{"id":"https://openalex.org/W7225466508","doi":"https://doi.org/10.64898/2026.11.06.764802","title":"Somatic Structural Variant Discovery from Tumor Specific Strings Computed Against a Draft Composite Germline Reference","display_name":"Somatic Structural Variant Discovery from Tumor Specific Strings Computed Against a Draft Composite Germline Reference","publication_year":2026,"publication_date":"2026-11-06","ids":{"openalex":"https://openalex.org/W7225466508","doi":"https://doi.org/10.64898/2026.11.06.764802"},"language":"en","primary_location":{"id":"doi:10.64898/2026.11.06.764802","doi":"https://doi.org/10.64898/2026.11.06.764802","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.06.764802","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/06/2026.11.06.764802.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/06/2026.11.06.764802.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060352558","display_name":"Davide Cesare Monti","orcid":"https://orcid.org/0009-0004-1710-5500","observed_orcids":["https://orcid.org/0009-0004-1710-5500"]},"institutions":[{"id":"https://openalex.org/I66752286","display_name":"University of Milano-Bicocca","ror":"https://ror.org/01ynf4891","country_code":"IT","type":"education","lineage":["https://openalex.org/I66752286"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Davide Cesare Monti","raw_affiliation_strings":["University of Milano-Bicocca;"],"raw_orcid":"https://orcid.org/0009-0004-1710-5500","affiliations":[{"raw_affiliation_string":"University of Milano-Bicocca;","institution_ids":["https://openalex.org/I66752286"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048411377","display_name":"Simone Ciccolella","orcid":"https://orcid.org/0000-0002-6469-4887","observed_orcids":["https://orcid.org/0000-0002-6469-4887"]},"institutions":[{"id":"https://openalex.org/I66752286","display_name":"University of Milano-Bicocca","ror":"https://ror.org/01ynf4891","country_code":"IT","type":"education","lineage":["https://openalex.org/I66752286"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Simone Ciccolella","raw_affiliation_strings":["University of Milano-Bicocca;"],"raw_orcid":"https://orcid.org/0000-0002-6469-4887","affiliations":[{"raw_affiliation_string":"University of Milano-Bicocca;","institution_ids":["https://openalex.org/I66752286"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021585705","display_name":"Davide Cozzi","orcid":"https://orcid.org/0000-0003-2439-0608","observed_orcids":["https://orcid.org/0000-0003-2439-0608"]},"institutions":[{"id":"https://openalex.org/I66752286","display_name":"University of Milano-Bicocca","ror":"https://ror.org/01ynf4891","country_code":"IT","type":"education","lineage":["https://openalex.org/I66752286"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Davide Cozzi","raw_affiliation_strings":["University of Milano-Bicocca;"],"raw_orcid":"https://orcid.org/0000-0003-2439-0608","affiliations":[{"raw_affiliation_string":"University of Milano-Bicocca;","institution_ids":["https://openalex.org/I66752286"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059679442","display_name":"Gianluca Della Vedova","orcid":"https://orcid.org/0000-0001-5584-3089","observed_orcids":["https://orcid.org/0000-0001-5584-3089"]},"institutions":[{"id":"https://openalex.org/I66752286","display_name":"University of Milano-Bicocca","ror":"https://ror.org/01ynf4891","country_code":"IT","type":"education","lineage":["https://openalex.org/I66752286"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Gianluca Della Vedova","raw_affiliation_strings":["University of Milano-Bicocca;"],"raw_orcid":"https://orcid.org/0000-0001-5584-3089","affiliations":[{"raw_affiliation_string":"University of Milano-Bicocca;","institution_ids":["https://openalex.org/I66752286"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038691764","display_name":"Paola Bonizzoni","orcid":"https://orcid.org/0000-0001-7289-4988","observed_orcids":["https://orcid.org/0000-0001-7289-4988"]},"institutions":[{"id":"https://openalex.org/I66752286","display_name":"University of Milano-Bicocca","ror":"https://ror.org/01ynf4891","country_code":"IT","type":"education","lineage":["https://openalex.org/I66752286"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Paola Bonizzoni","raw_affiliation_strings":["University of Milano-Bicocca;"],"raw_orcid":"https://orcid.org/0000-0001-7289-4988","affiliations":[{"raw_affiliation_string":"University