CRISPR 101: Validating Your Genome Edit

Posted by Melina Fan on Jul 30, 2015 10:30:00 AM

You’ve created your gRNA expression construct and used Cas9 to introduce it into your target cells. Hooray! You’re ready to begin reading out data, right? Almost. In this blog post we’ll explain how to verify that your cells were appropriately edited. We’ll also cover the basic techniques for detecting insertion, deletion, and mutation events.

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Process overview

The method for validating your genome edit will vary by species and the type of edit. In this post, we will focus on diploid mammalian cells, but many of the principles will hold across different model organisms.

Introducing Cas9 and a gRNA into your cells (possibly along with a donor template) will result in a mixed population of cells. Following the introduction of a Cas9-mediated double strand break (DSB) in mammalian cells, cellular machinery repair the DSB by non-homologous end joining (NHEJ) or homology directed repair (HDR). Repair via the NHEJ pathway predominates in mammalian cells resulting in the creation of indel errors, short heterogeneous insertions and deletions of nucleic acid sequences, at the site of the DSB. In addition to the heterogeneity of indels introduced at Cas9-induced DSBs, allelic editing frequencies will vary as well. The HDR pathway requires the presence of a repair template, which is used to fix the DSB in a more specific manner. HDR faithfully copies the sequence of the repair template to the cut target sequence. Some cells will not be edited, some will have one allele edited, and some will have both alleles edited.

Genome editing validation workflow. If Cas9 cuts the genome in the absence of an HDR donor, then an indel is created. Indels are detected by the mismatch cleavage assay and then cells with the desired mutations can be clonal expanded. If Cas9 cuts the genome in the presence of an HDR donor, then this donor may be introduced at the cut site due to homology directed repair of the DNA. PCR is then used to screen for cells that contain the desired insertion. Cells with the desired insertion can be clonal expanded.

The first step in the validation process is to quickly assess whether a significant number of the cells have been edited (see Figure 1). For indels, this is visualized using a mismatch cleavage assay (see Figure 2). For HDR, this is often visualized by a change in the restriction pattern at the site of interest or via a reporter readout. For deletions (see Figure 3), this is visualized by a decrease in size of a PCR product produced by primers flanking the region to be deleted.

Once you know that a portion of your cells have been edited, you can go on to create clonal cell lines. Serial dilutions can be used to isolate single cells followed by an expansion period to generate these lines. If you have a fluorescent protein marker on your plasmid, you can use FACS to enrich the cells that received Cas9 and your gRNA. After expansion, assay each cell line and sequence the region of interest in order to validate the genome edit as described in Figure 1. When possible, you should also assess protein expression via western blot as a further form of validation.

Mismatch Cleavage Assay to Detect Indels

Overview of the mismatch cleavage assay or Surveyor assay for detecting the creation of indels by CRISPR. The mutated region of DNA is amplified by PCR and then denatured and re-hybridized. Samples are then treated with the SURVEYOR nuclease which digests mismatched DNA. Samples are then run on a gel where cleaved DNA separates from uncleaved DNA.


A mismatch cleavage assay is a quick and easy way to detect indels. SurveyorTM nuclease is commonly used for this purpose, as it cleaves both DNA strands 3’ to any mismatches. It can detect indels of up to 12 nucleotides and is sensitive to mutations present at frequencies as low as 1 in 32 copies.

Mismatch cleavage assays typically consist of four steps: 1) PCR amplify the region of interest, 2) denature the strands and rehybridize to allow for the mutant and wild-type strands to anneal, 3) treat annealed DNA with SurveyorTM nuclease to cleave heteroduplexes, and 4) analyze DNA on an agarose gel or other instrument that separates DNA based on size. Figure 2 illustrates how the assay works. In this example, both +gRNA lanes contain cleaved fragments of the expected sizes, indicating that the gRNAs successfully produced indels in the target region. This assay is often used semi-quantitatively, and in this case, gRNA1 appears to be more efficient at producing indels than gRNA2.


Detect Homology Directed Repair

If you want to mutate your region of interest using HDR, it is advisable to first determine whether your gRNA is efficiently cutting your target sequence by creating indels and conducting a mismatch cleavage assay. Once you’ve selected your optimal gRNA, introduce it along with Cas9 and your repair template to drive HDR.

When designing your HDR donor template, plan ahead for detection of integration events. For instance, you could purposefully introduce or remove restriction sites which would alter the digestion pattern of PCR products. Alternatively, you could include a reporter element for detection of HDR at the DNA, RNA, or protein level. A large insertion or deletion after integration could also be detected by a size change in the PCR product. Single nucleotide changes can be quickly assayed using restriction digests if the polymorphism creates/removes a restriction digest site. Otherwise, single nucleotide changes can be detected by TA cloning and Sanger sequencing, next generation sequencing, or droplet digital PCR genotyping.

HDR events are generally less frequent than indels, so you will likely need to screen a larger number of colonies to create a clonal line. The number of clones that need to be screened will depend on both your transfection/transduction efficiency and HDR frequency. For example, if you have 40% transfection efficiency and 5% HDR efficiency, approximately 0.4x0.05=0.02 or 2% of your cells will have the recombined region. Thus, you should plan to screen at least 50 colonies. If you are able to select cells that have been successfully transfected/transduced using a marker, then you may be able to test fewer colonies.

Check Out Our Post on Sequencing Options for CRISPR Genotyping

PCR to detect deletions

Most deletions are created by using two gRNAs that direct Cas9 to cleave out the intervening region of DNA. The deletion can thus be detected by conducting a PCR using primers flanking the deleted region. The workflow is similar to that described in Figure 1. Figure 3 provides an example of PCR results obtained by screening a panel of clonal lines for deletions. In this example, clones 1, 5, and 7 are heterozygous for the deletion and clone 4 is homozygous for the deletion.

Using PCR to identify clones that contain desired CRISPR deletions.

Check Out Our Blog Post on Using Digital PCR to Validate Your Genome Edit

Next Generation Sequencing to validate edits and detect off-target effects 

If your lab has the resources, you can quantitatively assess genome edits in your target sequence and other regions of the genome using next generation sequencing (NGS). NGS is a good option if you have a large number of samples and/or want to simultaneously look at off-target changes. When using this method, it is important to keep a set of control cells as you will need to compare the sequencing reads from your edited sample to this untreated population. Software such as CRISPResso can help with the data analysis.

The techniques described in this post are not CRISPR-specific and can also be used for assessing genome edits created by TALEN or Zinc Finger Nucleases. Regardless of what method you use, validating your edit is time well spent as you prepare for your future experiments.

Thank you to David Scott (Dr. Feng Zhang's Lab), Joel McDade (Addgene),  and Marcy Patrick (Addgene) for helpful comments and edits.


1. Mutation detection using Surveyor nuclease. Qiu P, Shandilya H, D'Alessio JM, O'Connor K, Durocher J, Gerard GF. Biotechniques 2004 Apr; 36(4):702-7. PubMed

2. Genome engineering using the CRISPR-Cas9 system. Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA, Zhang F. Nature Protocols. 2013 Nov; 8(11):2281-2308. PubMed

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