Methylome analysis of congenital ectopic thyroids

To assess whether specific genes have relevant somatic genetic or epigenetic alterations in ectopic tissue, we used a combined analysis of transcriptome (confirmed by qRT-PCR on 68 genes), methylome, structural genome variations (copy number variants, CNVs) and miRNA profile of ectopic compared with orthotopic thyroids. The MeDIP-chip was performed using pair of enriched methylated fraction (IP) and nomal fraction (IN) of genomic DNA from the three available cases and the three controls. The methylated fraction of genomic DNA was enriched using the methylated DNA immunoprecipitation (MeDIP) assay (Weber et al. Nat Genetics, 2005) and interrogated on human Promoter plus CpG Island Tiling Arrays with a ChIP design for CpG islands and promoter regions (n=28,226) from HG18 using 385,020 Probes selected from CGH probe bank with a median spacing of 101bp (Roche NimbleGen, Madison, WI).