{"id":"https://openalex.org/W2566331076","doi":"https://doi.org/10.1186/s13029-016-0060-z","title":"PureCN: copy number calling and SNV classification using targeted short read sequencing","display_name":"PureCN: copy number calling and SNV classification using targeted short read sequencing","publication_year":2016,"publication_date":"2016-12-01","ids":{"openalex":"https://openalex.org/W2566331076","doi":"https://doi.org/10.1186/s13029-016-0060-z","mag":"2566331076","pmid":"https://pubmed.ncbi.nlm.nih.gov/27999612"},"language":"en","primary_location":{"id":"doi:10.1186/s13029-016-0060-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13029-016-0060-z","pdf_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/s13029-016-0060-z","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Source Code for Biology and Medicine","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/s13029-016-0060-z","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5069185084","display_name":"Markus Riester","orcid":"https://orcid.org/0000-0002-4759-8332"},"institutions":[{"id":"https://openalex.org/I4210117619","display_name":"Novartis (United States)","ror":"https://ror.org/028fhxy95","country_code":"US","type":"company","lineage":["https://openalex.org/I1283582996","https://openalex.org/I4210117619"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Markus Riester","raw_affiliation_strings":["Novartis Institutes for BioMedical Research, Cambridge, MA USA","Novartis Institutes for BioMedical Research, Cambridge, MA, USA"],"raw_orcid":"https://orcid.org/0000-0002-4759-8332","affiliations":[{"raw_affiliation_string":"Novartis Institutes for BioMedical Research, Cambridge, MA USA","institution_ids":["https://openalex.org/I4210117619"]},{"raw_affiliation_string":"Novartis Institutes for BioMedical Research, Cambridge, MA, USA","institution_ids":["https://openalex.org/I4210117619"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101568860","display_name":"Angad Singh","orcid":"https://orcid.org/0000-0002-3885-4779"},"institutions":[{"id":"https://openalex.org/I4210117619","display_name":"Novartis (United States)","ror":"https://ror.org/028fhxy95","country_code":"US","type":"company","lineage":["https://openalex.org/I1283582996","https://openalex.org/I4210117619"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Angad P. Singh","raw_affiliation_strings":["Novartis Institutes for BioMedical Research, Cambridge, MA USA","Novartis Institutes for BioMedical Research, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Novartis Institutes for BioMedical Research, Cambridge, MA USA","institution_ids":["https://openalex.org/I4210117619"]},{"raw_affiliation_string":"Novartis Institutes for BioMedical Research, Cambridge, MA, USA","institution_ids":["https://openalex.org/I4210117619"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090667008","display_name":"A. Rose Brannon","orcid":"https://orcid.org/0000-0003-4610-0149"},"institutions":[{"id":"https://openalex.org/I4210117619","display_name":"Novartis (United States)","ror":"https://ror.org/028fhxy95","country_code":"US","type":"company","lineage":["https://openalex.org/I1283582996","https://openalex.org/I4210117619"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"A. Rose Brannon","raw_affiliation_strings":["Novartis Institutes for BioMedical Research, Cambridge, MA USA","Novartis Institutes for BioMedical Research, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Novartis Institutes for BioMedical Research, Cambridge, MA USA","institution_ids":["https://openalex.org/I4210117619"]},{"raw_affiliation_string":"Novartis Institutes for BioMedical Research, Cambridge, MA, USA","institution_ids":["https://openalex.org/I4210117619"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100664136","display_name":"Kun Yu","orcid":"https://orcid.org/0009-0007-3344-7553"},"institutions":[{"id":"https://openalex.org/I4210117619","display_name":"Novartis (United States)","ror":"https://ror.org/028fhxy95","country_code":"US","type":"company","lineage":["https://openalex.org/I1283582996","https://openalex.org/I4210117619"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kun Yu","raw_affiliation_strings":["Novartis Institutes for BioMedical Research, Cambridge, MA USA","Novartis Institutes for BioMedical Research, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Novartis Institutes for BioMedical Research, Cambridge, MA USA","institution_ids":["https://openalex.org/I4210117619"]},{"raw_affiliation_string":"Novartis Institutes for BioMedical Research, Cambridge, MA, USA","institution_ids":["https://openalex.org/I4210117619"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084979512","display_name":"Catarina D. Campbell","orcid":"https://orcid.org/0000-0002-3863-9841"},"institutions":[{"id":"https://openalex.org/I4210117619","display_name":"Novartis (United States)","ror":"https://ror.org/028fhxy95","country_code":"US","type":"company","lineage":["https://openalex.org/I1283582996","https://openalex.org/I4210117619"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Catarina