{"id":"https://openalex.org/W4310167636","doi":"https://doi.org/10.1093/bioinformatics/btac756","title":"varAmpliCNV: analyzing variance of amplicons to detect CNVs in targeted NGS data","display_name":"varAmpliCNV: analyzing variance of amplicons to detect CNVs in targeted NGS data","publication_year":2022,"publication_date":"2022-11-25","ids":{"openalex":"https://openalex.org/W4310167636","doi":"https://doi.org/10.1093/bioinformatics/btac756","pmid":"https://pubmed.ncbi.nlm.nih.gov/36440912"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac756","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac756","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac756/48448975/btac756.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac756/48448975/btac756.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100632446","display_name":"Ajay Kumar","orcid":"https://orcid.org/0000-0002-0897-055X"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I149213910","display_name":"University of Antwerp","ror":"https://ror.org/008x57b05","country_code":"BE","type":"education","lineage":["https://openalex.org/I149213910"]},{"id":"https://openalex.org/I4210086966","display_name":"Open Targets","ror":"https://ror.org/000bp7q73","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210086966"]},{"id":"https://openalex.org/I4210102047","display_name":"Antwerp University Hospital","ror":"https://ror.org/01hwamj44","country_code":"BE","type":"funder","lineage":["https://openalex.org/I4210102047"]}],"countries":["BE","GB"],"is_corresponding":false,"raw_author_name":"Ajay Anand Kumar","raw_affiliation_strings":["Biomedical Informatics, Antwerp University Hospital , Antwerp (Wilrijk) 2610, Belgium","Center of Medical Genetics, University of Antwerp/Antwerp University Hospital , Antwerp (Edegem) 2650, Belgium","European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom","Open Targets , Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-0897-055X","affiliations":[{"raw_affiliation_string":"Biomedical Informatics, Antwerp University Hospital , Antwerp (Wilrijk) 2610, Belgium","institution_ids":["https://openalex.org/I4210102047"]},{"raw_affiliation_string":"Center of Medical Genetics, University of Antwerp/Antwerp University Hospital , Antwerp (Edegem) 2650, Belgium","institution_ids":["https://openalex.org/I149213910","https://openalex.org/I4210102047"]},{"raw_affiliation_string":"European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom","institution_ids":["https://openalex.org/I1303153112"]},{"raw_affiliation_string":"Open Targets , Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom","institution_ids":["https://openalex.org/I4210086966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042051309","display_name":"Bart Loeys","orcid":"https://orcid.org/0000-0003-3703-9518"},"institutions":[{"id":"https://openalex.org/I149213910","display_name":"University of Antwerp","ror":"https://ror.org/008x57b05","country_code":"BE","type":"education","lineage":["https://openalex.org/I149213910"]},{"id":"https://openalex.org/I4210102047","display_name":"Antwerp University Hospital","ror":"https://ror.org/01hwamj44","country_code":"BE","type":"funder","lineage":["https://openalex.org/I4210102047"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Bart Loeys","raw_affiliation_strings":["Center of Medical Genetics, University of Antwerp/Antwerp University Hospital , Antwerp (Edegem) 2650, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Medical Genetics, University of Antwerp/Antwerp University Hospital , Antwerp (Edegem) 2650, Belgium","institution_ids":["https://openalex.org/I149213910","https://openalex.org/I4210102047"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062965524","display_name":"Gerarda van de Beek","orcid":null},"institutions":[{"id":"https://openalex.org/I149213910","display_name":"University of Antwerp","ror":"https://ror.org/008x57b05","country_code":"BE","type":"education","lineage":["https://openalex.org/I149213910"]},{"id":"https://openalex.org/I4210102047","display_name":"Antwerp University Hospital","ror":"https://ror.org/01hwamj44","country_code":"BE","type":"funder","lineage":["https://openalex.org/I4210102047"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Gerarda Van De Beek","raw_affiliation_strings":["Center of Medical Genetics, University of Antwerp/Antwerp University Hospital , Antwerp (Edegem) 2650, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Medical Genetics, University of Antwerp/Antwerp University Hospital , Antwerp (Edegem) 2650, Belgium","institution_ids":["https://openalex.org/I149213910","https://openalex.org/I4210102047"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003024918","display_name":"Nils Peeters","orcid":null},"institutions":[{"id":"https://openalex.org/I149213910","display_name":"University of Antwerp","ror":"https://ror.org/008x57b05","country_code":"BE","type":"education","lineage":["https://openalex.org/I149213910"]},{"id":"https://openalex.org/I4210102047","display_name":"Antwerp University