甲醛固定石蜡包埋心脏组织的 DNA 质量评估用于 DNA 甲基化阵列分析。
DNA quality evaluation of formalin-fixed paraffin-embedded heart tissue for DNA methylation array analysis.
机构信息
Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
Section of Forensic Pathology, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
出版信息
Sci Rep. 2023 Feb 3;13(1):2004. doi: 10.1038/s41598-023-29120-y.
Archived formalin-fixed and paraffin-embedded (FFPE) heart tissue from autopsied individuals represents an important resource for investigating the DNA methylation of heart tissue of deceased individuals. The DNA quality of FFPE tissue from autopsies may be decreased, affecting the DNA methylation measurements. Therefore, inexpensive screening methods for estimating DNA quality are valuable. We investigated the correlation between the DNA quality of archived FFPE heart tissue examined with the Illumina Infinium HD FFPE QC assay (Infinium QC) and Thermo Fisher's Quantifiler Trio DNA Quantification kit (QuantifilerTrio), respectively, and the amount of usable DNA methylation data as measured by the probe detection rate (probe DR) obtained with the Illumina Infinium MethylationEPIC array. We observed a high correlation (r = 0.75; p < 10) between the QuantifilerTrio degradation index, DI, and the amount of usable DNA methylation data analysed with SeSAMe, whereas a much weaker correlation was observed between the Infinium QC and SeSAMe probe DR (r = 0.17; p < 0.05). Based on the results, QuantifilerTrio DI seems to predict the proportion of usable DNA methylation data analysed with the Illumina Infinium MethylationEPIC array and SeSAMe by a linear model: SeSAMe probe DR = 0.80-log(DI) × 0.25.
从尸检个体中存档的福尔马林固定和石蜡包埋 (FFPE) 心脏组织是研究已故个体心脏组织 DNA 甲基化的重要资源。尸检 FFPE 组织的 DNA 质量可能会降低，从而影响 DNA 甲基化测量。因此，具有成本效益的 DNA 质量估计筛选方法是很有价值的。我们分别研究了使用 Illumina Infinium HD FFPE QC 测定法 (Infinium QC) 和 Thermo Fisher 的 Quantifiler Trio DNA 定量试剂盒 (QuantifilerTrio) 检测的存档 FFPE 心脏组织的 DNA 质量与可用 DNA 甲基化数据量之间的相关性，后者通过 Illumina Infinium MethylationEPIC 阵列获得的探针检出率 (probe DR) 来衡量。我们观察到，QuantifilerTrio 的降解指数 (DI) 与 SeSAMe 分析的可用 DNA 甲基化数据量之间存在高度相关性 (r = 0.75; p < 0.05)，而 Infinium QC 与 SeSAMe 的探针 DR 之间的相关性要弱得多 (r = 0.17; p < 0.05)。基于这些结果，QuantifilerTrio DI 似乎可以通过线性模型预测 Illumina Infinium MethylationEPIC 阵列和 SeSAMe 分析的可用 DNA 甲基化数据比例：SeSAMe 探针 DR = 0.80-log(DI) × 0.25。
Zotero 插件