D. Campbell","raw_affiliation_strings":["Novartis Institutes for BioMedical Research, Cambridge, MA USA","Novartis Institutes for BioMedical Research, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Novartis Institutes for BioMedical Research, Cambridge, MA USA","institution_ids":["https://openalex.org/I4210117619"]},{"raw_affiliation_string":"Novartis Institutes for BioMedical Research, Cambridge, MA, USA","institution_ids":["https://openalex.org/I4210117619"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063447892","display_name":"Derek Y. Chiang","orcid":"https://orcid.org/0000-0002-1131-6065"},"institutions":[{"id":"https://openalex.org/I4210117619","display_name":"Novartis (United States)","ror":"https://ror.org/028fhxy95","country_code":"US","type":"company","lineage":["https://openalex.org/I1283582996","https://openalex.org/I4210117619"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Derek Y. Chiang","raw_affiliation_strings":["Novartis Institutes for BioMedical Research, Cambridge, MA USA","Novartis Institutes for BioMedical Research, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Novartis Institutes for BioMedical Research, Cambridge, MA USA","institution_ids":["https://openalex.org/I4210117619"]},{"raw_affiliation_string":"Novartis Institutes for BioMedical Research, Cambridge, MA, USA","institution_ids":["https://openalex.org/I4210117619"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058106214","display_name":"Michael Morrissey","orcid":null},"institutions":[{"id":"https://openalex.org/I4210117619","display_name":"Novartis (United States)","ror":"https://ror.org/028fhxy95","country_code":"US","type":"company","lineage":["https://openalex.org/I1283582996","https://openalex.org/I4210117619"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael P. Morrissey","raw_affiliation_strings":["Novartis Institutes for BioMedical Research, Cambridge, MA USA","Novartis Institutes for BioMedical Research, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Novartis Institutes for BioMedical Research, Cambridge, MA USA","institution_ids":["https://openalex.org/I4210117619"]},{"raw_affiliation_string":"Novartis Institutes for BioMedical Research, Cambridge, MA, USA","institution_ids":["https://openalex.org/I4210117619"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5069185084"],"corresponding_institution_ids":["https://openalex.org/I4210117619"],"apc_list":{"value":2040,"currency":"USD","value_usd":2040},"apc_paid":{"value":2040,"currency":"USD","value_usd":2040},"fwci":3.1754,"has_fulltext":true,"cited_by_count":172,"citation_normalized_percentile":{"value":0.92004367,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"11","issue":"1","first_page":"13","last_page":"13"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9557999968528748,"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":0.9557999968528748,"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/T11369","display_name":"Genetic factors in colorectal cancer","score":0.009100000374019146,"subfield":{"id":"https://openalex.org/subfields/2734","display_name":"Pathology and Forensic Medicine"},"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.0066999997943639755,"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/computer-science","display_name":"Computer science","score":0.6095196008682251},{"id":"https://openalex.org/keywords/copy-number-variation","display_name":"Copy-number variation","score":0.5246548652648926},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3818458616733551},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2278892695903778},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.21321937441825867},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.10682329535484314},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.06818440556526184}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6095196008682251},{"id":"https://openalex.org/C120821319","wikidata":"https://www.wikidata.org/wiki/Q1501491","display_name":"Copy-number variation","level":4,"score":0.5246548652648926},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3818458616733551},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2278892695903778},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.21321937441825867},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.10682329535484314},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.06818440556526184}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/s13029-016-0060-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13029-016-0060-z","pdf_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/s13029-016-0060-z","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Source Code for Biology and Medicine","raw_type":"journal-article"},{"id":"pmid:27999612","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27999612","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Source code for biology and medicine","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:5157099","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5157099","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"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":"Source Code Biol Med","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13029-016-0060-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13029-016-0060-z","pdf_url":"https://scfbm.biomedcentral.com/track/pdf/10.1186/s13029-016-0060-z","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Source Code for Biology and Medicine","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.4099999964237213}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2566331076.pdf","grobid_xml":"https://content.openalex.org/works/W2566331076.