Hospital","ror":"https://ror.org/01hwamj44","country_code":"BE","type":"funder","lineage":["https://openalex.org/I4210102047"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Nils Peeters","raw_affiliation_strings":["Center of Medical Genetics, University of Antwerp/Antwerp University Hospital , Antwerp (Edegem) 2650, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Medical Genetics, University of Antwerp/Antwerp University Hospital , Antwerp (Edegem) 2650, Belgium","institution_ids":["https://openalex.org/I149213910","https://openalex.org/I4210102047"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019374336","display_name":"Wim Wuyts","orcid":"https://orcid.org/0000-0002-4349-9038"},"institutions":[{"id":"https://openalex.org/I149213910","display_name":"University of Antwerp","ror":"https://ror.org/008x57b05","country_code":"BE","type":"education","lineage":["https://openalex.org/I149213910"]},{"id":"https://openalex.org/I4210102047","display_name":"Antwerp University Hospital","ror":"https://ror.org/01hwamj44","country_code":"BE","type":"funder","lineage":["https://openalex.org/I4210102047"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Wim Wuyts","raw_affiliation_strings":["Center of Medical Genetics, University of Antwerp/Antwerp University Hospital , Antwerp (Edegem) 2650, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Medical Genetics, University of Antwerp/Antwerp University Hospital , Antwerp (Edegem) 2650, Belgium","institution_ids":["https://openalex.org/I149213910","https://openalex.org/I4210102047"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023849845","display_name":"Lut Van Laer","orcid":"https://orcid.org/0000-0003-1394-9867"},"institutions":[{"id":"https://openalex.org/I149213910","display_name":"University of Antwerp","ror":"https://ror.org/008x57b05","country_code":"BE","type":"education","lineage":["https://openalex.org/I149213910"]},{"id":"https://openalex.org/I4210102047","display_name":"Antwerp University Hospital","ror":"https://ror.org/01hwamj44","country_code":"BE","type":"funder","lineage":["https://openalex.org/I4210102047"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Lut Van Laer","raw_affiliation_strings":["Center of Medical Genetics, University of Antwerp/Antwerp University Hospital , Antwerp (Edegem) 2650, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Medical Genetics, University of Antwerp/Antwerp University Hospital , Antwerp (Edegem) 2650, Belgium","institution_ids":["https://openalex.org/I149213910","https://openalex.org/I4210102047"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005620097","display_name":"Geert Vandeweyer","orcid":"https://orcid.org/0000-0002-6262-6522"},"institutions":[{"id":"https://openalex.org/I149213910","display_name":"University of Antwerp","ror":"https://ror.org/008x57b05","country_code":"BE","type":"education","lineage":["https://openalex.org/I149213910"]},{"id":"https://openalex.org/I4210102047","display_name":"Antwerp University Hospital","ror":"https://ror.org/01hwamj44","country_code":"BE","type":"funder","lineage":["https://openalex.org/I4210102047"]}],"countries":["BE"],"is_corresponding":true,"raw_author_name":"Geert Vandeweyer","raw_affiliation_strings":["Biomedical Informatics, Antwerp University Hospital , Antwerp (Wilrijk) 2610, Belgium","Center of Medical Genetics, University of Antwerp/Antwerp University Hospital , Antwerp (Edegem) 2650, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Informatics, Antwerp University Hospital , Antwerp (Wilrijk) 2610, Belgium","institution_ids":["https://openalex.org/I4210102047"]},{"raw_affiliation_string":"Center of Medical Genetics, University of Antwerp/Antwerp University Hospital , Antwerp (Edegem) 2650, Belgium","institution_ids":["https://openalex.org/I149213910","https://openalex.org/I4210102047"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044677354","display_name":"Maaike Alaerts","orcid":"https://orcid.org/0000-0002-1376-3635"},"institutions":[{"id":"https://openalex.org/I149213910","display_name":"University of Antwerp","ror":"https://ror.org/008x57b05","country_code":"BE","type":"education","lineage":["https://openalex.org/I149213910"]},{"id":"https://openalex.org/I4210102047","display_name":"Antwerp University Hospital","ror":"https://ror.org/01hwamj44","country_code":"BE","type":"funder","lineage":["https://openalex.org/I4210102047"]}],"countries":["BE"],"is_corresponding":true,"raw_author_name":"Maaike Alaerts","raw_affiliation_strings":["Center of Medical Genetics, University of Antwerp/Antwerp University Hospital , Antwerp (Edegem) 2650, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Medical Genetics, University of Antwerp/Antwerp University Hospital , Antwerp (Edegem) 