{"id":"https://openalex.org/W3135574759","doi":"https://doi.org/10.1200/jco.2021.39.6_suppl.464","title":"Single-cell DNA targeted sequencing (scDNA-seq) to test therapeutic vulnerabilities in urothelial cancer (UC) patient-derived organoids (PDO).","display_name":"Single-cell DNA targeted sequencing (scDNA-seq) to test therapeutic vulnerabilities in urothelial cancer (UC) patient-derived organoids (PDO).","publication_year":2021,"publication_date":"2021-02-20","ids":{"openalex":"https://openalex.org/W3135574759","doi":"https://doi.org/10.1200/jco.2021.39.6_suppl.464","mag":"3135574759"},"language":"en","primary_location":{"id":"doi:10.1200/jco.2021.39.6_suppl.464","doi":"https://doi.org/10.1200/jco.2021.39.6_suppl.464","is_oa":false,"landing_page_url":"https://doi.org/10.1200/jco.2021.39.6_suppl.464","pdf_url":null,"source":{"id":"https://openalex.org/S15137598","display_name":"Journal of Clinical Oncology","issn_l":"0732-183X","issn":["0732-183X","1527-7755"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315671","host_organization_name":"Lippincott Williams & Wilkins","host_organization_lineage":["https://openalex.org/P4310315671","https://openalex.org/P4310318547"],"host_organization_lineage_names":["Lippincott Williams & Wilkins","Wolters Kluwer"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Clinical Oncology","raw_type":"journal-article"},"volume":null,"type":"conference-abstract","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011483509","display_name":"Kyrillus Samaan Shohdy","orcid":"https://orcid.org/0000-0001-8627-3605","observed_orcids":["https://orcid.org/0000-0001-8627-3605"]},"institutions":[{"id":"https://openalex.org/I4387153466","display_name":"Weill Cornell Medicine","ror":"https://ror.org/02r109517","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295","https://openalex.org/I4387153466"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kyrillus Shohdy","raw_affiliation_strings":["Weill Cornell Medicine, New York, NY;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Weill Cornell Medicine, New York, NY;","institution_ids":["https://openalex.org/I4387153466"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074670112","display_name":"Weisi Liu","orcid":"https://orcid.org/0000-0002-4730-5448","observed_orcids":["https://orcid.org/0000-0002-4730-5448"]},"institutions":[{"id":"https://openalex.org/I4387153466","display_name":"Weill Cornell Medicine","ror":"https://ror.org/02r109517","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295","https://openalex.org/I4387153466"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Weisi Liu","raw_affiliation_strings":["Weill Cornell Medicine, New York, NY;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Weill Cornell Medicine, New York, NY;","institution_ids":["https://openalex.org/I4387153466"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Alicia Alonso","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4387153466","display_name":"Weill Cornell Medicine","ror":"https://ror.org/02r109517","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295","https://openalex.org/I4387153466"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alicia Alonso","raw_affiliation_strings":["Weill Cornell Medicine, New York, NY;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Weill Cornell Medicine, New York, NY;","institution_ids":["https://openalex.org/I4387153466"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036954977","display_name":"Jenny Xiang","orcid":"https://orcid.org/0000-0003-0484-2769","observed_orcids":["https://orcid.org/0000-0003-0484-2769"]},"institutions":[{"id":"https://openalex.org/I4387153466","display_name":"Weill Cornell Medicine","ror":"https://ror.org/02r109517","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295","https://openalex.org/I4387153466"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jenny Xiang","raw_affiliation_strings":["Weill Cornell Medicine, New York, NY;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Weill Cornell