Illumina Amplicon NGS
First, genomic DNA was sheared using sonication. Then, barcoded Y adapters were ligated to sheared genomic DNA and resulting DNA fragments were PCR-amplified using primers specific to the Y adapter and region of interest. Next, a second PCR reaction was performed to add sample specific barcodes and resulting Illumina PCR libraries were purified and samples run according to manufacturers instructions. NGS reads were demultiplexed and Read2 reads were filtered for an approximate donor sequence match (integration site nomination) or match to the intended target (translocation site nomination) prior to read pairing with seqkit and alignment to the hg38 genome with Bowtie2 for subsequent analysis (see detailed Methods in our manuscript).