
Crispr tweak may help gene-edited crops bypass biosafety regulation - cryoshon
http://www.nature.com/news/crispr-tweak-may-help-gene-edited-crops-bypass-biosafety-regulation-1.18590
======
nonbel
Link to actual paper:
[http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.338...](http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3389.html)

See figure 2D of the previous paper from the same group to see the treatment
is toxic (at least to some cell types):
[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4032847/](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4032847/)

They don't account for that possibility here. They report in the supplements
that ~1/100,000 cells are already mutants in the control group (Fig S1). This
may be an underestimate since they only detected ~7% mutant cells after
treatment using sequencing, but in fig 1c of the paper they report ~70% using
the T7 endonuclease assay. I don't see where this discrepancy is discussed,
but clearly one of these estimates is not reliable.

Anyway, as they write in the abstract: "The targeted sites contained germline-
transmissible small insertions or deletions that are indistinguishable from
naturally occurring genetic variation."

Yes, and they may very well be detecting natural variation by selecting for
the pre-existing mutants. Even using the .01 % pre-existing mutant value there
would be 10 mutants in the dish of ~10^5 cells. If the treatment kills 99.9%
of the normals you would be left with around 10 mutant and 100 normal
colonies. This is about the size of the observed effect according to the
sequencing method.

They need to report how many cells were remaining after the CRISPR-Cas9
treatment and figure out why the T7 endonuclease assay is disagreeing with the
sequencing by an order of magnitude.

