3 ms·

I asserted that saying that 10% of cells have an indel at any given site is equivalent to saying the per-base indel mutation rate is 10%. You posted an example

I asserted that saying that 10% of cells have an indel at any given site is equivalent to saying the per-base indel mutation rate is 10%. You posted an example purporting to disprove this, but instead, illustrated that you don't know what an indel is, and that the two statements are indeed equivalent -- at any given site, 12.5% of cells are mutant, and that the per-base mutation rate is 12.5%. The only one with Dunning-Kruger is you.

nonbel 8y ago
Here is what I am responding to (also keep in mind I was using indel to mean "indels and substitutions", ie whatever may be counted as an error during NHEJ): > "There's no way cells survive with indels at 10% of their base positions, that's not possible." > "How is the per-base indel rate not 10% if 10% of cells carry an indel at any given locus?" I figured you were referring to per base within each cell. Your overall "per base" rate is getting the average (across cells) number of mutated sites. The survival of a cell is determined by its own genome, not the average of the population its been grouped into. However, it is the case that if x% of cells have a mutation at any given site then there must be at least some cells in this group that contain x% or greater mutated sites. Is that what you meant? Because that's not a bad point. I don't know where that 10% value came from and have no attachment to it, just assume that one is measurement noise for now, but even cells with 0.1% of sites mutated seems like a lot. There doesn't seem to be many whole genome single cell sequencing results available yet, which is what I think is needed here. Here is one that reports ~ 15k SNVs, 50-100 "micro-CNVs" (ie 10-100 kb copy number variants, fig S4), and 290 indels: >"We call an SNV if there is a called NR allele and: (a) the total read depth in the bulk sample is above 15; (b) no bulk read has the NR allele; (c) if two SNVs are within 100bp from each other, both are discarded. With this procedure, we called 15,940 SNVs on the autosome of sample BJ1...We called 294 putative INDELs from the BJ1-BJ2 pair, the negative control" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5538131/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5538131/ So taking the smallest and biggest numbers of possible here gives: 100%*(15e3 + 50*10e3 + 290*1)/3e9 = 0.02% of bases affected 100%*(15e3 + 100*100e3 + 290*10e3)/3e9 = 0.4% of bases affected This seems to ignore any very small or large mutations that may affect a given site, and not all the mutations will simulate the effect of NHEJ... but this makes me think it isnt impossible for 0.001-1% to happen, especially in vitro.
nonbel 8y ago
typo in the last post: >"This seems to ignore any very small or large mutations" I wrote this before I added the "smallest" calculation. So only the very large structural changes are ignored (> 100 kb).

nonbel 8y ago

Here is what I am responding to (also keep in mind I was using indel to mean "indels and substitutions", ie whatever may be counted as an error during NHEJ): > "There's no way cells survive with indels at 10% of their base positions, that's not possible." > "How is the per-base indel rate not 10% if 10% of cells carry an indel at any given locus?" I figured you were referring to per base within each cell. Your overall "per base" rate is getting the average (across cells) number of mutated sites. The survival of a cell is determined by its own genome, not the average of the population its been grouped into. However, it is the case that if x% of cells have a mutation at any given site then there must be at least some cells in this group that contain x% or greater mutated sites. Is that what you meant? Because that's not a bad point. I don't know where that 10% value came from and have no attachment to it, just assume that one is measurement noise for now, but even cells with 0.1% of sites mutated seems like a lot. There doesn't seem to be many whole genome single cell sequencing results available yet, which is what I think is needed here. Here is one that reports ~ 15k SNVs, 50-100 "micro-CNVs" (ie 10-100 kb copy number variants, fig S4), and 290 indels: >"We call an SNV if there is a called NR allele and: (a) the total read depth in the bulk sample is above 15; (b) no bulk read has the NR allele; (c) if two SNVs are within 100bp from each other, both are discarded. With this procedure, we called 15,940 SNVs on the autosome of sample BJ1...We called 294 putative INDELs from the BJ1-BJ2 pair, the negative control" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5538131/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5538131/ So taking the smallest and biggest numbers of possible here gives: 100%*(15e3 + 50*10e3 + 290*1)/3e9 = 0.02% of bases affected 100%*(15e3 + 100*100e3 + 290*10e3)/3e9 = 0.4% of bases affected This seems to ignore any very small or large mutations that may affect a given site, and not all the mutations will simulate the effect of NHEJ... but this makes me think it isnt impossible for 0.001-1% to happen, especially in vitro.

nonbel 8y ago

typo in the last post: >"This seems to ignore any very small or large mutations" I wrote this before I added the "smallest" calculation. So only the very large structural changes are ignored (> 100 kb).