{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T23:22:33Z","timestamp":1773271353389,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1013368","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,8,22]],"date-time":"2025-08-22T00:00:00Z","timestamp":1755820800000}}],"reference-count":23,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2025,8,18]],"date-time":"2025-08-18T00:00:00Z","timestamp":1755475200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62472084"],"award-info":[{"award-number":["62472084"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Leading Technology Program of Jiangsu Province","award":["BK20222008"],"award-info":[{"award-number":["BK20222008"]}]},{"DOI":"10.13039\/501100004543","name":"China Scholarship Council","doi-asserted-by":"publisher","award":["202106090125"],"award-info":[{"award-number":["202106090125"]}],"id":[{"id":"10.13039\/501100004543","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Institut national de la sant\u00c3\u00a9 et de la recherche m\u00c3\u00a9dicale"},{"DOI":"10.13039\/501100004794","name":"Centre National de la Recherche Scientifique","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004794","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100009454","name":"Fondation de l'\u00c3\u2030cole Polytechnique","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100009454","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>G-quadruplexes (G4s) are nucleic acid secondary structures with important regulatory functions. Single-nucleotide variants (SNVs), one of the most common forms of genetic variation, can potentially impact the formation of G4 structures if they occur within G4 regions. However, there is currently a lack of software tools specifically designed to assess such effects. Here, we present an R\/Bioconductor package named G4SNVHunter, which enables rapid detection of variants that may disrupt G4 structures. This tool, based on the core principles of the G4Hunter algorithm, can provide precise quantitative assessment of the propensity for G4 formation within genomic sequences. Specialized experimental methods can then be designed based on the results provided by G4SNVHunter to further verify the specific functions of the affected G4 structures, facilitating deeper insights into the biological impacts of genetic variants from the perspective of G4 structures. To showcase the functionality of the G4SNVHunter package, we analyzed the Neandertal and Denisovan archaic introgressed variants detected by the Sprime software, and identified approximately 5,800 variants located within G4 regions, among which around 230 may impair G4 structure formation propensity. The source code for the G4SNVHunter package has been publicly released under the MIT license at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/rongxinzh\/G4SNVHunter\" xlink:type=\"simple\">https:\/\/github.com\/rongxinzh\/G4SNVHunter<\/jats:ext-link> and <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/bioconductor.org\/packages\/devel\/bioc\/html\/G4SNVHunter.html\" xlink:type=\"simple\">https:\/\/bioconductor.org\/packages\/devel\/bioc\/html\/G4SNVHunter.html<\/jats:ext-link>.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1013368","type":"journal-article","created":{"date-parts":[[2025,8,18]],"date-time":"2025-08-18T18:05:10Z","timestamp":1755540310000},"page":"e1013368","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":1,"title":["G4SNVHunter: An R\/Bioconductor Package for Evaluating SNV-Induced Disruption of G-Quadruplex Structures Leveraging the G4Hunter Algorithm"],"prefix":"10.1371","volume":"21","author":[{"given":"Rongxin","family":"Zhang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-0707-135X","authenticated-orcid":true,"given":"Wenyong","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ke","family":"Xiao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jean-Louis","family":"Mergny","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1048-7775","authenticated-orcid":true,"given":"Xiao","family":"Sun","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2025,8,18]]},"reference":[{"issue":"8","key":"pcbi.1013368.ref001","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1038\/s41580-020-0236-x","article-title":"The regulation and functions of DNA and RNA G-quadruplexes","volume":"21","author":"D Varshney","year":"2020","journal-title":"Nat Rev Mol Cell Biol"},{"issue":"2","key":"pcbi.1013368.ref002","article-title":"Where are G-quadruplexes located in the human transcriptome?","volume":"2","author":"A Vannutelli","year":"2020","journal-title":"NAR Genom Bioinform"},{"issue":"21","key":"pcbi.1013368.ref003","doi-asserted-by":"crossref","first-page":"7858","DOI":"10.1093\/nar\/gkq639","article-title":"How long is too long? 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