{"id":"https://openalex.org/W2048500586","doi":"https://doi.org/10.1093/bib/bbu002","title":"An assessment of computational methods for estimating purity and clonality using genomic data derived from heterogeneous tumor tissue samples","display_name":"An assessment of computational methods for estimating purity and clonality using genomic data derived from heterogeneous tumor tissue samples","publication_year":2014,"publication_date":"2014-02-20","ids":{"openalex":"https://openalex.org/W2048500586","doi":"https://doi.org/10.1093/bib/bbu002","mag":"2048500586","pmid":"https://pubmed.ncbi.nlm.nih.gov/24562872"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbu002","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbu002","pdf_url":"https://academic.oup.com/bib/article-pdf/16/2/232/679801/bbu002.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bib/article-pdf/16/2/232/679801/bbu002.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064937521","display_name":"Vinod Kumar Yadav","orcid":"https://orcid.org/0000-0001-6450-7036"},"institutions":[{"id":"https://openalex.org/I921990950","display_name":"University of Colorado Denver","ror":"https://ror.org/02hh7en24","country_code":"US","type":"education","lineage":["https://openalex.org/I921990950"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"V. K. Yadav","raw_affiliation_strings":["University of Colorado School of Medicine"],"affiliations":[{"raw_affiliation_string":"University of Colorado School of Medicine","institution_ids":["https://openalex.org/I921990950"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036093562","display_name":"Subhajyoti De","orcid":"https://orcid.org/0000-0002-2313-8593"},"institutions":[{"id":"https://openalex.org/I921990950","display_name":"University of Colorado Denver","ror":"https://ror.org/02hh7en24","country_code":"US","type":"education","lineage":["https://openalex.org/I921990950"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"S. De","raw_affiliation_strings":["University of Colorado School of Medicine"],"affiliations":[{"raw_affiliation_string":"University of Colorado School of Medicine","institution_ids":["https://openalex.org/I921990950"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5036093562"],"corresponding_institution_ids":["https://openalex.org/I921990950"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":2.5566,"has_fulltext":false,"cited_by_count":79,"citation_normalized_percentile":{"value":0.89099716,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"16","issue":"2","first_page":"232","last_page":"241"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":1.0,"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":1.0,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9997000098228455,"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"}},{"id":"https://openalex.org/T10231","display_name":"Pancreatic and Hepatic Oncology Research","score":0.9983999729156494,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"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/deconvolution","display_name":"Deconvolution","score":0.8345005512237549},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6619561314582825},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.6573599576950073},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4968595802783966},{"id":"https://openalex.org/keywords/complement","display_name":"Complement (music)","score":0.47364890575408936},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.46797066926956177},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.43014079332351685},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23526036739349365},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1303260326385498},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.0901036262512207}],"concepts":[{"id":"https://openalex.org/C174576160","wikidata":"https://www.wikidata.org/wiki/Q1183700","display_name":"Deconvolution","level":2,"score":0.8345005512237549},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6619561314582825},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.6573599576950073},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4968595802783966},{"id":"https://openalex.org/C112313634","wikidata":"https://www.wikidata.org/wiki/Q7886648","display_name":"Complement (music)","level":5,"score":0.47364890575408936},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.46797066926956177},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.43014079332351685},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23526036739349365},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1303260326385498},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.0901036262512207},{"id":"https://openalex.org/C188082640","wikidata":"https://www.wikidata.org/wiki/Q1780899","display_name":"Complementation","level":4,"score":0.0},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbu002","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbu002","pdf_url":"https://academic.oup.com/bib/article-pdf/16/2/232/679801/bbu002.