths to 2030: The Unexpected Burden of Thyroid, Liver, and Pancreas Cancers in the United States","volume":"74","author":"Rahib","year":"2014","journal-title":"Cancer Res."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"2008","DOI":"10.1016\/S0140-6736(20)30974-0","article-title":"Pancreatic Cancer","volume":"395","author":"Mizrahi","year":"2020","journal-title":"Lancet"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"9694","DOI":"10.3748\/wjg.v22.i44.9694","article-title":"Epidemiology of Pancreatic Cancer","volume":"22","author":"Ilic","year":"2016","journal-title":"World J. Gastroenterol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1039","DOI":"10.1056\/NEJMra1404198","article-title":"Pancreatic Adenocarcinoma","volume":"371","author":"Ryan","year":"2014","journal-title":"N. Engl. J. Med."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18063\/ghl.v2i1.243","article-title":"Pancreatic Cancer: Current Situation and Challenges","volume":"2","author":"Jin","year":"2020","journal-title":"Gastroenterol. Hepatol. Lett."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1016\/j.soc.2021.06.003","article-title":"Pathology and Molecular Characteristics of Pancreatic Cancer","volume":"30","author":"Kearney","year":"2021","journal-title":"Surg. Oncol. Clin."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1001\/jamasurg.2023.7010","article-title":"Optimal Surveillance Interval of Branch Duct Intraductal Papillary Mucinous Neoplasm of the Pancreas","volume":"159","author":"Han","year":"2024","journal-title":"JAMA Surg."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"891","DOI":"10.1097\/MEG.0000000000002415","article-title":"Diagnostic Value of Serum Carbohydrate Antigen 19-9 in Pancreatic Cancer: A Systematic Review and Meta-Analysis","volume":"34","author":"Zhao","year":"2022","journal-title":"Eur. J. Gastroenterol. Hepatol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1016\/S0953-6205(02)00002-X","article-title":"V High CA 19-9 Levels in Benign Biliary Tract Diseases. Report of Four Cases and Review of the Literature","volume":"13","author":"Katsanos","year":"2002","journal-title":"Eur. J. Intern. Med."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"5883","DOI":"10.21873\/anticanres.12931","article-title":"Relationship Between CA 19.9 and the Lewis Phenotype: Options to Improve Diagnostic Efficiency","volume":"38","author":"Santos","year":"2018","journal-title":"Anticancer Res."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1038\/s41392-024-02021-w","article-title":"Liquid Biopsy in Cancer: Current Status, Challenges and Future Prospects","volume":"9","author":"Ma","year":"2024","journal-title":"Signal Transduct. Target. Ther."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Boukovala, M., Westphalen, C.B., and Probst, V. (2024). Liquid Biopsy into the Clinics: Current Evidence and Future Perspectives. J. Liq. Biopsy, 4.","DOI":"10.1016\/j.jlb.2024.100146"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"243","DOI":"10.17816\/KMJ635015","article-title":"Liquid Biopsy in Pancreatic Ductal Adenocarcinoma and Precancerous Lesions","volume":"106","author":"Atayan","year":"2025","journal-title":"Kazan Med. J."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1007\/s12032-016-0745-9","article-title":"KRAS, BRAF, and PIK3CA Mutations, and Patient Prognosis in 126 Pancreatic Cancers: Pyrosequencing Technology and Literature Review","volume":"33","author":"Zhou","year":"2016","journal-title":"Med. Oncol."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Oketch, D.J.A., Giulietti, M., and Piva, F. (2024). Copy Number Variations in Pancreatic Cancer: From Biological Significance to Clinical Utility. Int. J. Mol. Sci., 25.","DOI":"10.3390\/ijms25010391"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1038\/s41588-019-0566-9","article-title":"Transcription Phenotypes of Pancreatic Cancer Are Driven by Genomic Events During Tumor Evolution","volume":"52","author":"Kim","year":"2020","journal-title":"Nat. Genet."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Mohan, S., Ayub, M., Rothwell, D.G., Gulati, S., Kilerci, B., Hollebecque, A., Sun Leong, H., Smith, N.K., Sahoo, S., and Descamps, T. (2019). Analysis of Circulating Cell-Free DNA Identifies KRAS Copy Number Gain and Mutation as a Novel Prognostic Marker in Pancreatic Cancer. Sci. Rep., 9.","DOI":"10.1038\/s41598-019-47489-7"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"e18581","DOI":"10.1097\/MD.0000000000018581","article-title":"Diagnostic Value of Various Liquid Biopsy Methods for Pancreatic Cancer: A Systematic Review and Meta-Analysis","volume":"99","author":"Zhu","year":"2020","journal-title":"Medicine"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"41","DOI":"10.23868\/gc321225","article-title":"Tumor Cell-Free DNA Detection-Based Liquid Biopsy of Plasma and Bile in Pancreatic Ductal Adenocarcinoma: A Pilot Study","volume":"18","author":"Jain","year":"2023","journal-title":"Genes Cells"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Jain, M., Atayan, D., Rakhmatullin, T., Dakhtler, T., Popov, P., Kim, P., Viborniy, M., Gontareva, I., Samokhodskaya, L., and Egorov, V. (2024). Cell-Free Tumor DNA Detection-Based Liquid Biopsy of Plasma and Bile in Patients with Various Pancreatic Neoplasms. Biomedicines, 12.","DOI":"10.3390\/biomedicines12010220"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1016\/j.suc.2009.12.004","article-title":"Palliation in Pancreatic Cancer","volume":"90","author":"Kruse","year":"2010","journal-title":"Surg. Clin. North Am."