title: HPV16 detection by qPCR method in relation to quantity and quality of DNA extracted from archival formalin fixed and paraffin embedded head and neck cancer tissues by three commercially available kits.
abstract: The aim of the present study was to compare HPV16 detection by quantitative polymerase chain reaction (qPCR) in relation to the quantity and quality of DNA isolated from 21 formalin fixed and paraffin embedded (FFPE) head and neck cancer tissues by three commercially available kits: EX-WAX™ DNA Extraction Kit (M) (Merck Millipore, Darmstadt, Germany), QIAamp(®) DNA FFPE Tissue (Q) (Qiagen, Hilden, Germany) and ReliaPrep™ FFPE gDNA Miniprep System (P) (Promega, Madison, USA). Quantity of extracted DNA was assessed spectrophometrically and fluorometrically. Its quality was analyzed using A260/280 and A260/230 ratios and the β-actin fragment amplifiability in qPCR. HPV16 presence was detected by qPCR, using specific primers and TaqMan probe. HPV infection was found in 8 DNA samples extracted with M kit (38.1%) and in 7 (33.3%) isolated with Q and P kits. Three samples from M and Q kits were characterized by HPV16 positivity and lack of β-actin amplifiability. They had significantly lower A260/280 ratio (M: 1.6±0.0, p=0.044 and Q: 1.7±0.0, p=0.016) compared to samples with both fragments amplification (M: 1.7±0.0 and Q: 1.9±0.0). Therefore, for HPV detection by qPCR in FFPE tissues we recommend ReliaPrep™ FFPE gDNA Miniprep System.
authors.affiliation: Department of Applied Radiobiology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Cracow Branch, 11 Garncarska Street, Cracow 31-115, Poland. Electronic address: z5biesag@cyfronet.pl.
authors.forename: Beata
authors.initials: B
authors.lastname: Biesaga
authors.affiliation: Department of Applied Radiobiology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Cracow Branch, 11 Garncarska Street, Cracow 31-115, Poland. Electronic address: janecka.zrk@gmail.com.
authors.forename: Anna
authors.initials: A
authors.lastname: Janecka
authors.affiliation: Department of Radiation Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Cracow Branch, 11 Garncarska Street, Cracow 31-115, Poland. Electronic address: annamucham@o2.pl.
authors.forename: Anna
authors.initials: A
authors.lastname: Mucha-Małecka
authors.affiliation: Department of Applied Radiobiology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Cracow Branch, 11 Garncarska Street, Cracow 31-115, Poland. Electronic address: a.adamczyk@yahoo.com.
authors.forename: Agnieszka
authors.initials: A
authors.lastname: Adamczyk
authors.affiliation: Department of Virology, Chair of Microbiology, Jagiellonian University Medical College, 18 Czysta Street, Cracow 31-121, Poland. Electronic address: sszostek@cm-uj.krakow.pl.
authors.forename: Sława
authors.initials: S
authors.lastname: Szostek
authors.affiliation: Department of Applied Radiobiology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Cracow Branch, 11 Garncarska Street, Cracow 31-115, Poland. Electronic address: z5slonin@cyfronet.pl.
authors.forename: Dorota
authors.initials: D
authors.lastname: Słonina
authors.affiliation: Department of Tumor Pathology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Cracow Branch, 11 Garncarska Street, Cracow 31-115, Poland. Electronic address: Krzysztofhalaszka@op.pl.
authors.forename: Krzysztof
authors.initials: K
authors.lastname: Halaszka
authors.affiliation: Department of Tumor Pathology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Cracow Branch, 11 Garncarska Street, Cracow 31-115, Poland. Electronic address: przewoznikmarcin@gmail.com.
authors.forename: Marcin
authors.initials: M
authors.lastname: Przewoźnik
mesh_terms: D004279:DNA, Viral / Q000235:genetics / Q000302:isolation & purification*; D006258:Head and Neck Neoplasms / Q000175:diagnosis* / Q000821:virology; D052162:Human papillomavirus 16 / Q000235:genetics / Q000302:isolation & purification*; D006801:Humans; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D030361:Papillomavirus Infections / Q000150:complications / Q000175:diagnosis*; D016612:Paraffin Embedding; D057089:Pathology, Molecular / Q000379:methods*; D011933:Reagent Kits, Diagnostic; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods*; D016707:Tissue Fixation
chemical_list: D004279:DNA, Viral; D011933:Reagent Kits, Diagnostic
keywords: DNA quality; FFPE tissue; HPV detection