Abstract: The invention relates to a method for determining the level and type of mutation events associated with the use of a targeted genetic modification, such as in the use of designer nucleases, to modify a target site of nucleic acid in a cell or virus population. The method comprises carrying out a mutation event determination on a targeted nucleic acid in a population of modified nucleic acids that have been treated with the targeted genetic modification, and a reference control analysis on a non-targeted nucleic acid. The invention further relates to the use of the method for screening of potential targeted genetic modification agents for therapeutic use and to estimate the genomic integrity and stability of a nucleic acid such as a viral vector or genomic DNA.