Influence of degree of DNA degradation in formalin-fixed and paraffin-embedded tissue samples on accuracy of genome-wide DNA methylation analysis
Influence of degree of DNA degradation in formalin-fixed and paraffin-embedded tissue samples on accuracy of genome-wide DNA methylation analysis
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DOI：
10.2217/epi-2020-0431
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发表时间：
2021-04-06
期刊：
影响因子：
3.8
通讯作者：
Ushijima, Toshikazu
中科院分区：
文献类型：
--
作者：
Ueda, Sho;Yamashita, Satoshi;Ushijima, Toshikazu
目的：根据福尔马林固定和石蜡包埋组织样品的DNA降解程度，评估Infinium MethylationEPIC BeadChip assay （Illumina， CA， USA）测量的准确性。材料与方法：采用Illumina质控法、DNA拷贝数和DNA完整性数值评价6个不同固定周期的福尔马林固定和石蜡包埋肺组织样品的DNA质量。从亚硫酸氢盐处理过的DNA中提取的微量元素数据与新鲜冷冻样本的数据进行了比较。结果：即使满足Illumina质量控制，相关系数也从0.993下降到0.970，取决于DNA降解程度。排除特定探针可以提高与组织的相关性。结论：DNA质量差可以用扩增DNA拷贝数和DNA完整性数来评价。探针过滤有可能提高测定的准确性。
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.