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.

[Pathological data of 92 rheumatic mitral valve after surgical ablation : comparison with pre-operative echocardiography results]. / Données morphométriques recueillies sur 92 valvulites mitrales rhumatismales après exérèse chirurgicale : les corrélations avec les données échocardiographiques pré-opératoires.

The echocardiographic information obtained pre-operatively with an electronic linear scanning system (Multiscan) was compared with the results of pathological examination of the excised mitral valve in 92 patients, and showed a close correlation. The way in which the pathological changes influence the various parameters usually used to distinguish this type of rheumatic valvular disease is demonstrated. Two-dimensional imagery provides precise information : this is shown by comparison of the still frames of the videoscopic recording and the photographs of the corresponding pathological specimens. Valve thickness, length and thickness of the chordae, calcification, mitral valve surface and commissural separation are well shown, especially at the anterior leaflet. Study of transverse incidences seems the most reliable method of estimating mitral valve area. Systolic separation of mitral valve echos, according to the usual criteria, is a good sign of associated mitral incompetence and was found in 83% of cases of mixed mitral valve disease. The mean values of anterior mitral leaflet excursion, diastolic slope and opening speeds were compared in three groups of mitral stanosis with preferential antatomical features and a control group of pure mitral stenosis with supple valves. No individual parameter was found to be specific for a particular antatomical feature, showing multiple correlations to be indispensable. The difficulty of diagnosis by isolated traditional echocardiography is confirmed and the association of two dimensional imagery would seem essential not only in making the diagnosis but also in the pre operative work up.