Medicine, New York, NY;","institution_ids":["https://openalex.org/I4387153466"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036851932","display_name":"M. Laura Mart\u00edn","orcid":"https://orcid.org/0000-0001-9359-5856","observed_orcids":["https://orcid.org/0000-0001-9359-5856"]},"institutions":[{"id":"https://openalex.org/I4387153466","display_name":"Weill Cornell Medicine","ror":"https://ror.org/02r109517","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295","https://openalex.org/I4387153466"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M. Laura Martin","raw_affiliation_strings":["Weill Cornell Medicine, New York, NY;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Weill Cornell Medicine, New York, NY;","institution_ids":["https://openalex.org/I4387153466"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061702711","display_name":"Olivier Elemento","orcid":"https://orcid.org/0000-0002-8061-9617","observed_orcids":["https://orcid.org/0000-0002-8061-9617"]},"institutions":[{"id":"https://openalex.org/I4387153466","display_name":"Weill Cornell Medicine","ror":"https://ror.org/02r109517","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295","https://openalex.org/I4387153466"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Olivier Elemento","raw_affiliation_strings":["Weill Cornell Medicine, New York, NY;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Weill Cornell Medicine, New York, NY;","institution_ids":["https://openalex.org/I4387153466"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040904315","display_name":"Bishoy M. Faltas","orcid":"https://orcid.org/0000-0002-6432-1693","observed_orcids":["https://orcid.org/0000-0002-6432-1693"]},"institutions":[{"id":"https://openalex.org/I4387153466","display_name":"Weill Cornell Medicine","ror":"https://ror.org/02r109517","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295","https://openalex.org/I4387153466"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bishoy Morris Faltas","raw_affiliation_strings":["Weill Cornell Medicine, New York, NY;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Weill Cornell Medicine, New York, NY;","institution_ids":["https://openalex.org/I4387153466"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I4387153466"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"39","issue":"6_suppl","first_page":"464","last_page":"464"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10458","display_name":"Bladder and Urothelial Cancer Treatments","score":0.7554000020027161,"subfield":{"id":"https://openalex.org/subfields/2746","display_name":"Surgery"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10458","display_name":"Bladder and Urothelial Cancer Treatments","score":0.7554000020027161,"subfield":{"id":"https://openalex.org/subfields/2746","display_name":"Surgery"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.22509999573230743,"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/T10417","display_name":"Lung Cancer Treatments and Mutations","score":0.004000000189989805,"subfield":{"id":"https://openalex.org/subfields/2740","display_name":"Pulmonary and Respiratory Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/urothelial-carcinoma","display_name":"urothelial carcinoma","score":0.9800000190734863},{"id":"https://openalex.org/keywords/bladder-cancer","display_name":"bladder cancer","score":0.7919999957084656},{"id":"https://openalex.org/keywords/patient-derived-organoids","display_name":"patient-derived organoids","score":0.9940000176429749},{"id":"https://openalex.org/keywords/single-cell-dna-sequencing","display_name":"single-cell DNA sequencing","score":0.7720000147819519},{"id":"https://openalex.org/keywords/therapeutic-vulnerabilities","display_name":"therapeutic vulnerabilities","score":0.5049999952316284},{"id":"https://openalex.org/keywords/fgfr3-mutation","display_name":"FGFR3 mutation","score":0.8059999942779541},{"id":"https://openalex.org/keywords/pik3ca-mutation","display_name":"PIK3CA