Its a cancer targeted panel, and these two are clearly two most prevalent observed mutations.
The most prevalent alteration is a cytosine to thymine transition caused by deamination of cytosines. The existence of these artifactual mutations can complicate analysis of next-generation sequencing (NGS) results, particularly when analyzing low-frequency mutations.
For this, Pretreatment of FFPE DNA with uracil-DNA glycosylase (UDG) can markedly reduce these C:G>T:A SNCs with a small panel of amplicons. This procedure has implications for massively parallel sequencing approaches to mutation detection from DNA.
You can find more details in below linked article: http://www.clinchem.org/content/59/9/1376.full.pdf
Do you have NGS data?
NextGenMap is a mapper that does extremely well handle any SNP concentration.
http://cibiv.github.io/NextGenMap/
Could you let me know about the expected mutation rate?
Do you expect to see homozygous pseudomutation, or heterozygous mutation as well
Any idea, if I can set up any allele freq cutoff to avoid such pseudo mutation calls...(its ion amplicon based sequencing)
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