{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,29]],"date-time":"2026-10-29T07:45:17Z","timestamp":1793259917976,"version":"4.5.0"},"reference-count":34,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2022,5,12]],"date-time":"2022-05-12T00:00:00Z","timestamp":1652313600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Diagnostics"],"abstract":"<jats:p>Recovery and amplification of nucleic acids from archived formalin-fixed tissue samples is the most developing field in retrospective genetic studies. We compared different deparaffinization methods and DNA isolation techniques, and intergroup comparisons were performed to evaluate the effectiveness of different storing methods for archival OSCC samples based on obtained mean DNA quantity, quality, and PCR amplification of the P53 gene. The study comprised 75 archival histologically diagnosed OSCC samples which were divided into Group I: Formalin-fixed paraffin-embedded tissue blocks and Group II: Long-term formalin-fixed tissue. A comparison of different deparaffinization methods showed that xylene deparaffinization is an efficient method to obtain suitable DNA. Comparing different DNA isolation techniques illustrated that the conventional phenol\u2013chloroform method gives better integrity to DNA in contrast with the kit method. Comparison between FFPET and long-term FFT samples demonstrated that samples fixed in formalin overnight and embedded in wax yield better quality and quantity DNA in comparison with long-term samples fixed in formalin. To obtain suitable integrity of DNA, tissue samples should be stored by fixing in formalin overnight followed by preparation of paraffin tissue blocks, deparaffinization by xylene, and subjecting them to the conventional phenol\u2013chloroform DNA isolation protocol.<\/jats:p>","DOI":"10.3390\/diagnostics12051219","type":"journal-article","created":{"date-parts":[[2022,5,12]],"date-time":"2022-05-12T21:46:53Z","timestamp":1652392013000},"page":"1219","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Evaluation and Comparison of Genomic DNA Extraction Methods and PCR Optimization on Archival Formalin-Fixed and Paraffin-Embedded Tissues of Oral Squamous Cell Carcinoma"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9199-9152","authenticated-orcid":false,"given":"Samar Saeed","family":"Khan","sequence":"first","affiliation":[{"name":"Division of Maxillofacial Surgery and Diagnostic Sciences, Department of Oral and Maxillofacial Pathology, College of Dentistry, Jazan University, Jazan 45142, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manisha","family":"Tijare","sequence":"additional","affiliation":[{"name":"Department of Dentistry, Government Medical College and Hospital, Gondia 441601, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sowmya","family":"Kasetty","sequence":"additional","affiliation":[{"name":"Oral Pathology Division, Oral Basic and Clinical Sciences, College of Dentistry, Qassim Private College, Buraidah 52571, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Megha","family":"Jain","sequence":"additional","affiliation":[{"name":"Department of Dentistry, Chhindwara Institute of Medical Sciences, Chhindwara 480001, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7459-5324","authenticated-orcid":false,"given":"Ahmed","family":"Alamoudi","sequence":"additional","affiliation":[{"name":"Department of Oral Biology, College of Dentistry, King Abdulaziz University, P.O. Box 80209, Jeddah 21589, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5946-5337","authenticated-orcid":false,"given":"Hammam Ahmed","family":"Bahammam","sequence":"additional","affiliation":[{"name":"Department of Pediatric Dentistry, College of Dentistry, King Abdulaziz University, P.O. Box 80209, Jeddah 21589, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah Ahmed","family":"Bahammam","sequence":"additional","affiliation":[{"name":"Department of Pediatric Dentistry and Orthodontics, College of Dentistry, Taibah University, Universities Road, P.O. Box 344, Medina 46526, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maha A.","family":"Bahammam","sequence":"additional","affiliation":[{"name":"Department of Periodontology, Faculty of Dentistry, King Abdulaziz University, P.O. Box 80209, Jeddah 21589, Saudi Arabia"},{"name":"Executive Presidency of Academic Affairs, Saudi Commission for Health Specialties, Riyadh 11614, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7051-1143","authenticated-orcid":false,"given":"Saranya","family":"Varadarajan","sequence":"additional","affiliation":[{"name":"Department of Oral Pathology and Microbiology, Sri Venkateswara Dental College and Hospital, Chennai 600130, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1079-1024","authenticated-orcid":false,"given":"A. Thirumal","family":"Raj","sequence":"additional","affiliation":[{"name":"Department of Oral Pathology and Microbiology, Sri Venkateswara Dental College and Hospital, Chennai 600130, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7246-5497","authenticated-orcid":false,"given":"Shankargouda","family":"Patil","sequence":"additional","affiliation":[{"name":"Department of Maxillofacial Surgery and Diagnostic Science, Division of Oral Pathology, College of Dentistry, Jazan University, Jazan 45142, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,5,12]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Huijsmans, C.J., Damen, J., van der Linden, J.C., Savelkoul, P.H., and Hermans, M.H. (2010). Comparative analysis of four methods to extract DNA from paraffin-embedded tissues: Effect on downstream molecular applications. BMC Res. 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