{"id":"https://openalex.org/W4392722985","doi":"https://doi.org/10.1158/2159-8290.c.6545849","title":"Data from High-Throughput Detection of Actionable Genomic Alterations in Clinical Tumor Samples by Targeted, Massively Parallel Sequencing","display_name":"Data from High-Throughput Detection of Actionable Genomic Alterations in Clinical Tumor Samples by Targeted, Massively Parallel Sequencing","publication_year":2023,"publication_date":"2023-04-03","ids":{"openalex":"https://openalex.org/W4392722985","doi":"https://doi.org/10.1158/2159-8290.c.6545849"},"language":"en","primary_location":{"id":"doi:10.1158/2159-8290.c.6545849","doi":"https://doi.org/10.1158/2159-8290.c.6545849","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1158/2159-8290.c.6545849","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"American Association for Cancer Research","raw_type":"posted-content"},"volume":null,"type":"other","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"http://dx.doi.org/10.1158/2159-8290.c.6545849","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068721624","display_name":"Nikhil Wagle","orcid":"https://orcid.org/0000-0003-3332-9438","observed_orcids":["https://orcid.org/0000-0003-3332-9438"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Nikhil Wagle","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104110846","display_name":"Michael Fabian Berger","orcid":"https://orcid.org/0009-0009-2032-9122","observed_orcids":["https://orcid.org/0009-0009-2032-9122"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Michael F. Berger","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082084895","display_name":"Matthew J. Davis","orcid":"https://orcid.org/0000-0002-3410-7100","observed_orcids":["https://orcid.org/0000-0002-3410-7100"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Matthew J. Davis","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011058943","display_name":"Brendan S. Blumenstiel","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Brendan Blumenstiel","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082031598","display_name":"Matthew T. DeFelice","orcid":"https://orcid.org/0009-0007-2481-8842","observed_orcids":["https://orcid.org/0009-0007-2481-8842"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Matthew DeFelice","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022656315","display_name":"Panisa Pochanard","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Panisa Pochanard","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022657765","display_name":"Matthew D. Ducar","orcid":"https://orcid.org/0000-0003-4635-1300","observed_orcids":["https://orcid.org/0000-0003-4635-1300"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Matthew Ducar","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004172458","display_name":"Paul Van Hummelen","orcid":"https://orcid.org/0000-0002-4801-8600","observed_orcids":["https://orcid.org/0000-0002-4801-8600"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Paul Van Hummelen","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088965709","display_name":"Laura E. MacConaill","orcid":"https://orcid.org/0000-0002-0220-4715","observed_orcids":["https://orcid.org/0000-0002-0220-4715"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Laura E. MacConaill","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063875415","display_name":"William C. Hahn","orcid":"https://orcid.org/0000-0003-2840-9791","observed_orcids":["https://orcid.org/0000-0003-2840-9791"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"William C. Hahn","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056373767","display_name":"Matthew M. Meyerson","orcid":"https://orcid.org/0000-0002-9133-8108","observed_orcids":["https://orcid.org/0000-0002-9133-8108"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Matthew Meyerson","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061030489","display_name":"Stacey Gabriel","orcid":"https://orcid.org/0000-0001-6939-2215","observed_orcids":["https://orcid.org/0000-0001-6939-2215"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Stacey B. Gabriel","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5055048393","display_name":"Levi A. Garraway","orcid":"https://orcid.org/0000-0003-3739-0471","observed_orcids":["https://orcid.org/0000-0003-3739-0471"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Levi A. Garraway","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9980000257492065,"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"}},"topics":[{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9980000257492065,"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":0.0010000000474974513,"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/T10769","display_name":"BRCA gene mutations in cancer","score":0.00019999999494757503,"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/targeted-deep-sequencing","display_name":"targeted deep sequencing","score":0.8920000195503235},{"id":"https://openalex.org/keywords/next-generation-sequencing","display_name":"next-generation sequencing","score":0.8090000152587891},{"id":"https://openalex.org/keywords/formalin-fixed-paraffin-embedded-tissue","display_name":"formalin-fixed paraffin-embedded tissue","score":0.9290000200271606},{"id":"https://openalex.org/keywords/single-nucleotide-variants","display_name":"single nucleotide variants","score":0.7670000195503235},{"id":"https://openalex.org/keywords/small-insertions-and-deletions","display_name":"small insertions and