What if I want to know whether an oncogene has acquired a single base mutation in a tumor, even if it's only present in 1 of every 10,000 cells? What if I want to know the prevalence of single nucleotide transcription errors for a specific transcript, even errors present at 1 in 20,000?
NGS technologies have an error rate of 1/1000 - 1/100 per base*read. Does this make the above two problems impossible to solve with NGS, even if I get millions of reads covering the regions in question?
I wanted to get the forum's thoughts on the above, in addition to hearing whether there are any publications addressing this, as I've found few. Can we think of any workarounds, either informatic or wet? How should we set thresholds for the minimum frequency at which a variant would be confidently detectable?
I look forward to anyone else's take,
Genly
(Wasn't sure what subforum to put this post in, so feel free to suggest another.)
NGS technologies have an error rate of 1/1000 - 1/100 per base*read. Does this make the above two problems impossible to solve with NGS, even if I get millions of reads covering the regions in question?
I wanted to get the forum's thoughts on the above, in addition to hearing whether there are any publications addressing this, as I've found few. Can we think of any workarounds, either informatic or wet? How should we set thresholds for the minimum frequency at which a variant would be confidently detectable?
I look forward to anyone else's take,
Genly
(Wasn't sure what subforum to put this post in, so feel free to suggest another.)
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