Disclosed is a method for high-throughput detection of genome-wide modifications in a nucleic acid genome obtained from a cell or tissue caused by the activity of a designer nuclease comprising the following steps: a) Extraction of the genomic DNA from cells that were exposed to a designer nuclease under conditions which allow the designer nuclease to introduce a DNA double-strand break (DSB) in the genomic DNA of the cell, b) fragmentation of the nucleic acid to obtain random fragments, c) performing an end repair in order to obtain blunt ends, d) ligation with a linker comprising a sequence complementary to a so called “linker primer”, e) performing a first nucleic acid amplification reaction with a “linker primer” and a so called “ON-target primer”, whereby one primer is located upstream and one primer is located downstream of the on-target site, wherein at least one decoy primer is present in the reaction mixture, f) performing a second nucleic acid amplification reaction whereby so called “nested primers” are added to the reaction mixture, whereby one primer is complementary to the on-target locus and one primer complementary to the linker sequence, g) performing a further nucleic acid amplification reaction whereby at least one code containing primers are added to the reaction mixture, h) sequencing of the nested and barcoded amplification product, and i) aligning the sequenced products with suitable bioinformatic means to a reference sequence to identify a chromosomal location that contains a genomic modification based on at least one DNA double strand break.