biostudies-literatureQuan ZJInnovation Fund for Medical SciencesNational Key R&D Program of ChinaChinese Academy of Medical SciencesNational Natural Science Foundation of China1221-1236https://www.ebi.ac.uk/biostudies/studies/S-EPMC11082256biostudies-literatureUnknown21(6)To achieve the enormous potential of gene-editing technology in clinical therapies, one needs to evaluate both the on-target efficiency and unintended editing consequences comprehensively. However, there is a lack of a pipelined, large-scale, and economical workflow for detecting genome editing outcomes, in particular insertion or deletion of a large fragment. Here, we describe an approach for efficient and accurate detection of multiple genetic changes after CRISPR/Cas9 editing by pooled nanopore sequencing of barcoded long-range PCR products. Recognizing the high error rates of Oxford nanopore sequencing, we developed a novel pipeline to capture the barcoded sequences by grepping reads of nanopore amplicon sequencing (GREPore-seq). GREPore-seq can assess nonhomologous end-joining (NHEJ)-Genomics, proteomics & bioinformaticsGREPore-seq: A Robust Workflow to Detect Changes After Gene Editing Through Long-range PCR and Nanopore Sequencing.PMC110822562019YFA0110800817701982019YFA0110204817300108189099082070115817300062016YFA01006002021-I2M-1-0412019-I2M-1-00681870149Zhang FCheng TYang ZXQuan ZJZhao JJLi GHZhang XBLi SAWen WfalseGREPore-seq: A Robust Workflow to Detect Changes After Gene Editing Through Long-range PCR and Nanopore Sequencing.To achieve the enormous potential of gene-editing technology in clinical therapies, one needs to evaluate both the on-target efficiency and unintended editing consequences comprehensively. However, there is a lack of a pipelined, large-scale, and economical workflow for detecting genome editing outcomes, in particular insertion or deletion of a large fragment. Here, we describe an approach for efficient and accurate detection of multiple genetic changes after CRISPR/Cas9 editing by pooled nanopore sequencing of barcoded long-range PCR products. Recognizing the high error rates of Oxford nanopore sequencing, we developed a novel pipeline to capture the barcoded sequences by grepping reads of nanopore amplicon sequencing (GREPore-seq). GREPore-seq can assess nonhomologous end-joining (NHEJ)-2023-01-01T00:00:00Z2023 Dec2026-03-17T15:21:01.106Z2025-08-16T03:06:31.142ZS-EPMC110822563575228910.1016/j.gpb.2022.06.002