High quality methylome-wide investigations through next-generation sequencing of DNA from a single archived dry blood spot

Abstract

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.

Genomic methylation patterns in archaeological barley show de-methylation as a time-dependent diagenetic process

“…The methyl-binding domain (MBD) bead-based method we used does not appear to discriminate in favour of large fragments during enrichment for target methylated molecules unlike column-based assays. In fact it has been suggested that smaller fragments are more efficiently captured using this method28, suggesting that our estimates of the contribution of DNA fragmentation to the reduction in methylation signal are too high. Therefore in all cases examined the extent of DNA fragmentation was insufficient to explain all the reduction in methylation signal.…”

Development of DNA Confirmatory and High-Risk Diagnostic Testing for Newborns Using Targeted Next-Generation DNA Sequencing

“…31,32 Using our methods, we see similarly high-quality TNGS performance of DNA isolated from DBS as compared with the standard 10 ml of whole blood and saliva (Supplementary Figure S1 online). With a control sample set, our protocols yielded ~450 ng doublestranded DNA (dsDNA) from one-half of a single saturated spot from the DBS card, representing 25 µl blood (as measured by the dsDNA-specific Qubit assay; Supplementary Table S2 online).…”

Epigenetics and Child Psychiatry: Ethical and Legal Issues

“…A good example of these issues has been the controversy over the retention and use of newborn screening blood spots. Newborn blood screening is routinely conducted for a variety of potential health concerns, and the dried blood samples are often retained and used in various research projects, including epigenetic epidemiologic surveys (Aberg et al, ). The use of retained samples without parental knowledge and use in research has resulted in lawsuits against state health departments (Carmichael, ).…”