of Milano-Bicocca;","institution_ids":["https://openalex.org/I66752286"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030595155","display_name":"Luca Denti","orcid":"https://orcid.org/0000-0001-8786-2276","observed_orcids":["https://orcid.org/0000-0001-8786-2276"]},"institutions":[{"id":"https://openalex.org/I74788687","display_name":"Comenius University Bratislava","ror":"https://ror.org/0587ef340","country_code":"SK","type":"education","lineage":["https://openalex.org/I74788687"]}],"countries":["SK"],"is_corresponding":false,"raw_author_name":"Luca Denti","raw_affiliation_strings":["Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava;"],"raw_orcid":"https://orcid.org/0000-0001-8786-2276","affiliations":[{"raw_affiliation_string":"Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava;","institution_ids":["https://openalex.org/I74788687"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005747594","display_name":"Fereydoun Hormozdiari","orcid":"https://orcid.org/0000-0003-2703-9274","observed_orcids":["https://orcid.org/0000-0003-2703-9274"]},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fereydoun Hormozdiari","raw_affiliation_strings":["UC-Davis"],"raw_orcid":"https://orcid.org/0000-0003-2703-9274","affiliations":[{"raw_affiliation_string":"UC-Davis","institution_ids":["https://openalex.org/I84218800"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5060352558"],"corresponding_institution_ids":["https://openalex.org/I66752286"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9053000211715698,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9053000211715698,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.04450000077486038,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.031700000166893005,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/somatic-structural-variants","display_name":"somatic structural variants","score":0.9670000076293945},{"id":"https://openalex.org/keywords/tumor-normal-comparison","display_name":"tumor-normal comparison","score":0.4749999940395355},{"id":"https://openalex.org/keywords/long-read-whole-genome-sequencing","display_name":"long-read whole-genome sequencing","score":0.8840000033378601},{"id":"https://openalex.org/keywords/complex-genomic-rearrangements","display_name":"complex genomic rearrangements","score":0.7699999809265137},{"id":"https://openalex.org/keywords/repetitive-regions","display_name":"repetitive regions","score":0.6919999718666077},{"id":"https://openalex.org/keywords/consensus-sequence-generation","display_name":"consensus sequence generation","score":0.6800000071525574},{"id":"https://openalex.org/keywords/cancer-genomics","display_name":"cancer genomics","score":0.628000020980835},{"id":"https://openalex.org/keywords/pacbio-hifi","display_name":"PacBio HiFi","score":0.7390000224113464}],"concepts":[{"id":"https://openalex.org/C109825262","wikidata":"https://www.wikidata.org/wiki/Q1139164","display_name":"Germline","level":3,"score":0.9000999927520752},{"id":"https://openalex.org/C134305767","wikidata":"https://www.wikidata.org/wiki/Q725508","display_name":"Somatic cell","level":3,"score":0.8522999882698059},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6704999804496765},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6360999941825867},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5091000199317932},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4611000120639801},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.45649999380111694},{"id":"https://openalex.org/C13514818","wikidata":"https://www.wikidata.org/wiki/Q5552256","display_name":"Germline mutation","level":4,"score":0.4262999892234802},{"id":"https://openalex.org/C132917006","wikidata":"https://www.wikidata.org/wiki/Q5250436","display_name":"Deep sequencing","level":4,"score":0.40799999237060547},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.3614000082015991},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.3589000105857849},{"id":"https://openalex.org/C151020129","wikidata":"https://www.wikidata.org/wiki/Q7625067","display_name":"Structural variation","level":4,"score":0.33799999952316284},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.27889999747276306},{"id":"https://openalex.org/C48720390","wikidata":"https://www.wikidata.org/wiki/Q5552250","display_name":"Germline mosaicism","level":4,"score":0.2768999934196472},{"id":"https://openalex.org/C47042493","wikidata":"https://www.wikidata.org/wiki/Q265799","display_name":"Human genetics","level":3,"score":0.25049999356269836}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.11.06.764802","doi":"https://doi.org/10.64898/2026.11.06.764802","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.06.764802","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/06/2026.11.06.764802.