Here's our G&D paper.
We use SNP FISH ala Levesque et al. to allow SNP detection. This has two problems. First, we need to solve the specificity problem of detecting single base mismatches with a 20-mer oligo. To solve this, we used a "mask" probe approach in which a "toehold" region allowed for greater discrimination.

Visualizing epigenetic mosaicism at the single cell level

By Arjun, Paul, Jenn, Marisa

Link to Manscript


Questions: all,
Using genetic crosses in which only one allele was available *Top left, bottom right*, we only detected a small number of off-targets. So the specificity of the technique is very good, probably around 5 percent.