DNA methylation episignatures: insight into copy number variation.

In this review we discuss epigenetic disorders that result from aberrations in genes linked to epigenetic regulation. We describe current testing methods for the detection of copy number variants (CNVs) in Mendelian disorders, dosage sensitivity, reciprocal phenotypes and the challenges of test selection and overlapping clinical features in genetic diagnosis. We discuss aberrations of DNA methylation and propose a role for episignatures as a novel clinical testing method in CNV disorders. Finally, we postulate that episignature mapping in CNV disorders may provide novel insights into the molecular mechanisms of disease and unlock key findings of the genome-wide impact on disease gene networks.

DNA methylation as the link between migration and the major noncommunicable diseases: the RODAM study.

Aim: We assessed epigenome-wide DNA methylation (DNAm) differences between migrant and non-migrant Ghanaians. Materials & methods: We used the Illumina Infinium® HumanMethylation450 BeadChip to profile DNAm of 712 Ghanaians in whole blood. We used linear models to detect differentially methylated positions (DMPs) associated with migration. We performed multiple post hoc analyses to validate our findings. Results: We identified 13 DMPs associated with migration (delta-beta values: 0.2-4.5%). Seven DMPs in CPLX2, EIF4E3, MEF2D, TLX3, ST8SIA1, ANG and CHRM3 were independent of extrinsic genomic influences in public databases. Two DMPs in NLRC5 were associated with duration of stay in Europe among migrants. All DMPs were biologically linked to migration-related factors. Conclusion: Our findings provide the first insights into DNAm differences between migrants and non-migrants.

Prevalence and determinants of type 2 diabetes among lean African migrants and non-migrants: the RODAM study.

BACKGROUND: Exposure to adverse conditions earlier in life-course can predispose to type 2 diabetes in adulthood, irrespective of body mass index (BMI). However, the burden of type 2 diabetes in lean Africans is not well understood despite higher exposure to adverse early life conditions. Mirroring ongoing epidemiological transition, we assessed the burden and determinants of type 2 diabetes in a homogenous group of lean Ghanaians residing in rural and urban Ghana, and as migrants in Europe. METHODS: Baseline data from 2179 RODAM study participants with BMI<25kg/m2 (25-70 years) were analyzed. Prevalence and determinants of type 2 diabetes were estimated using logistic regression analysis. Adjustments were made for socio-demographic and lifestyle factors, use of anti-diabetic medication and optimal blood glucose control. RESULTS: Prevalence of type 2 diabetes in rural, urban and migrant lean participants were 3.5%, 8.9% and 7.5% respectively, representing 55.4%, 35.6%, 13.2% of all participants with type 2 diabetes. Compared with lean rural participants, the odds of type 2 diabetes were higher in lean urban participants (adjusted OR = 8.81, 95% CI = 6.56-11.06), followed by migrants (5.27, 95% CI = 3.51-6.91). Irrespective of site, determinants of type 2 diabetes in lean participants include; presence of hypertension, physical inactivity, hypercholesterolemia and age (>45 years). CONCLUSIONS: Our study shows a high prevalence of type 2 diabetes among lean African populations in different geographical settings. Future studies are needed in-order to examine how contextual differences are related to the pathophysiology of type 2 diabetes in lean individuals.

DNA methylation abundantly associates with fetal alcohol spectrum disorder and its subphenotypes.

Aim: Fetal alcohol spectrum disorder (FASD) involves prenatal growth delay, impaired facial and CNS development and causes severe clinical, social-economic burdens. Here, we aim to detect DNA-methylation aberrations associated with FASD and potential FASD diagnostic and prognostic biomarkers. Patients & methods: The FASD diagnosis was established according to golden-standard protocols in a discovery and independent replication cohort. Genome-wide differential methylation association and replication analyses were performed. Results: We identified several loci that were robustly associated with FASD or one of its sub phenotypes. Our findings were evaluated using previously reported genome-wide surveys. Conclusion: We have detected robust FASD associated differentially methylated positions and differentially methylated regions for FASD in general and for FASD subphenotypes, in other words on growth delay, impaired facial and CNS development.

The idiopathic preterm delivery methylation profile in umbilical cord blood DNA.

BACKGROUND: Preterm delivery is the leading cause of neonatal morbidity and mortality. Two-thirds of preterm deliveries are idiopathic. The initiating molecular mechanisms behind spontaneous preterm delivery are unclear. Umbilical cord blood DNA samples are an easy source of material to study the neonatal state at birth. DNA methylation changes can be exploited as markers to identify spontaneous preterm delivery. To identify methylation differences specific to idiopathic preterm delivery, we assessed genome-wide DNA methylation changes in 24 umbilical cord blood samples (UCB) using the 450 K Illumina methylation array. After quality control, conclusions were based on 11 term and 11 idiopathic preterm born neonates. The differentially methylated positions (DMPs) specific for preterm/term delivery, neonatal sex, use of oxytocin and mode of initiation of labor were calculated by controlling the FDR p value at 0.05. RESULTS: The analysis identifies 1855 statistically significant DMPs between preterm and term deliveries of which 508 DMPs are also attributable to clinical variables other than preterm versus term delivery. 1347 DMPs are unique to term vs preterm delivery, of which 196 DMPs do not relate to gestational age as such. Pathway analysis indicated enrichment of genes involved in calcium signalling, myometrial contraction and relaxation pathways. The 1151 DMPs that correlate with advancing gestational age (p < 0.05) include 161 DMPs that match with two previously reported studies on UCB methylation. Additionally, 123 neonatal sex specific DMPs, 97 DMPs specific to the induction of labour and 42 DMPs specific to the mode of initiation of labor were also identified. CONCLUSION: This study identifies 196 DMPs in UCB DNA of neonates which do not relate to gestational age or any other clinical variable recorded and are specific to idiopathic preterm delivery. Furthermore, 161 DMPs from our study overlap with previously reported studies of which a subset is also reported to be differentially methylated at 18 years of age. A DMP on MYL4, encoding myosin light chain 4, is a robust candidate for the identification of idiopathic preterm labour as it is identified by all 3 independent studies.

Novel tools for extraction and validation of disease-related mutations applied to Fabry disease.

Genetic disorders are often caused by nonsynonymous nucleotide changes in one or more genes associated with the disease. Specific amino acid changes, however, can lead to large variability of phenotypic expression. For many genetic disorders this results in an increasing amount of publications describing phenotype-associated mutations in disorder-related genes. Keeping up with this stream of publications is essential for molecular diagnostics and translational research purposes but often impossible due to time constraints: there are simply too many articles to read. To help solve this problem, we have created Mutator, an automated method to extract mutations from full-text articles. Extracted mutations are crossreferenced to sequence data and a scoring method is applied to distinguish false-positives. To analyze stored and new mutation data for their (potential) effect we have developed Validator, a Web-based tool specifically designed for DNA diagnostics. Fabry disease, a monogenetic gene disorder of the GLA gene, was used as a test case. A structure-based sequence alignment of the alpha-amylase superfamily was used to validate results. We have compared our data with existing Fabry mutation data sets obtained from the HGMD and Swiss-Prot databases. Compared to these data sets, Mutator extracted 30% additional mutations from the literature.