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. 2019 Mar 6:4:44.
doi: 10.12688/wellcomeopenres.15136.1. eCollection 2019.

Assessment of dried blood spots for DNA methylation profiling

Rosie M Walker  1   2 , Louise MacGillivray  3 , Sarah McCafferty  3 , Nicola Wrobel  3 , Lee Murphy  3 , Shona M Kerr  1   4 , Stewart W Morris  1 , Archie Campbell  5 , Andrew M McIntosh  2   6 , David J Porteous #  1   2   5 , Kathryn L Evans #  1   2
Affiliations

Assessment of dried blood spots for DNA methylation profiling

Rosie M Walker et al. Wellcome Open Res. .

Abstract

Background: DNA methylation reflects health-related environmental exposures and genetic risk, providing insights into aetiological mechanisms and potentially predicting disease onset, progression and treatment response. An increasingly recognised need for large-scale, longitudinally-profiled samples collected world-wide has made the development of efficient and straightforward sample collection and storage procedures a pressing issue. An alternative to the low-temperature storage of EDTA tubes of venous blood samples, which are frequently the source of the DNA used in such studies, is to collect and store at room temperature blood samples using purpose built filter paper, such as Whatman FTA® cards. Our goal was to determine whether DNA stored in this manner can be used to generate DNA methylation profiles comparable to those generated using blood samples frozen in EDTA tubes. Methods: DNA methylation profiles were obtained from matched EDTA tube and Whatman FTA® card whole-blood samples from 62 Generation Scotland: Scottish Family Health Study participants using the Infinium HumanMethylation450 BeadChip. Multiple quality control procedures were implemented, the relationship between the two sample types assessed, and epigenome-wide association studies (EWASs) performed for smoking status, age and the interaction between these variables and sample storage method. Results: Dried blood spot (DBS) DNA methylation profiles were of good quality and DNA methylation profiles from matched DBS and EDTA tube samples were highly correlated (mean r = 0.991) and could distinguish between participants. EWASs replicated established associations for smoking and age, with no evidence for moderation by storage method. Conclusions: Our results support the use of Whatman FTA® cards for collecting and storing blood samples for DNA methylation profiling. This approach is likely to be particularly beneficial for large-scale studies and those carried out in areas where freezer access is limited. Furthermore, our results will inform consideration of the use of newborn heel prick DBSs for research use.

Keywords: DBS; DNA methylation; Generation Scotland; Guthrie cards; dried blood spots.

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Conflict of interest statement

No competing interests were disclosed.

Figures

Figure 1.
Figure 1.. Quality control plot showing median methylated and unmethylated raw signal intensities.
For each sample, the log median methylated signal intensity (y-axis) is plotted against the log median unmethylated signal intensity (x-axis). Each dot represents one sample with EDTA samples being represented in green and DBS samples in orange.
Figure 2.
Figure 2.. Density plots of the raw beta-values separated by probe type and methylation measurement unit.
Density plots are shown for the type 1 (green colour channel ( A); red colour channel ( B)) and type 2 ( C) probes. Each sample is represented by a separate line with EDTA samples indicated in green and dried blood spot (DBS) samples in orange.
Figure 3.
Figure 3.. Control probe plots for the bisulphite conversion (I and II) and non-polymorphic probe control probes.
The mean raw signal intensity for the bisulphite conversion (I and II) ( A and B) and non-polymorphic ( C) control probes are plotted for each array. EDTA samples are indicated in green and dried blood spot (DBS) samples in orange.
Figure 4.
Figure 4.. Unsupervised hierarchical clustering of methylation levels (beta-values) at variable probes.
A subset of 190,044 probes defined as variable using an approach described by Hannon et al. (2015) were used to perform unsupervised hierarchical clustering of the 124 samples. Each sample is labelled using the participants study identifier and a suffix indicating whether the sample was from DNA from whole blood stored as a dried blood spot (DBS) or in an EDTA tube.
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