mutation","score":0.9039999842643738},{"id":"https://openalex.org/keywords/cdkn2a-deletion","display_name":"CDKN2A deletion","score":0.9929999709129333},{"id":"https://openalex.org/keywords/alpelisib","display_name":"alpelisib","score":0.9390000104904175},{"id":"https://openalex.org/keywords/abemaciclib","display_name":"abemaciclib","score":0.9959999918937683},{"id":"https://openalex.org/keywords/erdafitinib","display_name":"erdafitinib","score":0.9940000176429749},{"id":"https://openalex.org/keywords/clonal-expansion","display_name":"clonal expansion","score":0.6769999861717224},{"id":"https://openalex.org/keywords/variant-allele-frequency","display_name":"variant allele frequency","score":0.8489999771118164},{"id":"https://openalex.org/keywords/combination-therapy","display_name":"combination therapy","score":0.5669999718666077},{"id":"https://openalex.org/keywords/rab31","display_name":"RAB31","score":0.625},{"id":"https://openalex.org/keywords/smad4","display_name":"SMAD4","score":0.9890000224113464},{"id":"https://openalex.org/keywords/rb1","display_name":"RB1","score":0.7059999704360962}],"concepts":[{"id":"https://openalex.org/C2780265364","wikidata":"https://www.wikidata.org/wiki/Q5009957","display_name":"CDKN2A","level":3,"score":0.8724247217178345},{"id":"https://openalex.org/C502942594","wikidata":"https://www.wikidata.org/wiki/Q3421914","display_name":"Cancer research","level":1,"score":0.6193352341651917},{"id":"https://openalex.org/C31695470","wikidata":"https://www.wikidata.org/wiki/Q11293125","display_name":"Organoid","level":2,"score":0.5663108825683594},{"id":"https://openalex.org/C3020745361","wikidata":"https://www.wikidata.org/wiki/Q2501186","display_name":"Urothelial cancer","level":4,"score":0.5200321674346924},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.5111539959907532},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.489139586687088},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.4733681380748749},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.43313106894493103},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4232298731803894},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.41457152366638184},{"id":"https://openalex.org/C153911025","wikidata":"https://www.wikidata.org/wiki/Q7202","display_name":"Molecular biology","level":1,"score":0.3892871141433716},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.29418885707855225},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.26948797702789307},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2385973334312439},{"id":"https://openalex.org/C2780352672","wikidata":"https://www.wikidata.org/wiki/Q504775","display_name":"Bladder cancer","level":3,"score":0.19086214900016785}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1200/jco.2021.39.6_suppl.464","doi":"https://doi.org/10.1200/jco.2021.39.6_suppl.464","is_oa":false,"landing_page_url":"https://doi.org/10.1200/jco.2021.39.6_suppl.464","pdf_url":null,"source":{"id":"https://openalex.org/S15137598","display_name":"Journal of Clinical Oncology","issn_l":"0732-183X","issn":["0732-183X","1527-7755"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310315671","host_organization_name":"Lippincott Williams & Wilkins","host_organization_lineage":["https://openalex.org/P4310315671","https://openalex.org/P4310318547"],"host_organization_lineage_names":["Lippincott Williams & Wilkins","Wolters Kluwer"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Clinical Oncology","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":1.0,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306239","display_name":"Conquer Cancer