{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Quan ZJ"],"funding":["Innovation Fund for Medical Sciences","National Key R&D Program of China","Chinese Academy of Medical Sciences","National Natural Science Foundation of China"],"pagination":["1221-1236"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC11082256"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["21(6)"],"pubmed_abstract":["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)-"],"journal":["Genomics, proteomics & bioinformatics"],"pubmed_title":["GREPore-seq: A Robust Workflow to Detect Changes After Gene Editing Through Long-range PCR and Nanopore Sequencing."],"pmcid":["PMC11082256"],"funding_grant_id":["2019YFA0110800","81770198","2019YFA0110204","81730010","81890990","82070115","81730006","2016YFA0100600","2021-I2M-1-041","2019-I2M-1-006","81870149"],"pubmed_authors":["Zhang F","Cheng T","Yang ZX","Quan ZJ","Zhao JJ","Li GH","Zhang XB","Li SA","Wen W"],"additional_accession":[]},"is_claimable":false,"name":"GREPore-seq: A Robust Workflow to Detect Changes After Gene Editing Through Long-range PCR and Nanopore Sequencing.","description":"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)-","dates":{"release":"2023-01-01T00:00:00Z","publication":"2023 Dec","modification":"2026-03-17T15:21:01.106Z","creation":"2025-08-16T03:06:31.142Z"},"accession":"S-EPMC11082256","cross_references":{"pubmed":["35752289"],"doi":["10.1016/j.gpb.2022.06.002"]}}