{"id":"https://openalex.org/W2748488591","doi":"https://doi.org/10.1145/3107411.3108203","title":"Pisces","display_name":"Pisces","publication_year":2017,"publication_date":"2017-08-20","ids":{"openalex":"https://openalex.org/W2748488591","doi":"https://doi.org/10.1145/3107411.3108203","mag":"2748488591"},"language":"en","primary_location":{"id":"doi:10.1145/3107411.3108203","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3107411.3108203","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics","raw_type":"proceedings-article"},"type":"article","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/A5055703028","display_name":"Tamsen Dunn","orcid":null},"institutions":[{"id":"https://openalex.org/I178645029","display_name":"Illumina (United States)","ror":"https://ror.org/05k34t975","country_code":"US","type":"company","lineage":["https://openalex.org/I178645029"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Tamsen Dunn","raw_affiliation_strings":["Illumina Inc., San Diego, CA, USA"],"affiliations":[{"raw_affiliation_string":"Illumina Inc., San Diego, CA, USA","institution_ids":["https://openalex.org/I178645029"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054066976","display_name":"Gwenn Berry","orcid":null},"institutions":[{"id":"https://openalex.org/I178645029","display_name":"Illumina (United States)","ror":"https://ror.org/05k34t975","country_code":"US","type":"company","lineage":["https://openalex.org/I178645029"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gwenn Berry","raw_affiliation_strings":["Illumina Inc., San Diego, CA, USA"],"affiliations":[{"raw_affiliation_string":"Illumina Inc., San Diego, CA, USA","institution_ids":["https://openalex.org/I178645029"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024241528","display_name":"Dorothea Emig-Agius","orcid":null},"institutions":[{"id":"https://openalex.org/I178645029","display_name":"Illumina (United States)","ror":"https://ror.org/05k34t975","country_code":"US","type":"company","lineage":["https://openalex.org/I178645029"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dorothea Emig-Agius","raw_affiliation_strings":["Illumina Inc., San Diego, CA, USA"],"affiliations":[{"raw_affiliation_string":"Illumina Inc., San Diego, CA, USA","institution_ids":["https://openalex.org/I178645029"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039921045","display_name":"Yu Jiang","orcid":"https://orcid.org/0000-0003-4821-3585"},"institutions":[{"id":"https://openalex.org/I178645029","display_name":"Illumina (United States)","ror":"https://ror.org/05k34t975","country_code":"US","type":"company","lineage":["https://openalex.org/I178645029"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yu Jiang","raw_affiliation_strings":["Illumina Inc., San Diego, CA, USA"],"affiliations":[{"raw_affiliation_string":"Illumina Inc., San Diego, CA, USA","institution_ids":["https://openalex.org/I178645029"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048475791","display_name":"Anita K. Iyer","orcid":null},"institutions":[{"id":"https://openalex.org/I178645029","display_name":"Illumina (United States)","ror":"https://ror.org/05k34t975","country_code":"US","type":"company","lineage":["https://openalex.org/I178645029"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anita Iyer","raw_affiliation_strings":["Illumina Inc., San Diego, CA, USA"],"affiliations":[{"raw_affiliation_string":"Illumina Inc., San Diego, CA, USA","institution_ids":["https://openalex.org/I178645029"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011864225","display_name":"Nitin Udar","orcid":"https://orcid.org/0000-0001-8533-9190"},"institutions":[{"id":"https://openalex.org/I178645029","display_name":"Illumina (United States)","ror":"https://ror.org/05k34t975","country_code":"US","type":"company","lineage":["https://openalex.org/I178645029"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nitin Udar","raw_affiliation_strings":["Illumina Inc., San Diego, CA, USA"],"affiliations":[{"raw_affiliation_string":"Illumina Inc., San Diego, CA, USA","institution_ids":["https://openalex.org/I178645029"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065499836","display_name":"Michael P. Str\u00f6mberg","orcid":null},"institutions":[{"id":"https://openalex.org/I178645029","display_name":"Illumina (United States)","ror":"https://ror.org/05k34t975","country_code":"US","type":"company","lineage":["https://openalex.org/I178645029"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Str\u00f6mberg","raw_affiliation_strings":["Illumina Inc., San