{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T01:39:18Z","timestamp":1790905158623,"version":"4.1.0"},"reference-count":37,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T00:00:00Z","timestamp":1777420800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"BMO Financial Chair in Precision Genomics","award":["BMO Financial Chair in Precision Genomics"],"award-info":[{"award-number":["BMO Financial Chair in Precision Genomics"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Circulating tumor DNA (ctDNA) has many potential applications in the management of cancer, including detection, monitoring, and treatment response assessment. This study evaluates pre-treatment ctDNA detection in a single-institution pan-cancer cohort using a highly sensitive tumor-informed ctDNA assay. Participant samples were collected at the University Health Network across six study cohorts. A total of 273 patients with stage II-IV cancers spanning 16 tumor types were analyzed using a personalized tumor-informed assay (RaDaR\u00ae). Harmonized methods were employed to mitigate the impact of variables known to influence ctDNA detection and its quantification. Pre-treatment ctDNA was detected in 83% of participants (226\/273) across all stages and cancer types. Detection rates varied by clinical characteristics, including cancer type and stage; ctDNA was detected in 100% of stage IV metastatic recurrent high-grade serous ovarian cancer (HGSOC) patients (n = 8\/8) and 54% of stage IV melanoma patients (n = 6\/11). The median estimated variant allele fraction (eVAF) across all patients with a positive ctDNA result was 0.25% (range: 0.000029\u201337.7%), varied by tumor type and increased with cancer stage. A total of 11% of positive samples (24\/226) had an eVAF of &lt;0.01%. This pan-cancer ctDNA analysis using a highly sensitive assay reveals high detection rates overall, including ~10% at low levels (&lt;0.01% eVAF), offering a reference for future clinical ctDNA applications and furthering our understanding of factors influencing ctDNA measurements.<\/jats:p>","DOI":"10.3390\/ijms27093979","type":"journal-article","created":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T15:01:18Z","timestamp":1777474878000},"page":"3979","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Pan-Cancer Pre-Treatment ctDNA Detection Using a Highly Sensitive Tumor-Informed Assay"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3618-9936","authenticated-orcid":false,"given":"Scott","family":"Strum","sequence":"first","affiliation":[{"name":"Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada"},{"name":"Department of Medical Oncology, Arthur J.E. Child Comprehensive Cancer Centre, University of Calgary, Calgary, AB T2N 5G2, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clodagh","family":"Murray","sequence":"additional","affiliation":[{"name":"NeoGenomics, Inc., Fort Myers, FL 33912, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sofia","family":"Genta","sequence":"additional","affiliation":[{"name":"Department of Oncology, Queen\u2019s School of Medicine, Queen\u2019s University, Kingston, ON K7L 3N6, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Enrique","family":"Sanz-Garcia","sequence":"additional","affiliation":[{"name":"Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Albiruni","family":"Razak","sequence":"additional","affiliation":[{"name":"Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephanie","family":"Lheureux","sequence":"additional","affiliation":[{"name":"Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christodoulos","family":"Pipinikas","sequence":"additional","affiliation":[{"name":"NeoGenomics, Inc., Fort Myers, FL 33912, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ben X.","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amber","family":"Chevalier","sequence":"additional","affiliation":[{"name":"NeoGenomics, Inc., Fort Myers, FL 33912, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7357-2737","authenticated-orcid":false,"given":"Christopher G.","family":"Smith","sequence":"additional","affiliation":[{"name":"NeoGenomics, Inc., Fort Myers, FL 33912, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3034-3042","authenticated-orcid":false,"given":"Anna","family":"Spreafico","sequence":"additional","affiliation":[{"name":"Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3500-0540","authenticated-orcid":false,"given":"Lillian L.","family":"Siu","sequence":"additional","affiliation":[{"name":"Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6711-7287","authenticated-orcid":false,"given":"Mitchell","family":"Elliott","sequence":"additional","affiliation":[{"name":"Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1080-0998","authenticated-orcid":false,"given":"David W.","family":"Cescon","sequence":"additional","affiliation":[{"name":"Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,4,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1617","DOI":"10.1016\/j.cell.2024.02.041","article-title":"Cancer biomarkers: Emerging trends and clinical implications for personalized treatment","volume":"187","author":"Passaro","year":"2024","journal-title":"Cell"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1038\/s41392-024-01823-2","article-title":"Tumor biomarkers for diagnosis, prognosis and targeted therapy","volume":"9","author":"Zhou","year":"2024","journal-title":"Signal Transduct. Target. Ther."