2650, Belgium","institution_ids":["https://openalex.org/I149213910","https://openalex.org/I4210102047"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5005620097","https://openalex.org/A5044677354"],"corresponding_institution_ids":["https://openalex.org/I149213910","https://openalex.org/I4210102047"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.5077,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.69715223,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"39","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.8501999974250793,"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"}},"topics":[{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.8501999974250793,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.051899999380111694,"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":0.011800000444054604,"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/amplicon","display_name":"Amplicon","score":0.7294386625289917},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6986232995986938},{"id":"https://openalex.org/keywords/copy-number-variation","display_name":"Copy-number variation","score":0.6205275058746338},{"id":"https://openalex.org/keywords/normalization","display_name":"Normalization (sociology)","score":0.6184845566749573},{"id":"https://openalex.org/keywords/principal-component-analysis","display_name":"Principal component analysis","score":0.5877596139907837},{"id":"https://openalex.org/keywords/false-positive-paradox","display_name":"False positive paradox","score":0.559170126914978},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.43018966913223267},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3970739245414734},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2953053414821625},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2477678656578064},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.17418411374092102},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15737760066986084},{"id":"https://openalex.org/keywords/polymerase-chain-reaction","display_name":"Polymerase chain reaction","score":0.1393214762210846},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13870838284492493}],"concepts":[{"id":"https://openalex.org/C8185291","wikidata":"https://www.wikidata.org/wiki/Q2844457","display_name":"Amplicon","level":4,"score":0.7294386625289917},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6986232995986938},{"id":"https://openalex.org/C120821319","wikidata":"https://www.wikidata.org/wiki/Q1501491","display_name":"Copy-number variation","level":4,"score":0.6205275058746338},{"id":"https://openalex.org/C136886441","wikidata":"https://www.wikidata.org/wiki/Q926129","display_name":"Normalization (sociology)","level":2,"score":0.6184845566749573},{"id":"https://openalex.org/C27438332","wikidata":"https://www.wikidata.org/wiki/Q2873","display_name":"Principal component analysis","level":2,"score":0.5877596139907837},{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.559170126914978},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.43018966913223267},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3970739245414734},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2953053414821625},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2477678656578064},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.17418411374092102},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15737760066986084},{"id":"https://openalex.org/C49105822","wikidata":"https://www.wikidata.org/wiki/Q176996","display_name":"Polymerase chain reaction","level":3,"score":0.1393214762210846},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13870838284492493},{"id":"https://openalex.org/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btac756","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac756","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac756/48448975/btac756.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36440912","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36440912","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9805572","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9805572","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":"Bioinformatics","raw_type":"Text"},{"id":"pmh:c:irua:192746","is_oa":false,"landing_page_url":"https://hdl.handle.net/10067/1927460151162165141","pdf_url":null,"source":{"id":"https://openalex.org/S4306401849","display_name":"Institutional Repository University of Antwerp (University of Antwerp)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149213910","host_organization_name":"University of Antwerp","host_organization_lineage":["https://openalex.org/I149213910"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac756","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac756","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac756/48448975/btac756.