{"id":"https://openalex.org/W7225455097","doi":"https://doi.org/10.64898/2026.11.06.26367303","title":"Benchmarking Structural Variant Detection in Whole-Exome Sequencing of 67 Multiple Myeloma Cell Lines","display_name":"Benchmarking Structural Variant Detection in Whole-Exome Sequencing of 67 Multiple Myeloma Cell Lines","publication_year":2026,"publication_date":"2026-11-06","ids":{"openalex":"https://openalex.org/W7225455097","doi":"https://doi.org/10.64898/2026.11.06.26367303"},"language":"en","primary_location":{"id":"doi:10.64898/2026.11.06.26367303","doi":"https://doi.org/10.64898/2026.11.06.26367303","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.06.26367303","pdf_url":"https://www.medrxiv.org/content/medrxiv/early/2026/11/06/2026.11.06.26367303.full.pdf","source":{"id":"https://openalex.org/S3005729997","display_name":"medRxiv","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core"],"host_organization":null,"host_organization_name":null,"host_organization_lineage":["https://openalex.org/P4310315909"],"host_organization_lineage_names":["Cold Spring Harbor Laboratory Press"],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"medRxiv","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.medrxiv.org/content/medrxiv/early/2026/11/06/2026.11.06.26367303.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5115819778","display_name":"Lokesha S. Pugalenthi","orcid":"https://orcid.org/0009-0001-0966-7157","observed_orcids":["https://orcid.org/0009-0001-0966-7157"]},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lokesh Srinivas Pugalenthi","raw_affiliation_strings":["College of Natural Sciences, University of Texas at Austin;"],"raw_orcid":"https://orcid.org/0009-0001-0966-7157","affiliations":[{"raw_affiliation_string":"College of Natural Sciences, University of Texas at Austin;","institution_ids":["https://openalex.org/I86519309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015374900","display_name":"Rahul Nanduri","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rahul Nanduri","raw_affiliation_strings":["College of Natural Sciences, University of Texas at Austin;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Natural Sciences, University of Texas at Austin;","institution_ids":["https://openalex.org/I86519309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5159781081","display_name":"Raymond Hong","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Raymond Hong","raw_affiliation_strings":["College of Natural Sciences, University of Texas at Austin;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Natural Sciences, University of Texas at Austin;","institution_ids":["https://openalex.org/I86519309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5093817851","display_name":"Maya Ylagan","orcid":"https://orcid.org/0009-0003-8995-2496","observed_orcids":["https://orcid.org/0009-0003-8995-2496"]},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Maya Ylagan","raw_affiliation_strings":["Department of Oncology, Dell Medical School, University of Texas at Austin,;"],"raw_orcid":"https://orcid.org/0009-0003-8995-2496","affiliations":[{"raw_affiliation_string":"Department of Oncology, Dell Medical School, University of Texas at Austin,;","institution_ids":["https://openalex.org/I86519309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5161254906","display_name":"Rohit Prasad","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rohit Prasad","raw_affiliation_strings":["College of Natural Sciences, University of Texas at Austin;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Natural Sciences, University of Texas at Austin;","institution_ids":["https://openalex.org/I86519309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045102506","display_name":"Dhivya Arasappan","orcid":"https://orcid.org/0009-0009-0488-6551","observed_orcids":["https://orcid.org/0009-0009-0488-6551"]},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dhivya Arasappan","raw_affiliation_strings":["Center for Biomedical Research Support, University of Texas at Austin;"],"raw_orcid":"https://orcid.org/0009-0009-0488-6551","affiliations":[{"raw_affiliation_string":"Center for Biomedical Research Support, University of Texas at Austin;","institution_ids":["https://openalex.org/I86519309"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019366387","display_name":"Jeanne Kowalski","orcid":"https://orcid.org/0000-0003-3458-3024","observed_orcids":["https://orcid.org/0000-0003-3458-3024"]},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jeanne Kowalski-Muegge","raw_affiliation_strings":["Department of Oncology, Dell Medical School, University of Texas at Austin"],"raw_orcid":"https://orcid.org/0000-0003-3458-3024","affiliations":[{"raw_affiliation_string":"Department of Oncology, Dell Medical School, University of Texas at