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1038\/nature05329","article-title":"Global Variation in Copy Number in the Human Genome","volume":"444","author":"Redon","year":"2006","journal-title":"Nature"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1126\/science.1098918","article-title":"Large-Scale Copy Number Polymorphism in the Human Genome","volume":"305","author":"Sebat","year":"2004","journal-title":"Science"},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Masood, D., Ren, L., Nguyen, C., Brundu, F.G., Zheng, L., Zhao, Y., Jaeger, E., Li, Y., Cha, S.W., and Halpern, A. (2024). Evaluation of Somatic Copy Number Variation Detection by NGS Technologies and Bioinformatics Tools on a Hyper-Diploid Cancer Genome. Genome Biol., 25.","DOI":"10.1186\/s13059-024-03294-8"},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Gilson, P., Merlin, J.L., and Harl\u00e9, A. (2022). Deciphering Tumour Heterogeneity: From Tissue to Liquid Biopsy. Cancers, 14.","DOI":"10.3390\/cancers14061384"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.1016\/j.asjsur.2019.12.011","article-title":"Complication Incidence of EUS-Guided Pancreas Biopsy: A Systematic Review and Meta-Analysis of 11 Thousand Population from 78 Cohort Studies","volume":"43","author":"Tian","year":"2020","journal-title":"Asian J. Surg."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"4303","DOI":"10.1158\/1078-0432.CCR-12-1075","article-title":"Genome-Wide Somatic Copy Number Alterations in Low-Grade PanINs and IPMNs from Individuals with a Family History of Pancreatic Cancer","volume":"18","author":"Hong","year":"2012","journal-title":"Clin. Cancer Res."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1760","DOI":"10.1038\/modpathol.2017.60","article-title":"Pancreatic Intraductal Tubulopapillary Neoplasm Is Genetically Distinct from Intraductal Papillary Mucinous Neoplasm and Ductal Adenocarcinoma","volume":"30","author":"Basturk","year":"2017","journal-title":"Mod. Pathol."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Driescher, C., Fuchs, K., Haeberle, L., Goering, W., Frohn, L., Opitz, F.V., Haeussinger, D., Knoefel, W.T., Keitel, V., and Esposito, I. (2020). Bile-Based Cell-Free DNA Analysis Is a Reliable Diagnostic Tool in Pancreatobiliary Cancer. Cancers, 13.","DOI":"10.3390\/cancers13010039"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"100275","DOI":"10.1016\/j.esmoop.2021.100275","article-title":"Cell-Free DNA from Bile Outperformed Plasma as a Potential Alternative to Tissue Biopsy in Biliary Tract Cancer","volume":"6","author":"Gou","year":"2021","journal-title":"ESMO Open"},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Grunvald, M.W., Jacobson, R.A., Kuzel, T.M., Pappas, S.G., and Masood, A. (2020). Current Status of Circulating Tumor DNA Liquid Biopsy in Pancreatic Cancer. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21207651"},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Toledano-Fonseca, M., Cano, M.T., Inga, E., Rodr\u00edguez-Alonso, R., G\u00f3mez-Espa\u00f1a, M.A., Guil-Luna, S., Mena-Osuna, R., de la Haba-Rodr\u00edguez, J.R., Rodr\u00edguez-Ariza, A., and Aranda, E. (2020). Circulating Cell-Free DNA-Based Liquid Biopsy Markers for the Non-Invasive Prognosis and Monitoring of Metastatic Pancreatic Cancer. Cancers, 12.","DOI":"10.3390\/cancers12071754"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1445","DOI":"10.1002\/ijc.32586","article-title":"Circulating Tumor DNA Quantity Is Related to Tumor Volume and Both Predict Survival in Metastatic Pancreatic Ductal Adenocarcinoma","volume":"146","author":"Strijker","year":"2019","journal-title":"Int. J. Cancer"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1507","DOI":"10.1200\/JCO.2019.37.15_suppl.1507","article-title":"Clonal Hematopoiesis of Indeterminate Potential (CHIP) Mutations in Solid Tumor Malignancies","volume":"37","author":"Conces","year":"2019","journal-title":"J. Clin. Oncol."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Roma, C., Sacco, A., Forgione, L., Esposito Abate, R., Lambiase, M., Dotolo, S., Maiello, M.R., Frezzetti, D., Nasti, G., and Morabito, A. (2022). Low Impact of Clonal Hematopoiesis on the Determination of RAS Mutations by Cell-Free DNA Testing in Routine Clinical Diagnostics. Diagnostics, 12.","DOI":"10.3390\/diagnostics12081956"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1016\/j.ajhg.2023.02.013","article-title":"Patterns of Mosaicism for Sequence and Copy-Number Variants Discovered Through Clinical Deep Sequencing of Disease-Related Genes in One Million Individuals","volume":"110","author":"Truty","year":"2023","journal-title":"Am. J. Hum. Genet."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"6499","DOI":"10.1007\/s00216-014-7835-3","article-title":"Towards Standardisation of Cell-Free DNA Measurement in Plasma: Controls for Extraction Efficiency, Fragment Size Bias and Quantification","volume":"406","author":"Devonshire","year":"2014","journal-title":"Anal. Bioanal. Chem."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/18\/8763\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T18:42:26Z","timestamp":1760035346000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/18\/8763"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,9,9]]},"references-count":38,"journal-issue":{"issue":"18","published-online":{"date-parts":[[2025,9]]}},"alternative-id":["ijms26188763"],"URL":"https:\/\/doi.org\/10.3390\/ijms26188763","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,9,9]]}}}