| Abstract: | A major concern in common disease epigenomics is distinguishing causal from consequential epigenetic variation. One means of addressing this issue is to identify the temporal origins of epigenetic variants via longitudinal analyses. However, prospective birth-cohort studies are expensive and time consuming. Here, we report DNA methylomics of archived Guthrie cards for the retrospective longitudinal analyses of in-utero-derived DNA methylation variation. We first validate two methodologies for generating comprehensive DNA methylomes from Guthrie cards. Then, using an integrated epigenomic/genomic analysis of Guthrie cards and follow-up samplings, we identify interindividual DNA methylation variation that is present both at birth and 3 yr later. These findings suggest that disease-relevant epigenetic variation could be detected at birth, i.e., before overt clinical disease. Guthrie card methylomics offers a potentially powerful and cost-effective strategy for studying the dynamics of interindividual epigenomic variation in a range of common human diseases.There is increasing interest in exploring the possibility that interindividual epigenetic variation plays a role in common human disease etiology (for review, see Petronis 2010; Rakyan et al. 2011). Consequently, epigenome-wide association studies (EWASs), analogous to genome-wide association studies (GWASs) for disease-associated genetic variants (Rakyan et al. 2011), are currently being conducted to systematically uncover epigenetic variants for a range of different diseases (www.roadmapepigenomics.org/participants lists some of the current NIH-funded EWASs). However, the disease process itself can also induce epigenetic changes. Therefore, an EWAS design that just compares post-disease affected with unaffected individuals will not distinguish causal from consequential disease-associated epigenetic variation. The inability to make this distinction will ultimately prove to be a significant barrier to establishing the etiological role or medical value for any disease-associated epigenetic variants.One way of addressing this issue is to determine whether the epigenetic variants are detectable before overt disease. Although such variants could arise at any point during an individual''s lifespan (Fraga et al. 2005), in-utero development is considered to be a period during which the epigenome is particularly susceptible to stochastic and/or environmental factors such as infection, poor diet, or stress (for review, see Warner and Ozanne 2010). A variety of common diseases have been proposed to have a component of in-utero origins including asthma, metabolic conditions including type 2 diabetes, and autoimmune disorders like multiple sclerosis (Heijmans et al. 2008; Warner and Ozanne 2010). Hence, being able to determine epigenomic profiles at birth, and by implication before overt disease, would be invaluable for elucidating the origins and potentially the etiological role of disease-associated epigenetic variants. In this regard, prospective birth-cohort studies are very useful but, unfortunately, are expensive, time-consuming, and difficult to establish.In 1963, Robert Guthrie proposed spotting a small amount of neonatal blood onto filter paper for the large-scale biochemical screening of various diseases such as phenylketonuria (Guthrie and Susi 1963). “Guthrie cards” are now routinely created by major national health authorities; e.g., since 2000, over 90% of all neonates in the United States had Guthrie cards made shortly after birth (Pollitt 2009). Remarkably, in many cases Guthrie cards are being stored indefinitely. This led us to consider genome-wide DNA methylation profiling—DNA methylomics—of Guthrie cards as a means of investigating the origins of disease-associated epigenetic variation. Crucially, this longitudinal investigation could be done retrospectively at a fraction of the cost and time investment required for prospective studies. |
