{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T19:28:30Z","timestamp":1780514910324,"version":"3.54.1"},"reference-count":47,"publisher":"MDPI AG","issue":"15","license":[{"start":{"date-parts":[[2025,7,29]],"date-time":"2025-07-29T00:00:00Z","timestamp":1753747200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004410","name":"TUB\u0130TAK, T\u00fcrkiye Bilimsel ve Teknolojik Ara\u015ft\u0131rma Kurumu","doi-asserted-by":"publisher","award":["120N391"],"award-info":[{"award-number":["120N391"]}],"id":[{"id":"10.13039\/501100004410","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Diagnostics"],"abstract":"<jats:p>Background: Cell-free DNA (cfDNA) has become a cornerstone of liquid biopsy applications, offering promise for early disease detection and monitoring. However, its widespread clinical adoption is limited by variability in pre-analytical processing, especially during isolation. Current extraction methods face challenges in yield, purity, and reproducibility. Methods: We developed and optimized SafeCAP 2.0, a novel magnetic bead-based cfDNA extraction kit, focusing on efficient recovery, minimal genomic DNA contamination, and PCR compatibility. Optimization involved systematic evaluation of magnetic bead chemistry, buffer composition, and reagent volumes. Performance was benchmarked against a commercial reference kit (Apostle MiniMax) using spiked oligonucleotides and plasma from patients with stage IV NSCLC. Results: The optimized protocol demonstrated superior recovery with a limit of detection (LoD) as low as 0.3 pg\/\u00b5L and a limit of quantification (LoQ) of 1 pg\/\u03bcL with no detectable PCR inhibition. In comparative studies, SafeCAP 2.0 showed equivalent or improved performance over the commercial kit. Clinical validation using 47 patient plasma samples confirmed robust cfDNA recovery and fragment integrity. Conclusions: SafeCAP 2.0 offers a cost-effective, high-performance solution for cfDNA extraction in both research and clinical workflows. Its design and validation address key pre-analytical barriers, supporting integration into routine diagnostics and precision medicine platforms.<\/jats:p>","DOI":"10.3390\/diagnostics15151897","type":"journal-article","created":{"date-parts":[[2025,7,29]],"date-time":"2025-07-29T08:00:41Z","timestamp":1753776041000},"page":"1897","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Design, Development, and Clinical Validation of a Novel Kit for Cell-Free DNA Extraction"],"prefix":"10.3390","volume":"15","author":[{"given":"Ekin","family":"\u00c7elik","sequence":"first","affiliation":[{"name":"Department of Medical Biology, Faculty of Medicine, K\u0131r\u015fehir Ahi Evran University, K\u0131r\u015fehir 40100, T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hande","family":"G\u00fcner","sequence":"additional","affiliation":[{"name":"ZipPrime Biotechnology Co., Eski\u015fehir 26190, T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gizem","family":"Kayal\u0131","sequence":"additional","affiliation":[{"name":"ZipPrime Biotechnology Co., Eski\u015fehir 26190, T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4391-1387","authenticated-orcid":false,"given":"Haktan Bagis","family":"Erdem","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics, Ankara Etlik City Hospital, Ankara 06170, T\u00fcrkiye"},{"name":"Department of Medical Genetics, Ankara Dr. Abdurrahman Yurtaslan Oncology Training and Research Hospital, University of Health Sciences, Ankara 06200, T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Taha","family":"Bahsi","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics, Ankara Dr. Abdurrahman Yurtaslan Oncology Training and Research Hospital, University of Health Sciences, Ankara 06200, T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hasan Huseyin","family":"Kazan","sequence":"additional","affiliation":[{"name":"Department of Medical Biology, Gulhane Faculty of Health Sciences, University of Health Sciences, Ankara 06010, T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,7,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"758","DOI":"10.1016\/j.tig.2021.04.005","article-title":"The nexus of cfDNA and nuclease biology","volume":"37","author":"Han","year":"2021","journal-title":"Trends Genet."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Kowal-Wisniewska, E., Jaskiewicz, K., Bartochowska, A., Kiwerska, K., Ustaszewski, A., Gorecki, T., Giefing, M., Paluszczak, J., Wierzbicka, M., and Jarmuz-Szymczak, M. 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