Influence of Degree of DNA Degradation in Formalin-Fixed and Paraffin-Embedded Tissue Samples on Accuracy of Genome-Wide DNA Methylation Analysis

Abstract

Aim: Depending upon the degree of DNA degradation of formalin-fixed and paraffin-embedded tissue samples, accuracy of measurement by Infinium MethylationEPIC BeadChip assay (Illumina, CA, USA) was assessed. Materials & methods: DNA quality of six formalin-fixed and paraffin-embedded lung tissue samples with different formalin fixation periods was assessed by Illumina quality control, DNA copy number and DNA integrity number value. Infinium data from restored bisulfite treated DNA were compared with datum from a fresh-frozen sample. Results: The correlation coefficient decreased from 0.993 to 0.970 depending upon DNA degradation, even if the Illumina quality control was met. Exclusion of specific probes improved the correlation regardless of tissue. Conclusion: Poor DNA quality can be assessed as an amplifiable DNA copy number and DNA integrity number value. Probe filtering has the potential to improve assay accuracy.

Keywords::

• DNA degradation
• epigenetic
• epigenomic
• genome wide
• microarray

Supplementary data

To view the supplementary data that accompany this paper please visit the journal website at: www.tandfonline.com/doi/suppl/10.2217/epi-2020-0431

Author contributions

S Ueda, S Yamashita, M Noguchi, Y Sato and T Ushijima designed the study. S Watanabe, N Motoi and S Sekine provided tissue and FFPE samples. S Ueda and M Wakabayashi performed experiments. S Ueda, S Yamashita, M Noguchi and Y Sato analyzed data. S Ueda and S Yamashita generated figures. S Ueda and T Ushijima wrote the manuscript. All authors gave final approval to the submitted and published versions.

Acknowledgments

The authors are grateful to K Tokita (Department of Diagnostic Pathology, National Cancer Center Hospital) for preparing formalin-fixed and paraffin-embedded tissue samples.

Financial & competing interests disclosure

The study was supported by JSPS KAKENHI Grant Number JP18H02704 (T.U.), and AMED under JP20bk0104097 and JP20ck0106490. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Ethical conduct of research

The authors state that they have obtained appropriate institutional review board approval or have followed the principles outlined in the Declaration of Helsinki for all human or animal experimental investigations. In addition, for investigations involving human subjects, informed consent has been obtained from the participants involved.

Additional information

Funding

The study was supported by JSPS KAKENHI Grant Number JP18H02704 (T.U.), and AMED under JP20bk0104097 and JP20ck0106490. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript.