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Investigation of the Methylation Status Around Parent-of-Origin Detectable SNPs in Imprinted Genes

NCJ Number
Forensic Science International: Genetics Volume: 3 Issue: 4 Dated: September 2009 Pages: 227-232
Nori Nakayashiki; Masataka Takamiya; Kirito Shimamoto; Yasuhiro Aoki; Masaki Hashiyada
Date Published
September 2009
This study examined the CpG methylation status around target single nucleotide polymorphisms (SNPs), not only on genomic DNA from peripheral blood, but also on DNA extracted from several human biological resources used in forensic investigation, in order to assess the reliability and specificity of the differentially methylated parental allele (DMPA) detection method.
The sequencing of the bisulphate-PCR product confirmed that more than 99 percent of the unmethylated cytosines in every tested DNA sequence were converted to uracil (corresponding to thymine in DNA), and therefore the remainder of the methylated CpGs could be easily discriminated. The methylation profile in each locus from every individual revealed generally hypermethylated or hypomethylated clones corresponding to either genotype, which would permit the reliability of this parent-of-origin detection method for each target SNP. In saliva DNA, most of the clones exhibited a hypermethylated or a hypomethylated status in each allele, which is consistent with the successful result of DMPA detection from saliva DNA described previously. On the other hand, DNAs from other sources (semen, finger nails, and hair) revealed quite different methylation profiles among the target genes, especially from semen samples. This indicates that it may be difficult to determine the parental origin from some gDNA sources by restriction-enzyme analysis (DMPA method). The descriptions of materials and methods address genomic DNA, candidate genes, PCR conditions, enzyme digestion, and sodium bisulphate treatment and bisulphate sequencing. 1 table, 3 figures, and 17 references