5-Hydroxymethylcytosine (5hmC), the first oxidized form of the well-known epigenetic modification 5-methylcytosine, is an independent regulator of gene expression and therefore a potential marker for disease. Here, we report on methods developed for a selective solid-state nanopore assay that enable direct analysis of global 5hmC content in human tissue. We first describe protocols for preparing genomic DNA derived from both healthy breast tissue and stage 1 breast tumor tissue and then use our approach to probe the net abundance of the modified base in each cohort. Then, we employ empirical data to adjust for the impact of nanopore diameter on the quantification. Correcting for variations in nanopore diameter among the devices used for analysis reveals no detectable difference in global 5hmC content between healthy and tumor tissue. These results suggest that 5hmC changes may not be associated with early-stage breast cancer and instead are a downstream consequence of the disease.

5-羟甲基胞嘧啶 (5hmC) 是众所周知的表观遗传修饰 5-甲基胞嘧啶的第一种氧化形式，是基因表达的独立调节因子，因此是疾病的潜在标志物。在这里，我们报告了为选择性固态纳米孔测定开发的方法，该方法能够直接分析人体组织中的整体 5hmC 含量。我们首先描述了从健康乳腺组织和一期乳腺肿瘤组织中制备基因组 DNA 的方案，然后使用我们的方法来探测每个队列中修饰碱基的净丰度。然后，我们利用经验数据来调整纳米孔径对定量的影响。校正用于分析的设备之间纳米孔径的变化表明，健康组织和肿瘤组织之间的总体 5hmC 含量没有可检测到的差异。这些结果表明 5hmC 变化可能与早期乳腺癌无关，而是该疾病的下游后果。