Computational protocol: DNA methylation changes at infertility genes in newborn twins conceived by in vitro fertilisation

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Protocol publication

[…] The contribution of additive genetic (A), common environmental (C), and unique environmental (E) factors to DNA methylation was estimated using the ACE model based on the classic twin design []. The model was fitted using the OpenMX statistical package []. RPM values without adjustment for covariates were used to estimate the ACE proportions. [...] Genomic DNA (500 ng) was bisulphite converted using the MethylEasy Exceed Rapid Bisulphite Modification Kit (Human Genetic Signatures, North Ryde, NSW, Australia). Primers to target the regions in TNP1 and C9orf3 were designed using the EpiDesigner tool (Sequenom Inc., Herston, QLD, Australia). The H19 CTCF6 region was the same used in a previous study []. Primers, genomic coordinates, and PCR conditions are shown in Additional file : Table S2. Methylation levels were determined by EpiTYPER on the MassARRAY System (Sequenom Inc., Herston, QLD, Australia). Statistical analysis considered the average of two to three technical replicates and were performed using data on single CpG sites. […]

Pipeline specifications

Software tools OpenMx, EpiDesigner
Applications Miscellaneous, BS-seq analysis
Organisms Homo sapiens
Diseases Infertility, Infertility, Male