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.11.06.764802","doi":"https://doi.org/10.64898/2026.11.06.764802","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.06.764802","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/06/2026.11.06.764802.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.8048999905586243}],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7225466508.pdf","grobid_xml":"https://content.openalex.org/works/W7225466508.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4408409095","https://openalex.org/W7225389925","https://openalex.org/W6944363499","https://openalex.org/W4409689268","https://openalex.org/W2252413964","https://openalex.org/W2567361949","https://openalex.org/W7130360751","https://openalex.org/W4392966795","https://openalex.org/W2056286145","https://openalex.org/W7110679117"],"abstract_inverted_index":{"Somatic":[0],"structural":[1],"variants":[2,32],"(SVs)":[3],"are":[4,51,144],"among":[5],"the":[6,85,182,193,203,209],"most":[7],"clinically":[8],"relevant":[9],"genomic":[10,23,26,231],"alterations":[11,232],"in":[12,29,56,233],"cancer.":[13,234],"However,":[14],"their":[15],"accurate":[16,218],"detection":[17],"remains":[18],"challenging":[19],"due":[20],"to":[21,53,92,156],"complex":[22,61,230],"rearrangements,":[24],"repetitive":[25,57],"regions,":[27],"difficulties":[28],"distinguishing":[30],"somatic":[31,48,104,116,158,171,219],"from":[33,80,106,123],"germline":[34,93,140],"variation":[35],"and":[36,39,59,73,147,153,179,185,199,222],"sequencing":[37,41,111],"artifacts,":[38],"limited":[40],"support":[42],"for":[43,102,217,228],"low-frequency":[44],"events.":[45],"Existing":[46],"mapping-based":[47],"SV":[49,62,94,117,172,220],"callers":[50],"susceptible":[52],"alignment":[54],"ambiguities":[55],"regions":[58],"near":[60],"breakpoints,":[63],"while":[64],"approaches":[65],"relying":[66],"on":[67,84,161,181],"comparisons":[68],"of":[69,87,197,211],"independently":[70],"generated":[71],"tumor":[72,124],"normal":[74],"variant":[75],"callsets":[76],"may":[77],"propagate":[78],"errors":[79],"both":[81],"callsets.":[82],"Building":[83],"concept":[86],"specific":[88,120,212],"strings,":[89],"previously":[90],"applied":[91],"discovery,":[95],"we":[96],"introduce":[97],"VESPA-SS,":[98],"a":[99,127,138,224],"novel":[100],"approach":[101],"detecting":[103],"SVs":[105],"paired":[107],"tumor-normal":[108],"long-read":[109],"whole-genome":[110],"data.":[112],"VESPA-SS":[113,168,235],"directly":[114],"extracts":[115],"signals":[118,143],"using":[119],"strings":[121],"computed":[122],"reads":[125],"against":[126],"Draft":[128],"Composite":[129],"Germline":[130],"Reference,":[131],"without":[132],"requiring":[133],"initial":[134],"read":[135],"mapping":[136],"or":[137],"high-quality":[139],"assembly.":[141],"These":[142,206],"subsequently":[145],"clustered":[146],"refined":[148],"through":[149],"consensus":[150],"sequence":[151],"generation":[152],"alignment-based":[154],"procedures":[155],"identify":[157],"SVs.":[159],"Evaluation":[160],"real":[162],"PacBio":[163],"HiFi":[164],"datasets":[165],"demonstrates":[166],"that":[167],"outperforms":[169],"state-of-the-art":[170],"callers,":[173],"achieving":[174],"F1":[175,195],"scores":[176,196],"exceeding":[177],"0.92":[178],"0.90":[180],"well-characterized":[183],"HG008":[184],"COLO829":[186],"cancer":[187],"cell":[188],"lines,":[189],"respectively,":[190],"compared":[191],"with":[192],"highest":[194],"0.86":[198],"0.85":[200],"achieved":[201],"by":[202],"evaluated":[204],"methods.":[205],"results":[207],"demonstrate":[208],"effectiveness":[210],"string":[213],"based":[214],"signal":[215],"extraction":[216],"discovery":[221],"establish":[223],"new":[225],"computational":[226],"paradigm":[227],"identifying":[229],"is":[236],"freely":[237],"available":[238],"at":[239],"https://github.com/dcmonti/VESPA.":[240]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-11-08T00:00:00"}
