{"doi":"10.1101/2022.11.08.515732","title":"Flap-enabled next-generation capture (FENGC): precision targeted single-molecule profiling of epigenetic heterogeneity, chromatin dynamics, and genetic variation","abstract":"Abstract Targeted sequencing is an increasingly sought technology. Available methods, however, are often costly and yield high proportions of off-target reads. Here, we present FENGC, a scalable, multiplexed method in which target sequences are assembled into 5′ flaps for precise excision by flap endonuclease. Recovery of length-matched sequences, amplification with universal primers, and exonucleolytic removal of non-targeted genomic regions mitigate amplification biases and consistently yield ≥ 80% on-target sequencing. Furthermore, optimized sequential reagent addition and purifications minimize sample loss and facilitate rapid processing of sub-microgram quantities of DNA for detection of genetic variants and DNA methylation. Treatment of cultured human glioblastoma cells and primary murine monocytes with GC methyltransferase followed by FENGC and high-coverage enzymatic methyl sequencing provides single-molecule, long-read detection of differential endogenous CG methylation, dynamic nucleosome repositioning, and transcription factor binding. FENGC provides a versatile and cost-effective platform for targeted sequence enrichment for analysis of genetic and/or epigenetic heterogeneity.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2022,"id":299602,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":4,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9509,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":989957,"name":"Nancy Nabilsi","orcid":null,"position":1,"is_corresponding":false},{"id":458826,"name":"Anqi Wang","orcid":"0009-0000-5321-8917","position":2,"is_corresponding":false},{"id":258271,"name":"Marie‐Pierre L. Gauthier","orcid":"0009-0002-1936-2231","position":3,"is_corresponding":false},{"id":747395,"name":"Kevin Murray","orcid":"0000-0003-1863-0708","position":4,"is_corresponding":false},{"id":989496,"name":"Hassan Azari","orcid":"0000-0002-8021-3166","position":5,"is_corresponding":false},{"id":989958,"name":"William S. Owens","orcid":null,"position":6,"is_corresponding":false},{"id":307664,"name":"Jeremy R. B. Newman","orcid":"0000-0001-8486-2801","position":7,"is_corresponding":false},{"id":989497,"name":"Francisco J. Pardo-Palacios","orcid":"0000-0002-3067-0166","position":8,"is_corresponding":false},{"id":20402,"name":"Ana Conesa","orcid":"0000-0001-9597-311X","position":9,"is_corresponding":false},{"id":77359,"name":"Alberto Riva","orcid":"0000-0001-9150-8333","position":10,"is_corresponding":false},{"id":461302,"name":"Thomas L. Clanton","orcid":"0000-0003-0600-7150","position":11,"is_corresponding":false},{"id":932719,"name":"Brent A. Reynolds","orcid":"0000-0001-6273-7014","position":12,"is_corresponding":false},{"id":395853,"name":"Patrick Concannon","orcid":"0000-0002-5801-1859","position":13,"is_corresponding":false},{"id":989498,"name":"Jason O. Brant","orcid":"0000-0002-9800-9251","position":14,"is_corresponding":false},{"id":86476,"name":"Rhonda Bacher","orcid":"0000-0001-5787-476X","position":15,"is_corresponding":false},{"id":447551,"name":"Michael P. Kladde","orcid":"0000-0001-7951-9291","position":16,"is_corresponding":false},{"id":989495,"name":"Mingqi Zhou","orcid":"0000-0002-4605-5467","position":0,"is_corresponding":true}],"reference_count":62,"raw_metadata":null,"created_at":"2026-07-19T00:31:44.904250Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}