Austin","institution_ids":["https://openalex.org/I86519309"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5019366387"],"corresponding_institution_ids":["https://openalex.org/I86519309"],"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":0.8695999979972839,"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":0.8695999979972839,"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":0.08009999990463257,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.02239999920129776,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/structural-variant-calling","display_name":"structural variant calling","score":0.9580000042915344},{"id":"https://openalex.org/keywords/whole-exome-sequencing","display_name":"exome sequencing","score":0.8230000138282776},{"id":"https://openalex.org/keywords/multiple-myeloma-cell-lines","display_name":"multiple myeloma cell lines","score":0.925000011920929},{"id":"https://openalex.org/keywords/chromosomal-abnormalities","display_name":"chromosomal abnormalities","score":0.6480000019073486},{"id":"https://openalex.org/keywords/manta","display_name":"Manta","score":0.9810000061988831},{"id":"https://openalex.org/keywords/delly","display_name":"Delly","score":0.6420000195503235},{"id":"https://openalex.org/keywords/pindel","display_name":"Pindel","score":0.8510000109672546},{"id":"https://openalex.org/keywords/cancer-genomics","display_name":"cancer genomics","score":0.5080000162124634}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6044999957084656},{"id":"https://openalex.org/C16671776","wikidata":"https://www.wikidata.org/wiki/Q5420592","display_name":"Exome sequencing","level":4,"score":0.5952000021934509},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5909000039100647},{"id":"https://openalex.org/C10590036","wikidata":"https://www.wikidata.org/wiki/Q417664","display_name":"Exome","level":5,"score":0.5764999985694885},{"id":"https://openalex.org/C2776364478","wikidata":"https://www.wikidata.org/wiki/Q467635","display_name":"Multiple myeloma","level":2,"score":0.508899986743927},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.43849998712539673},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4235999882221222},{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.4221000075340271},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.40130001306533813},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.400299996137619},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.38850000500679016},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.36059999465942383},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.35989999771118164},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.3546999990940094},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3440999984741211},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.33730000257492065},{"id":"https://openalex.org/C205270622","wikidata":"https://www.wikidata.org/wiki/Q17082639","display_name":"Cancer genome sequencing","level":5,"score":0.336899995803833},{"id":"https://openalex.org/C2993561819","wikidata":"https://www.wikidata.org/wiki/Q5097977","display_name":"Pediatric cancer","level":3,"score":0.2996000051498413},{"id":"https://openalex.org/C64618202","wikidata":"https://www.wikidata.org/wiki/Q3733697","display_name":"Genetic heterogeneity","level":4,"score":0.2971000075340271},{"id":"https://openalex.org/C2994372470","wikidata":"https://www.wikidata.org/wiki/Q4118072","display_name":"Cancer cell lines","level":4,"score":0.2782000005245209},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.26930001378059387},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.25200000405311584},{"id":"https://openalex.org/C151020129","wikidata":"https://www.wikidata.org/wiki/Q7625067","display_name":"Structural variation","level":4,"score":0.2515999972820282},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.25099998712539673}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.11.06.26367303","doi":"https://doi.org/10.64898/2026.11.06.26367303","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.06.26367303","pdf_url":"https://www.medrxiv.org/content/medrxiv/early/2026/11/06/2026.11.06.26367303.full.pdf","source":{"id":"https://openalex.org/S3005729997","display_name":"medRxiv","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core"],"host_organization":null,"host_organization_name":null,"host_organization_lineage":["https://openalex.org/P4310315909"],"host_organization_lineage_names":["Cold Spring Harbor Laboratory Press"],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"medRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.11.06.26367303","doi":"https://doi.org/10.64898/2026.11.06.26367303","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.06.26367303","pdf_url":"https://www.medrxiv.org/content/medrxiv/early/2026/11/06/2026.11.06.26367303.full.pdf","source":{"id":"https://openalex.org/S3005729997","display_name":"medRxiv","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core"],"host_organization":null,"host_organization_name":null,"host_organization_lineage":["https://openalex.org/P4310315909"],"host_organization_lineage_names":["Cold Spring Harbor Laboratory