Sho Ueda1,2,3, Satoshi Yamashita1, Shun-Ichi Watanabe4, Mika Wakabayashi1, Noriko Motoi5, Masayuki Noguchi2, Shigeki Sekine5, Yukio Sato3, Toshikazu Ushijima1. 1. Division of Epigenomics, National Cancer Center Research Institute, Tokyo 104 0045, Japan. 2. Department of Pathology, Faculty of Medicine, University of Tsukuba, Ibaraki 305 8575, Japan. 3. Department of Thoracic Surgery, Faculty of Medicine, University of Tsukuba, Ibaraki 305 8575, Japan. 4. Department of Thoracic Surgery, National Cancer Center Hospital, Tokyo 104 0045, Japan. 5. Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo 104 0045, Japan.
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.
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.
Entities:
Keywords:
DNA degradation; epigenetic; epigenomic; genome wide; microarray