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"600","DOI":"10.1038\/s41571-022-00660-y","article-title":"Circulating tumour DNA\u2014Looking beyond the blood","volume":"19","author":"Tivey","year":"2022","journal-title":"Nat. Rev. Clin. Oncol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"101883","DOI":"10.1016\/j.tranon.2024.101883","article-title":"Corresponding ctDNA and tumor burden dynamics in metastatic melanoma patients on systemic treatment","volume":"42","author":"Egger","year":"2024","journal-title":"Transl. Oncol."},{"key":"ref_5","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_6","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1080\/15384047.2021.1963166","article-title":"Clinical and biological determinants of circulating tumor DNA detection and prognostication using a next-generation sequencing panel assay","volume":"22","author":"Hsiehchen","year":"2021","journal-title":"Cancer Biol. Ther."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1016\/j.cell.2020.09.001","article-title":"Noninvasive Early Identification of Therapeutic Benefit from Immune Checkpoint Inhibition","volume":"183","author":"Nabet","year":"2020","journal-title":"Cell"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"985","DOI":"10.1038\/nm.1789","article-title":"Circulating mutant DNA to assess tumor dynamics","volume":"14","author":"Diehl","year":"2008","journal-title":"Nat. Med."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1016\/j.lungcan.2022.01.013","article-title":"Exploitation of treatment induced tumor lysis to enhance the sensitivity of ctDNA analysis: A first-in-human pilot study","volume":"165","author":"Breadner","year":"2022","journal-title":"Lung Cancer"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1016\/S1470-2045(20)30726-9","article-title":"Circulating tumour DNA in patients with advanced melanoma treated with dabrafenib or dabrafenib plus trametinib: A clinical validation study","volume":"22","author":"Syeda","year":"2021","journal-title":"Lancet Oncol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1016\/j.annonc.2020.11.007","article-title":"Circulating tumor DNA in neoadjuvant-treated breast cancer reflects response and survival","volume":"32","author":"Magbanua","year":"2020","journal-title":"Ann. Oncol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"2261","DOI":"10.1056\/NEJMoa2200075","article-title":"Circulating Tumor DNA Analysis Guiding Adjuvant Therapy in Stage II Colon Cancer","volume":"386","author":"Tie","year":"2022","journal-title":"N. Engl. J. Med."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"e154941","DOI":"10.1172\/JCI154941","article-title":"Circulating tumor DNA: Current challenges for clinical utility","volume":"132","author":"Dang","year":"2022","journal-title":"J. Clin. Investig."},{"key":"ref_14","first-page":"263","article-title":"Minimal residual disease in colorectal cancer. Tumor-informed versus tumor-agnostic approaches: Unraveling the optimal strategy","volume":"36","author":"Camblor","year":"2024","journal-title":"Ann. Oncol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"eabi8618","DOI":"10.1126\/sciadv.abi8618","article-title":"Monitoring and adapting cancer treatment using circulating tumor DNA kinetics: Current research, opportunities, and challenges","volume":"8","author":"Zhao","year":"2022","journal-title":"Sci. Adv."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Chan, H.T., Nagayama, S., Otaki, M., Chin, Y.M., Fukunaga, Y., Ueno, M., Nakamura, Y., and Low, S.K. (2023). Tumor-informed or tumor-agnostic circulating tumor DNA as a biomarker for risk of recurrence in resected colorectal cancer patients. Front. Oncol., 12.","DOI":"10.3389\/fonc.2022.1055968"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"e16505","DOI":"10.15252\/emmm.202216505","article-title":"Comparison of tumor-informed and tumor-na\u00efve sequencing assays for ctDNA detection in breast cancer","volume":"15","author":"Santonja","year":"2023","journal-title":"EMBO Mol. Med."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1038\/s41467-020-20162-8","article-title":"Pan-cancer circulating tumor DNA detection in over 10,000 Chinese patients","volume":"12","author":"Zhang","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"224ra24","DOI":"10.1126\/scitranslmed.3007094","article-title":"Detection of circulating tumor DNA in early- and late-stage human malignancies","volume":"6","author":"Bettegowda","year":"2014","journal-title":"Sci. Transl. Med."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"18682","DOI":"10.1038\/s41598-020-75792-1","article-title":"Circulating tumor DNA (ctDNA) detection is associated with shorter progression-free survival in advanced melanoma patients","volume":"10","author":"Marczynski","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1130","DOI":"10.1093\/annonc\/mdx026","article-title":"Circulating tumour DNA predicts response to anti-PD1 antibodies in metastatic melanoma","volume":"28","author":"Lee","year":"2017","journal-title":"Ann. Oncol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"103109","DOI":"10.1016\/j.critrevonc.2020.103109","article-title":"ctDNA as a cancer biomarker: A broad overview","volume":"155","author":"Pessoa","year":"2020","journal-title":"Crit. Rev. Oncol. Hematol."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"S\u00e1nchez-Herrero, E., Serna-Blasco, R., Robado de Lope, L., Gonz\u00e1lez-Rumayor, V., Romero, A., and Provencio, M. (2022). Circulating Tumor DNA as a Cancer Biomarker: An Overview of Biological Features and Factors That may Impact on ctDNA Analysis. Front. Oncol., 12.","DOI":"10.3389\/fonc.2022.943253"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"107830","DOI":"10.1016\/j.celrep.2020.107830","article-title":"Senescence, Necrosis, and Apoptosis Govern Circulating Cell-free DNA Release Kinetics","volume":"31","author":"Rostami","year":"2020","journal-title":"Cell Rep."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"266","DOI":"10.1158\/1078-0432.CCR-18-1941","article-title":"Clinical Significance of Extracellular Vesicles in Plasma from Glioblastoma Patients","volume":"25","author":"Osti","year":"2019","journal-title":"Clin. Cancer Res."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Logozzi, M., Mizzoni, D., Di Raimo, R., Giuliani, A., Maggi, M., Sciarra, A., and Fais, S. (2021). Plasmatic Exosome Number and Size Distinguish Prostate Cancer Patients From Healthy Individuals: A Prospective Clinical Study. Front. Oncol., 11.","DOI":"10.3389\/fonc.2021.727317"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"e89829","DOI":"10.1172\/jci.insight.89829","article-title":"The head and neck cancer immune landscape and its immunotherapeutic implications","volume":"1","author":"Mandal","year":"2016","journal-title":"JCI Insight"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"56781","DOI":"10.18632\/oncotarget.10788","article-title":"Gene expression analysis of TIL rich HPV-driven head and neck tumors reveals a distinct B-cell signature when compared to HPV independent tumors","volume":"7","author":"Wood","year":"2016","journal-title":"Oncotarget"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1837","DOI":"10.1038\/s41467-025-56658-4","article-title":"Longitudinal evaluation of circulating tumor DNA in patients undergoing neoadjuvant therapy for early breast cancer using a tumor-informed assay","volume":"16","author":"Elliott","year":"2025","journal-title":"Nat. Commun."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1038\/s41523-025-00783-2","article-title":"Personalized ctDNA monitoring in metastatic HR+\/HER2- breast cancer patients during endocrine and CDK4\/6 inhibitor therapy","volume":"11","author":"Elliott","year":"2025","journal-title":"NPJ Breast Cancer"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"460","DOI":"10.1038\/s41418-024-01272-y","article-title":"Multimodal detection of molecular residual disease in high-risk locally advanced squamous cell carcinoma of the head and neck","volume":"31","author":"Zou","year":"2024","journal-title":"Cell Death Differ."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"103978","DOI":"10.1016\/j.esmoop.2024.103978","article-title":"Bespoke ctDNA for longitudinal detection of molecular residual disease in high-risk melanoma patients","volume":"9","author":"Genta","year":"2024","journal-title":"ESMO Open"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1016\/j.ejca.2023.04.014","article-title":"Circulating tumour DNA kinetics in recurrent\/metastatic head and neck squamous cell cancer patients","volume":"188","author":"Taylor","year":"2023","journal-title":"Eur. J. Cancer"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"2737","DOI":"10.1038\/s41591-025-03735-2","article-title":"Early detection of multiple cancer types using multidimensional cell-free DNA fragmentomics","volume":"31","author":"Bao","year":"2025","journal-title":"Nat. Med."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"e766","DOI":"10.1002\/mco2.766","article-title":"Circulating tumor DNA methylation detection as biomarker and its application in tumor liquid biopsy: Advances and challenges","volume":"5","author":"Li","year":"2024","journal-title":"MedComm"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1038\/s41698-026-01309-0","article-title":"Personalized ctDNA analysis for detection of residual disease and recurrence in surgically treated HNSCC patients","volume":"10","author":"Flach","year":"2026","journal-title":"NPJ Precis. Oncol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1186\/s40425-019-0541-0","article-title":"An interim report on the investigator-initiated phase 2 study of pembrolizumab immunological response evaluation (INSPIRE)","volume":"7","author":"Clouthier","year":"2019","journal-title":"J. Immunother. Cancer"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/9\/3979\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T04:20:14Z","timestamp":1778214014000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/9\/3979"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,4,29]]},"references-count":37,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,5]]}},"alternative-id":["ijms27093979"],"URL":"https:\/\/doi.org\/10.3390\/ijms27093979","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,4,29]]}}}