Press"],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"medRxiv","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":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7225455097.pdf","grobid_xml":"https://content.openalex.org/works/W7225455097.grobid-xml"},"referenced_works_count":1,"referenced_works":["https://openalex.org/W4394666350"],"related_works":["https://openalex.org/W3139338482","https://openalex.org/W3135072270","https://openalex.org/W3092805463","https://openalex.org/W2906753728","https://openalex.org/W3208597274","https://openalex.org/W1985532455","https://openalex.org/W3185087055","https://openalex.org/W2127999963","https://openalex.org/W2997199169","https://openalex.org/W4411187682"],"abstract_inverted_index":{"Background.":[0],"Although":[1],"the":[2,51,101,178,191,199,228,242,252,262,278,288,306,325,410,419],"majority":[3],"of":[4,53,113,142,184,236,254,265,282,301,316,318,335,353,402,421],"structural":[5],"variant":[6],"(SV)":[7],"workflows":[8,416],"have":[9,34,97],"been":[10,47],"derived":[11,138],"based":[12],"on":[13,349,366],"whole":[14,25],"genome":[15],"sequencing":[16,91,102,395],"(WGS)":[17],"data,":[18],"they":[19],"continue":[20,397],"to":[21,24,63,67,90,120,166,173,211,219,232,384,398,417],"be":[22,106,370],"applied":[23,62],"exome":[26],"sequence":[27,85],"(WES)":[28],"data":[29,86,93,103,122,137,368],"for":[30,78,130,163,413],"which":[31],"many":[32,392],"studies":[33],"evaluated":[35,150,341],"their":[36,164,385,400],"performance":[37],"in":[38,123,177,204,209,251,378,388],"cancer.":[39],"An":[40],"equally":[41],"important":[42],"consideration":[43],"that":[44,104,213,391],"has":[45],"not":[46,70],"well":[48],"studied":[49],"is":[50],"impact":[52],"cancer":[54,82,95,128,414],"context":[55],"specific":[56],"features":[57,99],"among":[58,116,187],"WGS-derived":[59,117,152],"SV":[60,72,114,118,153,230,237,342,364],"callers":[61,73,119,365],"WES":[64,121,136,367],"data.":[65],"Similar":[66],"personalized":[68],"medicine,":[69],"all":[71,81,340],"are":[74],"alike":[75],"and":[76,84,161,172,182,195,224,272,274,294,299],"optimal":[77],"use":[79,387],"with":[80,257,280,305,404],"types":[83,96],"types.":[87],"In":[88],"addition":[89],"related":[92],"features,":[94],"embedded":[98],"withing":[100],"should":[105,369],"considered.":[107],"Herein,":[108],"we":[109,149],"performed":[110],"an":[111],"analysis":[112],"heterogeneity":[115],"multiple":[124],"myeloma":[125],"(MM),":[126],"a":[127,140,234],"known":[129,169,302,336],"its":[131],"genetically":[132],"heterogeneous":[133],"nature.":[134],"Using":[135],"from":[139],"panel":[141],"67":[143],"Multiple":[144],"Myeloma":[145],"(MM)":[146],"cell":[147,355],"lines,":[148,356],"seven":[151,192],"detection":[154,343],"tools":[155,212,249,308,344],"(Delly,":[156],"SvABA,":[157],"BreakDancer,":[158],"Smoove,":[159],"LUMPY":[160],"Manta)":[162],"ability":[165],"identify":[167,233],"cytogenetically":[168],"genetic":[170],"abnormalities":[171],"characterize":[174],"overall":[175],"differences":[176],"number,":[179],"length,":[180],"type,":[181],"runtime":[183],"SVs":[185,255,281,360],"called":[186],"them.":[188],"Results.":[189],"Among":[190],"tools,":[193],"Smoove":[194,226],"Manta":[196],"both":[197],"had":[198],"shortest":[200,263],"runtime,":[201],"processing":[202],"files":[203],"less":[205,266,283,317,319],"than":[206,216,267,284,320,333],"2":[207],"minutes,":[208],"contrast":[210],"required":[214],"more":[215,332],"two":[217],"hours":[218],"run":[220],"such":[221,422],"as":[222],"SvABA":[223,240],"Pindel.":[225],"was":[227,241],"only":[229,246],"caller":[231],"range":[235],"types,":[238],"while":[239],"most":[243],"restrictive,":[244],"calling":[245,420],"breakends.":[247],"All":[248],"differed":[250],"length":[253,264],"called,":[256],"SvABA's":[258,291,310],"unfiltered":[259,292],"output":[260,276,293,296,381],"including":[261,277],"10":[268],"base":[269],"pairs":[270],"(bps),":[271],"Delly":[273],"BreakDancer's":[275],"longest,":[279],"1,000":[285],"bps.":[286],"At":[287],"chromosome":[289],"level,":[290,328],"Delly's":[295],"included":[297],"78%":[298],"27.5%":[300],"SVs,":[303],"respectively,":[304],"remaining":[307],"(including":[309],"filtered":[311],"output)":[312],"achieved":[313,345],"recall":[314,347],"rates":[315,348],"10%.":[321],"By":[322],"comparison,":[323],"at":[324],"genomics":[326],"coordinate":[327],"no":[329],"tool":[330],"identified":[331],"20%":[334],"SVs.":[337],"Conclusions.":[338],"As":[339],"poor":[346],"this":[350,357],"comprehensive":[351],"catalog":[352],"MM":[354],"study":[358],"implies":[359],"detected":[361],"by":[362],"WGS-based":[363],"confirmed":[371],"experimentally":[372],"before":[373],"being":[374],"declared":[375],"legitimate.":[376],"Heterogeneity":[377],"these":[379],"tools'":[380],"lends":[382],"support":[383],"combined":[386],"practice.":[389],"Considering":[390],"clinical":[393],"grade":[394],"panels":[396],"expand":[399],"repertoire":[401],"rearrangements":[403],"therapeutic":[405],"implications,":[406],"our":[407],"results":[408],"prompt":[409],"potential":[411],"need":[412],"type-matched":[415],"evaluate":[418],"rearrangements.":[423]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-11-08T00:00:00"}