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Amplicon length andnumber of Methylation sitesthe greater the number of potential methylation sites in an amplicon, the larger the tm difference between pcr products from highly methylated and unmethylated dna samples. this makes it easy to distinguish melt profiles; however, it may also contribute to pcr bias. including too few CpG dinucleotides, on the other hand, may produce melt profiles that are too similar to be useful for methylation analysis. pcr bias is based on the observation that, in general, dna fragments with high c content are not amplified as efficiently as fragments with high u / t content. after bisulfite conversion, unmethylated stretches of dna will be significantly enriched for u / t nucleotides and may be amplified to the exclusion of their methylated counterparts [2]. pcr bias is very hard to predict; in some cases it is directly related to the number of CpG dinucleotides in the amplicon, but not always. in addition, methylation may be heterogeneous, i.e., only some potential sites are actually methylated. it is difficult to calculate accurate methylation values for fragments derived from heterogeneously methylated sequences.the optimally number of potential methylation sites in amplicons must be determined empirically because it varies significantly among different genomic regions, for reasons that are not well understood. successful ms hrm assays have been published with 100–200 bp amplicons and up to 16 methylation sites.
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