Methods of detecting a mutation comprise introducing a Cas endonuclease complex to a nucleic acid sample, wherein guide RNA in the Cas endonuclease complex bind to a location of a suspected mutation. Unbound nucleic acid in the sample is degraded or separated from the bound complex, and presence of the mutation is detected by detecting bound Cas endonuclease complex. The Cas endonuclease complex comprises a Cas endonuclease and guide RNA. The guide RNA is designed to bind to the location of the suspected mutation. In some instances, the Cas endonuclease complex comprises a detectable label, such as a fluorescent label. Therefore, detecting presence of the mutation comprises detecting presence of the label. An exonuclease may be used to degrade or digest unbound nucleic acid and isolate the mutation. Methods include further analysis of the isolated mutation.
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