Abstract
BackgroundIn utero and early-life experienced environmental exposures are suggested to play an important role in many multifactorial diseases potentially mediated through lasting effects on the epigenome. As the epigenome in addition remains modifiable throughout life, identifying specific disease-relevant biomarkers may prove challenging. This has led to an increased interest in epigenome-wide association studies using dried blood spots (DBS) routinely collected in perinatal screening programs. Such programs are in place in numerous countries around the world producing large and unique biobanks. However, availability of this biological material is highly limited as each DBS is made only from a few droplets of blood and storage conditions may be suboptimal for epigenetic studies. Furthermore, as relevant markers may reside outside gene bodies, epigenome-wide interrogation is needed.ResultsHere we demonstrate, as a proof of principle, that genome-wide interrogation of the methylome based on methylated DNA immunoprecipitation coupled with next-generation sequencing (MeDIP-seq) is feasible using a single 3.2 mm DBS punch (60 ng DNA) from filter cards archived for up to 16 years. The enrichment profile, sequence quality and distribution of reads across genetic regions were comparable between samples archived 16 years, 4 years and a freshly prepared control sample.ConclusionsIn summary, we show that high-quality MeDIP-seq data is achievable from neonatal screening filter cards stored at room temperature, thereby providing information on annotated as well as on non-RefSeq genes and repetitive elements. Moreover, the quantity of DNA from one DBS punch proved sufficient allowing for multiple epigenome studies using one single DBS.Electronic supplementary materialThe online version of this article (doi:10.1186/s13148-016-0242-1) contains supplementary material, which is available to authorized users.
Highlights
In utero and early-life experienced environmental exposures are suggested to play an important role in many multifactorial diseases potentially mediated through lasting effects on the epigenome
With mounting evidence of epigenetic variations playing an important role in the etiology of common complex diseases such as cancer, diabetes and psychiatric disorders, the interest in epigenome-wide association studies (EWAS), with regard to DNA methylation, has increased extensively
methylated DNA immunoprecipitation (MeDIP) sequencing quality from dried blood spots (DBS) samples Genomic DNA was extracted from one 3.2 mm punch from each of the three Whatman 903 filter cards (Table 1), being a freshly prepared “homemade” sample, a short-term (4 years at room temperature) stored sample and a long-term (16 years at room temperature) stored sample
Summary
In utero and early-life experienced environmental exposures are suggested to play an important role in many multifactorial diseases potentially mediated through lasting effects on the epigenome. As the epigenome in addition remains modifiable throughout life, identifying specific disease-relevant biomarkers may prove challenging. This has led to an increased interest in epigenome-wide association studies using dried blood spots (DBS) routinely collected in perinatal screening programs. Such programs are in place in numerous countries around the world producing large and unique biobanks. With mounting evidence of epigenetic variations playing an important role in the etiology of common complex diseases such as cancer, diabetes and psychiatric disorders, the interest in epigenome-wide association studies (EWAS), with regard to DNA methylation, has increased extensively. Interrogation of the epigenetic profile is, preferably done before disease onset and ideally perinatally
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