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:24562872","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24562872","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:3764130","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4794615","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbu002","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbu002","pdf_url":"https://academic.oup.com/bib/article-pdf/16/2/232/679801/bbu002.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.5699999928474426,"id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G3892583714","display_name":null,"funder_award_id":"IRG 57-001-53","funder_id":"https://openalex.org/F4320306095","funder_display_name":"American Cancer Society"},{"id":"https://openalex.org/G40421540","display_name":null,"funder_award_id":"57-001-53","funder_id":"https://openalex.org/F4320306095","funder_display_name":"American Cancer Society"}],"funders":[{"id":"https://openalex.org/F4320306095","display_name":"American Cancer Society","ror":"https://ror.org/02e463172"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2048500586.pdf","grobid_xml":"https://content.openalex.org/works/W2048500586.grobid-xml"},"referenced_works_count":56,"referenced_works":["https://openalex.org/W1599494094","https://openalex.org/W1773728303","https://openalex.org/W1986888627","https://openalex.org/W1987012261","https://openalex.org/W1987370132","https://openalex.org/W1988785484","https://openalex.org/W1995086037","https://openalex.org/W1998728654","https://openalex.org/W2006288875","https://openalex.org/W2009720434","https://openalex.org/W2022495797","https://openalex.org/W2026523107","https://openalex.org/W2029943952","https://openalex.org/W2030781210","https://openalex.org/W2032518018","https://openalex.org/W2032980774","https://openalex.org/W2033642329","https://openalex.org/W2041380745","https://openalex.org/W2041993682","https://openalex.org/W2065709676","https://openalex.org/W2068661079","https://openalex.org/W2070310570","https://openalex.org/W2088580309","https://openalex.org/W2096283457","https://openalex.org/W2096478492","https://openalex.org/W2099377894","https://openalex.org/W2101741321","https://openalex.org/W2105644651","https://openalex.org/W2109135251","https://openalex.org/W2112706474","https://openalex.org/W2114495858","https://openalex.org/W2115232436","https://openalex.org/W2116642156","https://openalex.org/W2119192314","https://openalex.org/W2124704227","https://openalex.org/W2127214385","https://openalex.org/W2129631522","https://openalex.org/W2129905934","https://openalex.org/W2130430382","https://openalex.org/W2130996300","https://openalex.org/W2137605677","https://openalex.org/W2138601221","https://openalex.org/W2143093088","https://openalex.org/W2145347221","https://openalex.org/W2146244933","https://openalex.org/W2146290346","https://openalex.org/W2147730364","https://openalex.org/W2148241659","https://openalex.org/W2150078021","https://openalex.org/W2151571079","https://openalex.org/W2151794156","https://openalex.org/W2155388222","https://openalex.org/W2158549544","https://openalex.org/W2166493347","https://openalex.org/W2170490448","https://openalex.org/W2171501288"],"related_works":["https://openalex.org/W4251527294","https://openalex.org/W3090782779","https://openalex.org/W4296701479","https://openalex.org/W4231036715","https://openalex.org/W3149087629","https://openalex.org/W2032074591","https://openalex.org/W1986156575","https://openalex.org/W4242983818","https://openalex.org/W2970288912","https://openalex.org/W2053972265"],"abstract_inverted_index":{"Solid":[0],"tumor":[1,105],"samples":[2,51],"typically":[3],"contain":[4],"multiple":[5],"distinct":[6],"clonal":[7],"populations":[8,42],"of":[9,21,43,46,68,83],"cancer":[10,23],"cells,":[11],"and":[12,15,25,34,36,70,97,100],"also":[13,77],"stromal":[14],"immune":[16],"cell":[17],"contamination.":[18],"A":[19],"majority":[20],"the":[22],"genomics":[24,96],"transcriptomics":[26],"studies":[27],"do":[28],"not":[29],"explicitly":[30],"consider":[31],"genetic":[32],"heterogeneity":[33],"impurity,":[35],"draw":[37],"inferences":[38],"based":[39],"on":[40],"mixed":[41],"cells.":[44],"Deconvolution":[45],"genomic":[47,69],"data":[48,72],"from":[49,73],"heterogeneous":[50,74],"provides":[52],"a":[53,79],"powerful":[54],"tool":[55],"to":[56,93],"address":[57],"this":[58],"limitation.":[59],"We":[60,76],"discuss":[61],"several":[62],"computational":[63],"tools,":[64],"which":[65],"enable":[66],"deconvolution":[67],"transcriptomic":[71],"samples.":[75],"performed":[78],"systematic":[80],"comparative":[81],"assessment":[82],"these":[84,89],"tools.":[85],"If":[86],"properly":[87],"used,":[88],"tools":[90],"have":[91],"potentials":[92],"complement":[94],"single-cell":[95],"immunoFISH":[98],"analyses,":[99],"provide":[101],"novel":[102],"insights":[103],"into":[104],"heterogeneity.":[106]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":10},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":8},{"year":2014,"cited_by_count":6}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}