Methylation haplotypes of the insulin gene promoter in children and adolescents with type 1 diabetes: could a dimensionality reduction approach predict the disease?

The aim of the present study was to identify insulin gene promoter (IGP) methyl-haplotypes among children and adolescents with T1D and suggest a predictive model for the discrimination of cases and controls according to methyl-haplotypes. Fourty individuals (20 T1D) participated. IGP-region from peripheral whole blood DNA of 40 participants (20 T1D) was sequenced by next generation sequencing, sequences were read using FASTQ files, and methylation status was calculated by python-based pipeline for targeted deep bisulfite sequenced amplicons (ampliMethProfiler). Methylation profile at 10 CpG sites proximal to transcription start site of the IGP was recorded and coded as 0 for unmethylation or 1 for methylation. A single read could result in “1111111111” methyl-haplotype (all methylated), “000000000” methyl-haplotype (all unmethylated) or any other combination.