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4593400399","display_name":null,"funder_award_id":"ERC-COG-2017-771945","funder_id":"https://openalex.org/F4320321730","funder_display_name":"Fonds Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G5995622719","display_name":null,"funder_award_id":"12 CVD 03","funder_id":"https://openalex.org/F4320320890","funder_display_name":"Fondation Leducq"},{"id":"https://openalex.org/G6290902372","display_name":null,"funder_award_id":"2013T093","funder_id":"https://openalex.org/F4320321642","funder_display_name":"Hartstichting"}],"funders":[{"id":"https://openalex.org/F4320320890","display_name":"Fondation Leducq","ror":"https://ror.org/01czwga19"},{"id":"https://openalex.org/F4320321642","display_name":"Hartstichting","ror":"https://ror.org/05nxhgm70"},{"id":"https://openalex.org/F4320321730","display_name":"Fonds Wetenschappelijk Onderzoek","ror":"https://ror.org/03qtxy027"},{"id":"https://openalex.org/F4320324595","display_name":"Universiteit Antwerpen","ror":"https://ror.org/008x57b05"},{"id":"https://openalex.org/F4320327336","display_name":"Vlaamse regering","ror":null},{"id":"https://openalex.org/F4320338335","display_name":"H2020 European Research Council","ror":"https://ror.org/0472cxd90"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4310167636.pdf","grobid_xml":"https://content.openalex.org/works/W4310167636.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W32279435","https://openalex.org/W2001725705","https://openalex.org/W2002843742","https://openalex.org/W2012151892","https://openalex.org/W2018604728","https://openalex.org/W2054744711","https://openalex.org/W2055798820","https://openalex.org/W2060114404","https://openalex.org/W2101844137","https://openalex.org/W2106149075","https://openalex.org/W2110374888","https://openalex.org/W2133174470","https://openalex.org/W2133257334","https://openalex.org/W2158931791","https://openalex.org/W2166657289","https://openalex.org/W2167278603","https://openalex.org/W2168893192","https://openalex.org/W2169744057","https://openalex.org/W2337209831","https://openalex.org/W2338102768","https://openalex.org/W2519126396","https://openalex.org/W2551190949","https://openalex.org/W2608516201","https://openalex.org/W2791559636","https://openalex.org/W3005768323","https://openalex.org/W3036487724","https://openalex.org/W6601306115"],"related_works":["https://openalex.org/W2995118009","https://openalex.org/W1557094818","https://openalex.org/W2786748503","https://openalex.org/W2011298649","https://openalex.org/W2036617847","https://openalex.org/W1975632186","https://openalex.org/W2591697403","https://openalex.org/W3088281179","https://openalex.org/W1966203981","https://openalex.org/W2513883126"],"abstract_inverted_index":{"MOTIVATION:":[0],"Computational":[1],"identification":[2],"of":[3,22,63,80,88,93,107,164,170],"copy":[4],"number":[5],"variants":[6],"(CNVs)":[7],"in":[8,52,60,155],"sequencing":[9],"data":[10,56,106,213],"is":[11,191],"a":[12,43,131,178],"challenging":[13],"task.":[14],"Existing":[15],"CNV-detection":[16,51],"methods":[17,100],"account":[18],"for":[19,50],"various":[20],"sources":[21],"variation":[23],"and":[24,32,103,152,167,197],"perform":[25],"different":[26],"normalization":[27],"strategies.":[28],"However,":[29],"their":[30],"applicability":[31],"predictions":[33],"are":[34,175,214],"restricted":[35],"to":[36,77,157,181],"specific":[37],"enrichment":[38,58],"protocols.":[39],"Here,":[40],"we":[41,126],"introduce":[42],"novel":[44],"tool":[45,190],"named":[46],"varAmpliCNV,":[47],"specifically":[48],"designed":[49],"amplicon-based":[53],"targeted":[54],"resequencing":[55],"(Haloplex\u2122":[57],"protocol)":[59],"the":[61,128],"absence":[62],"matched":[64],"controls.":[65,146],"VarAmpliCNV":[66,94,147],"utilizes":[67],"principal":[68],"component":[69],"analysis":[70],"(PCA)":[71],"and/or":[72],"metric":[73],"dimensional":[74],"scaling":[75],"(MDS)":[76],"control":[78,123],"variances":[79],"amplicon":[81],"associated":[82],"read":[83],"counts":[84],"enabling":[85],"effective":[86],"detection":[87],"CNV":[89,165],"signals.":[90],"RESULTS:":[91],"Performance":[92],"was":[95],"compared":[96],"against":[97],"three":[98],"existing":[99],"(ConVaDING,":[101],"ONCOCNV":[102],"DECoN)":[104],"on":[105,130,140],"167":[108],"samples":[109],"run":[110,139],"with":[111],"an":[112],"aortic":[113],"aneurysm":[114],"gene":[115,134],"panel":[116,135],"(n":[117,136],"=":[118,137],"30),":[119],"including":[120],"9":[121],"positive":[122,145],"samples.":[124],"Additionally,":[125],"validated":[127],"performance":[129],"large":[132],"deafness":[133],"145)":[138],"138":[141],"samples,":[142],"containing":[143],"4":[144],"achieved":[148],"higher":[149],"sensitivity":[150],"(100%)":[151],"specificity":[153],"(99.78%)":[154],"comparison":[156],"competing":[158],"methods.":[159],"In":[160],"addition,":[161],"unsupervised":[162],"clustering":[163],"segments":[166],"visualization":[168],"plots":[169],"amplicons":[171],"spanning":[172],"these":[173],"regions":[174],"included":[176],"as":[177],"downstream":[179],"strategy":[180],"filter":[182],"out":[183],"false":[184],"positives.":[185],"AVAILABILITY":[186],"AND":[187],"IMPLEMENTATION:":[188],"The":[189],"freely":[192],"available":[193,215],"through":[194],"galaxy":[195],"toolshed":[196],"at:":[198],"https://hub.docker.com/r/cmgantwerpen/varamplicnv.":[199],"Supplementary":[200,205,212],"Data":[201,206],"File":[202,207],"S1:":[203],"https://tinyurl.com/2yzswyhh;":[204],"S2:":[208],"https://tinyurl.com/ycyf2fb4.":[209],"SUPPLEMENTARY":[210],"INFORMATION:":[211],"at":[216],"Bioinformatics":[217],"online.":[218]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}