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Updated: Nov 11, 2025
Chromogenic In Situ Hybridization as a Tool for HPV-Related Head and Neck Cancer Diagnosis
Published on: June 14, 2019
Human DNA decays faster with time than viral dsDNA: an analysis on HPV16 using pathology archive samples spanning
Sara Nicolás-Párraga1, Montserrat Torres2, Laia Alemany3,4,5
1Infections and Cancer Laboratory, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Granvia de L'Hospitalet 199-203, 08908, L'Hospitalet de Llobregat, Spain. sara.nicolas.parraga@gmail.com.
Background:
Quality of the nucleic acids extracted from Formalin Fixed Paraffin Embedded (FFPE) samples largely depends on pre-analytic, fixation and storage conditions. We assessed the differential sensitivity of viral and human double stranded DNA (dsDNA) to degradation with storage time.
Methods:
We randomly selected forty-four HPV16-positive invasive cervical cancer (ICC) FFPE samples collected between 1930 and 1935 and between 2000 and 2004. We evaluated through qPCR the amplification within the same sample of two targets of the HPV16 L1 gene (69 bp, 134 bp) compared with two targets of the human tubulin-β gene (65 bp, 149 bp).
Results:
Both viral and human, short and long targets were amplified from all samples stored for 15 years. In samples archived for 85 years, we observed a significant decrease in the ability to amplify longer targets and this difference was larger in human than in viral DNA: longer fragments were nine times (CI 95% 2.6-35.2) less likely to be recovered from human DNA compared with 1.6 times (CI 95% 1.1-2.2) for viral DNA.
Conclusions:
We conclude that human and viral DNA show a differential decay kinetics in FFPE samples. The faster degradation of human DNA should be considered when assessing viral DNA prevalence in long stored samples, as HPV DNA detection remains a key biomarker of viral-associated transformation.
Insights
Human DNA degrades faster than viral DNA in aged Formalin Fixed Paraffin Embedded (FFPE) samples. This differential decay impacts HPV DNA detection accuracy in long-term studies.
Area of Science:
- Molecular Biology
- Genomics
- Pathology
Background:
- Nucleic acid quality from FFPE samples depends on pre-analytic, fixation, and storage.
- Assessing viral and human double-stranded DNA (dsDNA) degradation over time is crucial.
Purpose of the Study:
- To evaluate the differential degradation of viral (HPV16) and human DNA in FFPE samples stored for extended periods.
- To understand the impact of storage time on DNA fragment amplification.
Main Methods:
- Selected 44 HPV16-positive invasive cervical cancer FFPE samples from 1930-1935 and 2000-2004.
- Used qPCR to amplify short (69/65 bp) and long (134/149 bp) targets of HPV16 L1 and human tubulin-β genes.
Main Results:
- Short and long targets of both viral and human DNA amplified from samples stored for 15 years.
- In samples stored for 85 years, amplification of longer fragments decreased significantly.
- Longer human DNA fragments were 9x less likely to be recovered compared to 1.6x for viral DNA.
Conclusions:
- Human and viral DNA exhibit distinct degradation rates in FFPE tissues.
- Faster human DNA decay necessitates consideration in long-term viral DNA prevalence studies.
- Accurate HPV DNA detection, a key biomarker, relies on understanding FFPE sample degradation kinetics.
