{"doi":"10.1101/2024.04.18.590093","title":"Long-read sequencing and structural variant characterization in 1,019 samples from the 1000 Genomes Project","abstract":"Structural variants (SVs) contribute significantly to human genetic diversity and disease 1–4 . Previously, SVs have remained incompletely resolved by population genomics, with short-read sequencing facing limitations in capturing the whole spectrum of SVs at nucleotide resolution 5–7 . Here we leveraged nanopore sequencing 8 to construct an intermediate coverage resource of 1,019 long-read genomes sampled within 26 human populations from the 1000 Genomes Project. By integrating linear and graph-based approaches for SV analysis via pangenome graph-augmentation, we uncover 167,291 sequence-resolved SVs in these samples, considerably advancing SV characterization compared to population-wide short-read sequencing studies 3,4 . Our analysis details diverse SV classes—deletions, duplications, insertions, and inversions—at population-scale. LINE-1 and SVA retrotransposition activities frequently mediate transductions 9,10 of unique sequences, with both mobile element classes transducing sequences at either the 3′- or 5′-end, depending on the source element locus. Furthermore, analyses of SV breakpoint junctions suggest a continuum of homology-mediated rearrangement processes are integral to SV formation, and highlight evidence for SV recurrence involving repeat sequences. Our open-access dataset underscores the transformative impact of long-read sequencing in advancing the characterisation of polymorphic genomic architectures, and provides a resource for guiding variant prioritisation in future long-read sequencing-based disease studies.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2024,"id":483907,"datarank":1.2871211833405969,"base_score":3.6635616461296463,"endowment":3.6635616461296463,"self_citation_contribution":0.5495342469194471,"citation_network_contribution":0.7375869364211499,"self_endowment_contribution":0.5495342469194471,"citer_contribution":0.7375869364211499,"corpus_percentile":83.97926819834456,"corpus_rank":2072,"citation_count":38,"citer_count":32,"citers_with_citation_signal":22,"citers_with_endowment":22,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.7803,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1324955,"name":"Samarendra Pani","orcid":"0009-0002-2037-2533","position":1,"is_corresponding":false},{"id":14431,"name":"Bernardo Rodríguez–Martín","orcid":"0000-0003-4693-3140","position":2,"is_corresponding":false},{"id":231857,"name":"Jana Ebler","orcid":"0000-0002-0382-3702","position":3,"is_corresponding":false},{"id":1324956,"name":"Carsten Hain","orcid":"0000-0002-6206-9906","position":4,"is_corresponding":false},{"id":19731,"name":"Vasiliki Tsapalou","orcid":"0009-0002-3588-7003","position":5,"is_corresponding":false},{"id":19728,"name":"Arda Soylev","orcid":"0000-0003-2198-1920","position":6,"is_corresponding":false},{"id":1324957,"name":"Patrick Hüther","orcid":"0000-0003-3315-2484","position":7,"is_corresponding":false},{"id":19709,"name":"Hufsah Ashraf","orcid":"0000-0001-7760-0627","position":8,"is_corresponding":false},{"id":19699,"name":"Timofey Prodanov","orcid":"0000-0001-7469-6651","position":9,"is_corresponding":false},{"id":456998,"name":"Mila Asparuhova","orcid":"0000-0002-8597-4116","position":10,"is_corresponding":false},{"id":19717,"name":"Sarah E. Hunt","orcid":"0000-0002-8350-1235","position":11,"is_corresponding":false},{"id":13956,"name":"Tobias Rausch","orcid":"0000-0001-5773-5620","position":12,"is_corresponding":false},{"id":6321,"name":"Tobias Marschall","orcid":"0000-0002-9376-1030","position":13,"is_corresponding":false},{"id":108507,"name":"Jan O. Korbel","orcid":"0000-0002-2798-3794","position":14,"is_corresponding":false},{"id":630807,"name":"Siegfried Schloissnig","orcid":"0000-0003-4574-8330","position":0,"is_corresponding":true}],"reference_count":111,"raw_metadata":null,"created_at":"2026-07-19T02:07:33.718973Z","pmid":"38659906","pmcid":"PMC11042266","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":[]}