deletions","score":0.9419999718666077},{"id":"https://openalex.org/keywords/copy-number-alterations","display_name":"copy number alterations","score":0.8930000066757202},{"id":"https://openalex.org/keywords/drug-target-identification","display_name":"drug target identification","score":0.41499999165534973},{"id":"https://openalex.org/keywords/precision-oncology","display_name":"precision oncology","score":0.718999981880188},{"id":"https://openalex.org/keywords/drug-sensitivity-and-resistance","display_name":"drug sensitivity and resistance","score":0.6159999966621399}],"concepts":[{"id":"https://openalex.org/C192800701","wikidata":"https://www.wikidata.org/wiki/Q6784807","display_name":"Massive parallel sequencing","level":4,"score":0.787484347820282},{"id":"https://openalex.org/C190475519","wikidata":"https://www.wikidata.org/wiki/Q544384","display_name":"Massively parallel","level":2,"score":0.773066520690918},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.6892978549003601},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5287135243415833},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5063780546188354},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.49285435676574707},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.32331228256225586},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.29178154468536377},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2286587357521057},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.20673152804374695},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.07714161276817322},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1158/2159-8290.c.6545849","doi":"https://doi.org/10.1158/2159-8290.c.6545849","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1158/2159-8290.c.6545849","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"American Association for Cancer Research","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.1158/2159-8290.c.6545849","doi":"https://doi.org/10.1158/2159-8290.c.6545849","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1158/2159-8290.c.6545849","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"American Association for Cancer Research","raw_type":"posted-content"},"sustainable_development_goals":[{"score":0.979200005531311,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2130940380","https://openalex.org/W2591104734","https://openalex.org/W7100567998","https://openalex.org/W2080960707","https://openalex.org/W2321356509","https://openalex.org/W2120856515","https://openalex.org/W2328735098","https://openalex.org/W2939064943","https://openalex.org/W2566220083","https://openalex.org/W2101248947"],"abstract_inverted_index":{"Abstract":[0],"Knowledge":[1],"of":[2,33,44,128,147,183,197],"\u201cactionable\u201d":[3],"somatic":[4],"genomic":[5,35,63,103,158,169],"alterations":[6,18,64,87,159,170],"present":[7],"in":[8,65,98,119,171,186,222],"each":[9,120],"tumor":[10,62,69,121,130,157,173],"(e.g.,":[11],"point":[12,46],"mutations,":[13],"small":[14,82],"insertions/deletions,":[15,83],"and":[16,78,84,114,180,190,214],"copy-number":[17],"that":[19,107],"direct":[20],"therapeutic":[21,149],"options)":[22],"should":[23],"facilitate":[24],"individualized":[25],"approaches":[26],"to":[27,60,112,153,167],"cancer":[28,140,198],"treatment.":[29,141],"However,":[30],"clinical":[31,99,129,135,181],"implementation":[32],"systematic":[34,151],"profiling":[36],"has":[37],"rarely":[38],"been":[39],"achieved":[40],"beyond":[41],"limited":[42],"numbers":[43],"oncogene":[45],"mutations.":[47],"To":[48],"address":[49],"this":[50,210],"challenge,":[51],"we":[52],"utilized":[53],"a":[54,164,192],"targeted,":[55],"massively":[56],"parallel":[57],"sequencing":[58,127,185],"approach":[59,166],"detect":[61],"formalin-fixed,":[66],"paraffin-embedded":[67],"(FFPE)":[68],"samples.":[70,174],"Nearly":[71],"400-fold":[72],"mean":[73],"sequence":[74,80],"coverage":[75],"was":[76],"achieved,":[77],"single-nucleotide":[79],"variants,":[81],"chromosomal":[85],"copynumber":[86],"were":[88,117],"detected":[89,118],"simultaneously":[90],"with":[91,95],"high":[92],"accuracy":[93],"compared":[94],"other":[96],"methods":[97,152],"use.":[100],"Putatively":[101],"actionable":[102],"alterations,":[104],"including":[105],"those":[106],"predict":[108],"sensitivity":[109],"or":[110],"resistance":[111],"established":[113],"experimental":[115],"therapies,":[116],"sample":[122],"tested.":[123],"Thus,":[124],"targeted":[125,148,184],"deep":[126],"material":[131],"may":[132],"enable":[133],"mutation-driven":[134],"trials":[136],"and,":[137],"ultimately,":[138],"\u201cpersonalized\u201d":[139],"Significance:":[142],"Despite":[143],"the":[144,178,187,207,223],"rapid":[145],"proliferation":[146],"agents,":[150],"profile":[154],"clinically":[155],"relevant":[156],"remain":[160],"underdeveloped.":[161],"We":[162],"describe":[163],"sequencing-based":[165],"identifying":[168],"FFPE":[172],"These":[175],"studies":[176],"affirm":[177],"feasibility":[179],"utility":[182],"oncology":[188],"arena":[189],"provide":[191],"foundation":[193],"for":[194],"genomics-based":[195],"stratification":[196],"patients.":[199],"Cancer":[200],"Discovery;":[201],"2(1);":[202],"82\u201393.":[203],"\u00a92011":[204],"AACR.":[205],"Read":[206],"Commentary":[208],"on":[209],"article":[211,219],"by":[212],"Corless":[213],"Spellman,":[215],"p.":[216,228],"23":[217],"This":[218,225],"is":[220],"highlighted":[221],"In":[224],"Issue":[226],"feature,":[227],"1":[229]},"counts_by_year":[],"updated_date":"2026-10-17T09:40:24.721904","created_date":"2024-03-13T00:00:00"}