The application of epiphenotyping approaches to DNA methylation array studies of the human placenta.

BACKGROUND: Genome-wide DNA methylation (DNAme) profiling of the placenta with Illumina Infinium Methylation bead arrays is often used to explore the connections between in utero exposures, placental pathology, and fetal development. However, many technical and biological factors can lead to signals of DNAme variation between samples and between cohorts, and understanding and accounting for these factors is essential to ensure meaningful and replicable data analysis. Recently, "epiphenotyping" approaches have been developed whereby DNAme data can be used to impute information about phenotypic variables such as gestational age, sex, cell composition, and ancestry. These epiphenotypes offer avenues to compare phenotypic data across cohorts, and to understand how phenotypic variables relate to DNAme variability. However, the relationships between placental epiphenotyping variables and other technical and biological variables, and their application to downstream epigenome analyses, have not been well studied. RESULTS: Using DNAme data from 204 placentas across three cohorts, we applied the PlaNET R package to estimate epiphenotypes gestational age, ancestry, and cell composition in these samples. PlaNET ancestry estimates were highly correlated with independent polymorphic ancestry-informative markers, and epigenetic gestational age, on average, was estimated within 4 days of reported gestational age, underscoring the accuracy of these tools. Cell composition estimates varied both within and between cohorts, as well as over very long placental processing times. Interestingly, the ratio of cytotrophoblast to syncytiotrophoblast proportion decreased with increasing gestational age, and differed slightly by both maternal ethnicity (lower in white vs. non-white) and genetic ancestry (lower in higher probability European ancestry). The cohort of origin and cytotrophoblast proportion were the largest drivers of DNAme variation in this dataset, based on their associations with the first principal component. CONCLUSIONS: This work confirms that cohort, array (technical) batch, cell type proportion, self-reported ethnicity, genetic ancestry, and biological sex are important variables to consider in any analyses of Illumina DNAme data. We further demonstrate the specific utility of epiphenotyping tools developed for use with placental DNAme data, and show that these variables (i) provide an independent check of clinically obtained data and (ii) provide a robust approach to compare variables across different datasets. Finally, we present a general framework for the processing and analysis of placental DNAme data, integrating the epiphenotype variables discussed here.

Prevalence and characteristics of adults with fetal alcohol spectrum disorder in corrections: a Canadian case ascertainment study.

BACKGROUND: Individuals with fetal alcohol spectrum disorder (FASD) experience a range of cognitive, affective, and physical deficits following prenatal alcohol exposure. They are thought to be overrepresented in criminal justice settings. However, limited evidence is available to inform prevalence. We sought to estimate the prevalence of FASD in a Northern Canadian correctional population. METHODS: Using an active case ascertainment approach we recruited a representative sample of 80 justice-involved adults (ages 18-40, 85% male) over an 18-month period from 2013 to 2015. Participants completed interdisciplinary clinical assessments comprising medical and psychological evaluations that adhered to the 2005 Canadian FASD Diagnostic Guidelines. RESULTS: We identified a high rate of FASD (17.5, 95% CI [9.2, 25.8%]) in this sample, and this rate could have been as high as 31.2% with confirmation of prenatal alcohol exposure. Most participants in this study presented with significant neurodevelopmental and cognitive deficits in at least two domains of functioning, irrespective of diagnosis, with only five of 80 participants (6.3%) demonstrating no cognitive impairment. CONCLUSIONS: Findings showed disproportionately high estimated FASD prevalence in this representative sample compared to general population estimates in both Canada and the U.S. (2-5%), underscoring the need for improved FASD screening and diagnosis in correctional settings, and education for clinicians working in the justice context. Strengthened health prevention and intervention efforts to support the needs of individuals with FASD outside the criminal justice context are needed.