Foundation","ror":"https://ror.org/027327e78"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4379281611","https://openalex.org/W4226250964","https://openalex.org/W3007592474","https://openalex.org/W4404282294","https://openalex.org/W4397013178","https://openalex.org/W2489345005","https://openalex.org/W7131800869","https://openalex.org/W4400108731","https://openalex.org/W4379283390","https://openalex.org/W2049306725"],"abstract_inverted_index":{"464":[0],"Background:":[1],"Genomic":[2],"alterations":[3],"in":[4,13,33,82,99,160,192,285,331,364,377],"FGFR3,":[5],"PIK3CA,":[6],"and":[7,28,61,77,105,197,211,232,337,373],"CDKN2A":[8,62],"are":[9],"common":[10],"actionable":[11],"targets":[12],"urothelial":[14],"cancer":[15,35],"(UC).":[16],"We":[17,44,70,189,216,223,264],"aimed":[18],"to":[19,85,96,116,182,244,281,358],"determine":[20,86],"the":[21,52,56,87,100,250,271,291,294,311,341,349,360],"efficacy":[22,333],"of":[23,74,139,162,268,306,334,343,351,371],"alpelisib,":[24,75],"a":[25,30,46,303,355],"PIK3CA":[26,57,272,374,381],"inhibitor,":[27],"abemaciclib,":[29,76],"CDK4/6":[31,372],"inhibitor":[32],"bladder":[34],"patient-derived":[36,47,365],"organoid":[37,49],"using":[38,67,352],"single-cell":[39],"targeted":[40],"DNA":[41],"sequencing.":[42,69],"Methods:":[43],"established":[45,348],"UC":[48,366],"(PDO)":[50],"harboring":[51,172,227,236],"FGFR3":[53,80,173,206,295],"mutation":[54,273],"(p.Y375C),":[55],"(p.":[58],"E452K)":[59],"mutation,":[60],"deletion,":[63],"which":[64,277],"we":[65,164,248,289],"characterized":[66],"whole-genome":[68],"generated":[71],"dose-response":[72],"curves":[73],"erdafitinib":[78,134,149,179],"(an":[79],"inhibitor)":[81],"PDO":[83,130,218],"cells":[84,131,142,146,152,171,184,219,237,251,269,308],"IC50":[88],"concentrations.":[89],"The":[90,109,234],"scDNA-seq":[91,125,353],"(Tapsteri)":[92],"platform":[93],"was":[94,114,126,302],"used":[95,115],"measure":[97],"changes":[98,284],"variant":[101],"allele":[102],"frequencies":[103],"(VAF)":[104],"clonal":[106,167,203,361],"fractions":[107],"post-treatment.":[108,287],"Chi-square":[110],"test":[111,117,328],"for":[112,118,255],"trend":[113,120,299,327],"linear":[119],"across":[121,310],"ordered":[122],"categories.":[123],"Results:":[124],"performed":[127],"after":[128,241],"treating":[129],"with":[132,148,154,202,220,252,261,340],"3uM":[133,221],"or":[135,259],"DMSO.":[136],"A":[137],"total":[138],"7000":[140],"single":[141],"were":[143,200,238],"obtained":[144],"(4179":[145],"treated":[147,153,217,249],"vs.":[150,186,209,213,317,320,323,325],"2821":[151],"DMSO).":[155],"After":[156],"removing":[157],"variants":[158],"mutated":[159],"<50%":[161],"cells,":[163],"identified":[165,190,224,265],"94":[166],"variants.":[168],"As":[169],"expected,":[170],"Y375C":[174,296],"have":[175],"significantly":[176,239],"decreased":[177,240],"post":[178],"treatment":[180],"compared":[181,243],"DMSO-treated":[183],"(66.05%":[185],"82.36%,":[187],"p<0.0001).":[188],"mutations":[191],"two":[193],"genes":[194,226],"(":[195,229],"RAB31":[196],"SMAD4)":[198],"that":[199,266],"associated":[201],"expansion":[204],"following":[205],"inhibition":[207,370,382],"(12%":[208],"53%":[210],"13%":[212],"26%,":[214],"respectively).":[215],"abemaciclib.":[222,344],"three":[225,312],"SNVs":[228,235],"RB1,":[230],"GNAQ,":[231],"SMAD4).":[233],"abemaciclib":[242,262,314],"DMSO":[245,321],"(p<0.0001).":[246],"Then,":[247],"1uM":[253],"alpelisib":[254,316,318,335],"72":[256],"hours":[257],"alone":[258,319,336],"combined":[260],"(0.1uM).":[263],"100%":[267],"harbored":[270],"E452K":[274],"at":[275],"pre-treatment,":[276],"limited":[278],"our":[279],"ability":[280],"detect":[282],"significant":[283,304,338],"VAF":[286],"Instead,":[288],"analyzed":[290],"effect":[292],"on":[293],"clone.":[297],"Using":[298],"analysis,":[300],"there":[301],"reduction":[305],"FGFR3-mutant":[307],"observed":[309],"conditions,":[313],"+":[315],"(74%":[322],"85%":[324],"92%,":[326],"p<0.0001),":[329],"suggesting":[330],"vitro":[332,378],"synergism":[339],"addition":[342],"Conclusions:":[345],"This":[346],"study":[347,359],"feasibility":[350],"as":[354],"promising":[356],"tool":[357],"evolution":[362],"patterns":[363],"organoids.":[367],"Combined":[368],"pharmacologic":[369],"showed":[375],"more":[376],"sensitivity":[379],"than":[380],"alone.":[383]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2026-10-14T16:39:01.820549","created_date":"2021-03-15T00:00:00"}
