Assessment of dried blood spots for DNA methylation profiling

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.

Epigenetic aging in children from a small‐scale farming society in The Congo Basin: Associations with child growth and family conflict

“…Finally, our measures of EAA were derived from DBS samples, rather than whole blood collection, which is the more widely used approach, particularly in research done in laboratory and clinical settings, as opposed to at field sites such as ours. However, recent research found that matched DBS and EDTA tube samples were highly correlated for DNA methylation (r = 0.99), so we are confident that our results reflect those measured in blood (Walker et al, 2019).…”

DNA methylome-wide association study of genetic risk for depression implicates antigen processing and immune responses

“…Quality control (QC) and normalisation were conducted using R packages ‘ShinyMethyl’ (version 1.28.0) [ 34 ], ‘watermelon’ (version 1.36.0) [ 35 ] and ‘meffil’ (version 1.1.1) [ 36 ]. Details of the protocol are described elsewhere [ 37 ]. In summary, quality control procedures removed probes if there was an outlying log median methylated signal intensity against unmethylated signal for each array, or a bead count <3 in ≥5 % of the total probe sample, or a detection p -value >0.05 for set 1 and p -value >0.01 for set 2 in ≥0.5% of the total sample in each respective set.…”

“…Self-reported smoking status, smoking pack years, DNAm-estimated white-blood cell proportions (CD8+T, CD4+T, natural killer cells, B cells and granulocytes) [ 37 ], batch, the first 20 principal component derived from the M -values, the first 10 principal components derived from the imputed genetic data, age and sex were included as covariates for the discovery methylome-wide association analysis (see Additional file 1 : Supplementary Methods and Additional file 1 : Table S3 for details). Where possible, the same covariates were used in the replication analyses, although only smoking status (and not pack years) was available in LBC 1921, LBC 1936 and ALSPAC.…”

DNA Methylation in Healthy Older Adults With a History of Childhood Adversity—Findings From the Women 40+ Healthy Aging Study

“…We used the DBS technique, which is a relatively new sampling method in the context of methylation analyses. The latest publications are promising and suggest that this handy and simple technique is reliable and valid in the assessment of methylation marks (reviewed in 54, 63). As mentioned above, cell composition can be a potential confounder, which was not controlled for in the present analyses and therefore needs to be considered as a limitation.…”

“…Cytosine methylation was assessed from dried blood spot (DBS) DNA samples, as previously described elsewhere (see, e.g., 61, 62, 63). The Qiagen QIAamp DNA Investigator Kit (Qiagen, Hombrechtikon, Switzerland) was used to extract genomic DNA from three punches of blood-soaked filter paper (each 3 mm in diameter).…”