I've had "radio silence on this blog for a while. Time to start it back up!

I've been reading and responding to a lot of questions about the 2015 protocol, we published and I hope to soon start posting these responses to the blog.

The most common question has been "what are low-cost alternatives to HRMA?"

In our paper, we indicated that a "standard" qPCR machine could be used to do HRMA-like analysis. A recent paper by D'Agostino et al demonstrated that this is indeed true.

If you're interested, take a look at this short paper: 
A Rapid and Cheap Methodology for CRISPR/Cas9 Zebrafish Mutant Screening.

Upside: Less upfront costs, fast
Downside: not very good at detecting small indels.
While this method can identify F0 carriers, it seems best-suited for F1 analysis.



A somewhat older paper provides another alternative method to HRMA:
An Efficient Genotyping Method for Genome-modified Animals and Human Cells Generated with CRISPR/Cas9 System

In this paper, Zhu et al. 2014, the authors show that acrylamide gels do an excellent job of identifying heteroduplex DNA, as is seen in F1 CRISPR injected embryos.
Simply do a PCR, and then run out the products on a 15% PAGE gel.

According to personal communications from Rich Londraville, this method also does a good job of identifying heterozygotes in F0

Upside: Very low cost, fast
Downside: May be less capable of distinguishing alleles from one another than HRMA.

I hope that the blog's readers find these methods helpful.