Diego, CA, USA"],"affiliations":[{"raw_affiliation_string":"Illumina Inc., San Diego, CA, USA","institution_ids":["https://openalex.org/I178645029"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5055703028"],"corresponding_institution_ids":["https://openalex.org/I178645029"],"apc_list":null,"apc_paid":null,"fwci":0.172,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.49454052,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"595","last_page":"595"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.8323000073432922,"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":0.8323000073432922,"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":0.13459999859333038,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.004600000102072954,"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/computer-science","display_name":"Computer science","score":0.4822600483894348}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4822600483894348}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3107411.3108203","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3107411.3108203","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.6499999761581421,"display_name":"Reduced inequalities","id":"https://metadata.un.org/sdg/10"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W4391913857","https://openalex.org/W2350741829","https://openalex.org/W2530322880"],"abstract_inverted_index":{"A":[0],"method":[1],"for":[2,79,128,235,294],"robustly":[3],"and":[4,28,71,94,152,157,188,203,226,251,262,297],"accurately":[5],"detecting":[6,80,129],"rare":[7],"DNA":[8],"mutations":[9,43,82,112,132],"in":[10,47,89,286],"tumor":[11,26,271],"samples":[12],"is":[13,55,153],"critical":[14],"to":[15,39,59,106,167,185,208,240],"cancer":[16],"research.":[17,60],"Because":[18],"many":[19],"clinical":[20,269],"tissue":[21,35],"repositories":[22],"have":[23,183,189],"only":[24],"FFPE-degraded":[25],"samples,":[27,261,272],"no":[29],"matched":[30,52],"normal":[31,53,104],"sample":[32,54,105],"from":[33,44,113,133,255,263],"healthy":[34],"available,":[36],"being":[37],"able":[38],"discriminate":[40,108],"low":[41,109,130],"frequency":[42,110,131],"background":[45],"noise":[46],"the":[48,64,90,103,145,159,168,178,213,221,231,256],"absence":[49],"of":[50,56,63,92,144,194,258,266,289],"a":[51,84,120,192,199,264,287],"particular":[57],"importance":[58],"Current":[61],"state":[62],"art":[65],"variant":[66,76,100,122,180,195,215,223,242,275,299],"callers":[67],"such":[68],"as":[69],"GATK":[70],"VarScan":[72],"focus":[73,96],"on":[74,97,155,158,170,249],"germline":[75,252,298],"calling":[77,101,181,196,224],"(used":[78],"inherited":[81],"following":[83],"Mendelian":[85],"inheritance":[86],"pattern)":[87],"or,":[88],"case":[91],"FreeBayes":[93],"MuTect,":[95],"tumor-normal":[98],"joint":[99],"(using":[102],"help":[107],"somatic":[111,241,250,296],"back":[114],"ground":[115],"noise).":[116],"We":[117,229,244,291],"present":[118],"Pisces,":[119,187],"tumor-only":[121],"caller":[123],"exclusively":[124],"developed":[125],"at":[126],"Illumina":[127,146],"next":[134],"generation":[135],"sequencing":[136,161],"data.":[137],"Pisces":[138,163,179,222,236,247,281,293],"has":[139,164],"been":[140,165],"an":[141],"integral":[142],"part":[143],"Truseq":[147],"Amplicon":[148],"workflow":[149],"since":[150,172],"2012,":[151],"available":[154,166,191],"BaseSpace":[156],"MiSeq":[160],"platforms.":[162],"public":[169],"github,":[171],"2015.":[173],"(https://github.com/Illumina/Pisces)":[174],"Since":[175],"that":[176,280],"time,":[177],"team":[182],"continued":[184],"develop":[186],"made":[190],"suite":[193],"tools,":[197],"including":[198],"ReadStitcher,":[200],"Variant":[201,204],"Phaser,":[202],"Quality":[205],"Recalibration":[206],"tool,":[207],"be":[209],"used":[210],"along":[211],"with":[212],"core":[214,227],"caller,":[216],"Pisces.":[217],"Here,":[218],"we":[219],"describe":[220,230],"tools":[225],"algorithms.":[228],"common":[232],"use":[233],"cases":[234],"(not":[237],"necessarily":[238],"restricted":[239],"calling).":[243],"also":[245],"evaluate":[246],"performance":[248],"datasets,":[253],"both":[254],"titration":[257],"well":[259],"characterized":[260],"corpus":[265],"500":[267],"FFPE-treated":[268],"trial":[270],"against":[273],"other":[274],"callers.":[276],"Our":[277],"results":[278,285],"show":[279],"gives":[282],"highly":[283],"accurate":[284],"variety":[288],"contexts.":[290],"recommend":[292],"amplicon":[295],"calling.":[300]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1}],"updated_date":"2026-03-03T08:47:05.690250","created_date":"2017-08-31T00:00:00"}