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W1973094248","https://openalex.org/W2006288875","https://openalex.org/W2044702943","https://openalex.org/W2065388551","https://openalex.org/W2096283457","https://openalex.org/W2096746187","https://openalex.org/W2097331151","https://openalex.org/W2103684001","https://openalex.org/W2109991075","https://openalex.org/W2115919763","https://openalex.org/W2117656191","https://openalex.org/W2119180969","https://openalex.org/W2131478115","https://openalex.org/W2133339454","https://openalex.org/W2134151441","https://openalex.org/W2135643214","https://openalex.org/W2136939537","https://openalex.org/W2138601221","https://openalex.org/W2144759168","https://openalex.org/W2155943701","https://openalex.org/W2160981405","https://openalex.org/W2170490448","https://openalex.org/W2202187342","https://openalex.org/W2281123440","https://openalex.org/W2286981607","https://openalex.org/W2405513305","https://openalex.org/W2560367415"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2513883126","https://openalex.org/W3118014344","https://openalex.org/W2160911017","https://openalex.org/W2763474833","https://openalex.org/W2387464095","https://openalex.org/W2507940864","https://openalex.org/W2390279801","https://openalex.org/W1526237818","https://openalex.org/W2358668433"],"abstract_inverted_index":{"BACKGROUND:":[0],"Matched":[1],"sequencing":[2,107,154,184],"of":[3,15,57,70,126,134,192,211],"both":[4],"tumor":[5,58,94,121,171,193],"and":[6,37,72,97,114,129,131,142,164,169,179,195],"normal":[7,61,200],"tissue":[8],"is":[9,148,174,215],"routinely":[10],"used":[11,25],"to":[12,79],"classify":[13],"variants":[14,48,137],"uncertain":[16],"significance":[17],"(VUS)":[18],"into":[19],"somatic":[20,32,73,140,160],"vs.":[21],"germline.":[22],"However,":[23,89],"assays":[24],"in":[26,34,64,66,206],"molecular":[27],"diagnostics":[28],"focus":[29],"on":[30,176,180],"known":[31],"alterations":[33],"cancer":[35],"genes":[36],"often":[38],"only":[39],"sequence":[40],"tumors.":[41],"Therefore,":[42],"an":[43],"algorithm":[44,188],"that":[45],"reliably":[46],"classifies":[47],"would":[49],"be":[50,77],"helpful":[51],"for":[52,85,92,103,119,132,150,167],"retrospective":[53],"exploratory":[54],"analyses.":[55],"Contamination":[56],"samples":[59,201],"with":[60,158],"cells":[62],"results":[63],"differences":[65],"expected":[67],"allelic":[68],"fractions":[69],"germline":[71],"variants,":[74],"which":[75],"can":[76],"exploited":[78],"accurately":[80],"infer":[81],"genotypes":[82],"after":[83],"adjusting":[84],"local":[86],"copy":[87,98,123],"number.":[88],"existing":[90],"algorithms":[91],"determining":[93],"purity,":[95,122],"ploidy":[96],"number":[99],"are":[100,202],"not":[101,203],"designed":[102],"unmatched":[104,170],"short":[105,152],"read":[106,153],"data.":[108,185],"RESULTS:":[109],"We":[110],"describe":[111],"a":[112],"methodology":[113],"corresponding":[115],"open":[116,218],"source":[117,219],"software":[118,214],"estimating":[120],"number,":[124],"loss":[125],"heterozygosity":[127],"(LOH),":[128],"contamination,":[130],"classification":[133,210],"single":[135],"nucleotide":[136],"(SNVs)":[138],"by":[139],"status":[141],"clonality.":[143],"This":[144,205],"R":[145],"package,":[146],"PureCN,":[147],"optimized":[149],"targeted":[151],"data,":[155],"integrates":[156],"well":[157],"standard":[159],"variant":[161],"detection":[162],"pipelines,":[163],"has":[165],"support":[166],"matched":[168,199],"samples.":[172],"Accuracy":[173],"demonstrated":[175],"simulated":[177],"data":[178],"real":[181],"whole":[182],"exome":[183],"CONCLUSIONS:":[186],"Our":[187],"provides":[189],"accurate":[190,209],"estimates":[191],"purity":[194],"ploidy,":[196],"even":[197],"if":[198],"available.":[204],"turn":[207],"allows":[208],"SNVs.":[212],"The":[213],"provided":[216],"as":[217],"(Artistic":[220],"License":[221],"2.0)":[222],"R/Bioconductor":[223],"package":[224],"PureCN":[225],"(http://bioconductor.org/packages/PureCN/).":[226]},"counts_by_year":[{"year":2026,"cited_by_count":14},{"year":2025,"cited_by_count":20},{"year":2024,"cited_by_count":30},{"year":2023,"cited_by_count":30},{"year":2022,"cited_by_count":18},{"year":2021,"cited_by_count":21},{"year":2020,"cited_by_count":12},{"year":2019,"cited_by_count":16},{"year":2018,"cited_by_count":11}],"updated_date":"2026-08-19T15:00:24.278416","created_date":"2025-10-10T00:00:00"}
