Evaluation and Comparison of Genomic DNA Extraction Methods and PCR Optimization on Archival Formalin-Fixed and Paraffin-Embedded Tissues of Oral Squamous Cell Carcinoma
Samar Saeed Khan,
Manisha Tijare,
Sowmya Kasetty,
Megha Jain,
Ahmed Alamoudi,
Hammam Ahmed Bahammam,
Sarah Ahmed Bahammam,
Maha A. Bahammam,
Saranya Varadarajan,
A. Thirumal Raj,
Shankargouda Patil
Affiliations
Samar Saeed Khan
Division of Maxillofacial Surgery and Diagnostic Sciences, Department of Oral and Maxillofacial Pathology, College of Dentistry, Jazan University, Jazan 45142, Saudi Arabia
Manisha Tijare
Department of Dentistry, Government Medical College and Hospital, Gondia 441601, India
Sowmya Kasetty
Oral Pathology Division, Oral Basic and Clinical Sciences, College of Dentistry, Qassim Private College, Buraidah 52571, Saudi Arabia
Megha Jain
Department of Dentistry, Chhindwara Institute of Medical Sciences, Chhindwara 480001, India
Ahmed Alamoudi
Department of Oral Biology, College of Dentistry, King Abdulaziz University, P.O. Box 80209, Jeddah 21589, Saudi Arabia
Hammam Ahmed Bahammam
Department of Pediatric Dentistry, College of Dentistry, King Abdulaziz University, P.O. Box 80209, Jeddah 21589, Saudi Arabia
Sarah Ahmed Bahammam
Department of Pediatric Dentistry and Orthodontics, College of Dentistry, Taibah University, Universities Road, P.O. Box 344, Medina 46526, Saudi Arabia
Maha A. Bahammam
Department of Periodontology, Faculty of Dentistry, King Abdulaziz University, P.O. Box 80209, Jeddah 21589, Saudi Arabia
Saranya Varadarajan
Department of Oral Pathology and Microbiology, Sri Venkateswara Dental College and Hospital, Chennai 600130, India
A. Thirumal Raj
Department of Oral Pathology and Microbiology, Sri Venkateswara Dental College and Hospital, Chennai 600130, India
Shankargouda Patil
Department of Maxillofacial Surgery and Diagnostic Science, Division of Oral Pathology, College of Dentistry, Jazan University, Jazan 45142, Saudi Arabia
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–chloroform 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–chloroform DNA isolation protocol.
