Center for Biomarker Research and Personalized Medicine, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA.
Epigenetics. 2013 May;8(5):542-7. doi: 10.4161/epi.24508. Epub 2013 Apr 18.
The potential importance of DNA methylation in the etiology of complex diseases has led to interest in the development of methylome-wide association studies (MWAS) aimed at interrogating all methylation sites in the human genome. When using blood as biomaterial for a MWAS the DNA is typically extracted directly from fresh or frozen whole blood that was collected via venous puncture. However, DNA extracted from dry blood spots may also be an alternative starting material. In the present study, we apply a methyl-CpG binding domain (MBD) protein enrichment-based technique in combination with next generation sequencing (MBD-seq) to assess the methylation status of the ~27 million CpGs in the human autosomal reference genome. We investigate eight methylomes using DNA from blood spots. This data are compared with 1,500 methylomes previously assayed with the same MBD-seq approach using DNA from whole blood. When investigating the sequence quality and the enrichment profile across biological features, we find that DNA extracted from blood spots gives comparable results with DNA extracted from whole blood. Only if the amount of starting material is ≤ 0.5µg DNA we observe a slight decrease in the assay performance. In conclusion, we show that high quality methylome-wide investigations using MBD-seq can be conducted in DNA extracted from archived dry blood spots without sacrificing quality and without bias in enrichment profile as long as the amount of starting material is sufficient. In general, the amount of DNA extracted from a single blood spot is sufficient for methylome-wide investigations with the MBD-seq approach.
DNA 甲基化在复杂疾病病因学中的潜在重要性，促使人们产生了开展全基因组甲基化关联研究（MWAS）的兴趣，旨在检测人类基因组中的所有甲基化位点。当使用血液作为 MWAS 的生物材料时，通常直接从通过静脉穿刺采集的新鲜或冷冻全血中提取 DNA。然而，从干血斑中提取的 DNA 也可能是另一种起始材料。在本研究中，我们应用基于甲基化 CpG 结合域（MBD）蛋白富集的技术结合下一代测序（MBD-seq），评估人类常染色体参考基因组中约 2700 万个 CpG 的甲基化状态。我们使用血斑中的 DNA 研究了 8 个甲基组。将这些数据与之前使用相同的 MBD-seq 方法从全血中检测到的 1500 个甲基组进行了比较。当研究序列质量和跨生物学特征的富集情况时，我们发现从血斑中提取的 DNA 与从全血中提取的 DNA 给出了可比的结果。只有当起始材料的量≤0.5μg DNA 时，我们才观察到该检测方法的性能略有下降。总之，我们表明，只要起始材料充足，使用 MBD-seq 可以在从存档的干血斑中提取的 DNA 上进行高质量的全基因组甲基化研究，而不会牺牲质量或富集谱的偏倚。一般来说，使用 MBD-seq 进行全基因组甲基化研究，从单个血斑中提取的 DNA 量就足够了。
