{"id":"https://openalex.org/W2035593347","doi":"https://doi.org/10.1186/1471-2105-10-80","title":"CNV-seq, a new method to detect copy number variation using high-throughput sequencing","display_name":"CNV-seq, a new method to detect copy number variation using high-throughput sequencing","publication_year":2009,"publication_date":"2009-03-06","ids":{"openalex":"https://openalex.org/W2035593347","doi":"https://doi.org/10.1186/1471-2105-10-80","mag":"2035593347","pmid":"https://pubmed.ncbi.nlm.nih.gov/19267900"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-10-80","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-80","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-80","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"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":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-80","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103744058","display_name":"Chao Xie","orcid":null},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Chao Xie","raw_affiliation_strings":["Department of Biological Sciences, National University of Singapore, Singapore. xie@nus.edu.sg","Department of Biological Sciences, National University of Singapore, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, National University of Singapore, Singapore. xie@nus.edu.sg","institution_ids":["https://openalex.org/I165932596"]},{"raw_affiliation_string":"Department of Biological Sciences, National University of Singapore, Singapore","institution_ids":["https://openalex.org/I165932596"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046347871","display_name":"Martti T. Tammi","orcid":null},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]},{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["SE","SG"],"is_corresponding":true,"raw_author_name":"Martti T Tammi","raw_affiliation_strings":["Department of Biochemistry, National University of Singapore, Singapore","Department of Biological Sciences, National University of Singapore, Singapore","Karolinska Institutet, Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, National University of Singapore, Singapore","institution_ids":["https://openalex.org/I165932596"]},{"raw_affiliation_string":"Department of Biological Sciences, National University of Singapore, Singapore","institution_ids":["https://openalex.org/I165932596"]},{"raw_affiliation_string":"Karolinska Institutet, Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden","institution_ids":["https://openalex.org/I28166907"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5046347871"],"corresponding_institution_ids":["https://openalex.org/I165932596","https://openalex.org/I28166907"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":17.0297,"has_fulltext":true,"cited_by_count":609,"citation_normalized_percentile":{"value":0.99405165,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"10","issue":"1","first_page":"80","last_page":"80"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.9901000261306763,"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":0.9901000261306763,"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":0.002300000051036477,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.002199999988079071,"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/copy-number-variation","display_name":"Copy-number variation","score":0.8889386653900146},{"id":"https://openalex.org/keywords/shotgun-sequencing","display_name":"Shotgun sequencing","score":0.6152687072753906},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.5735582709312439},{"id":"https://openalex.org/keywords/comparative-genomic-hybridization","display_name":"Comparative genomic hybridization","score":0.555973470211029},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5404937863349915},{"id":"https://openalex.org/keywords/structural-variation","display_name":"Structural variation","score":0.509157121181488},{"id":"https://openalex.org/keywords/copy-number-analysis","display_name":"Copy number analysis","score":0.4965079426765442},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.47976717352867126},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4774949252605438},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.43208983540534973},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.42405954003334045},{"id":"https://openalex.org/keywords/human-genome","display_name":"Human genome","score":0.4170586168766022},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.40954962372779846},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1644711196422577}],"concepts":[{"id":"https://openalex.org/C120821319","wikidata":"https://www.wikidata.org/wiki/Q1501491","display_name":"Copy-number variation","level":4,"score":0.8889386653900146},{"id":"https://openalex.org/C101985253","wikidata":"https://www.wikidata.org/wiki/Q1073526","display_name":"Shotgun sequencing","level":4,"score":0.6152687072753906},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5735582709312439},{"id":"https://openalex.org/C124942203","wikidata":"https://www.wikidata.org/wiki/Q656638","display_name":"Comparative genomic hybridization","level":4,"score":0.555973470211029},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5404937863349915},{"id":"https://openalex.org/C151020129","wikidata":"https://www.wikidata.org/wiki/Q7625067","display_name":"Structural variation","level":4,"score":0.509157121181488},{"id":"https://openalex.org/C166608930","wikidata":"https://www.wikidata.org/wiki/Q5169175","display_name":"Copy number analysis","level":5,"score":0.4965079426765442},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.47976717352867126},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4774949252605438},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.43208983540534973},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.42405954003334045},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.4170586168766022},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.40954962372779846},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1644711196422577},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"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":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"D018628","descriptor_name":"Gene Dosage","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018628","descriptor_name":"Gene Dosage","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018628","descriptor_name":"Gene Dosage","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-10-80","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-80","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-80","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"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":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19267900","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19267900","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:2667514","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2667514","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":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:scholarbank.nus.edu.sg:10635/100291","is_oa":false,"landing_page_url":"http://scholarbank.nus.edu.sg/handle/10635/100291","pdf_url":null,"source":{"id":"https://openalex.org/S7407052290","display_name":"National University of Singapore","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Scopus","raw_type":"Article"},{"id":"pmh:oai:doaj.org/article:06b8bec29fc3446ca169733c8960bb24","is_oa":false,"landing_page_url":"https://doaj.org/article/06b8bec29fc3446ca169733c8960bb24","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 10, Iss 1, p 80 (2009)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-10-80","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-80","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-80","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"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":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320698","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2035593347.pdf","grobid_xml":"https://content.openalex.org/works/W2035593347.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W1484187172","https://openalex.org/W1976823255","https://openalex.org/W1983253191","https://openalex.org/W1984708728","https://openalex.org/W1989568035","https://openalex.org/W2002875415","https://openalex.org/W2005129098","https://openalex.org/W2022385074","https://openalex.org/W2028079794","https://openalex.org/W2039716761","https://openalex.org/W2045160632","https://openalex.org/W2047765648","https://openalex.org/W2092784580","https://openalex.org/W2096525273","https://openalex.org/W2102877882","https://openalex.org/W2107233609","https://openalex.org/W2113649367","https://openalex.org/W2114752404","https://openalex.org/W2115610250","https://openalex.org/W2116753165","https://openalex.org/W2119923823","https://openalex.org/W2121016876","https://openalex.org/W2121211805","https://openalex.org/W2122232025","https://openalex.org/W2124873881","https://openalex.org/W2128114769","https://openalex.org/W2129795133","https://openalex.org/W2135196291","https://openalex.org/W2136145671","https://openalex.org/W2142642738","https://openalex.org/W2154431984","https://openalex.org/W2155707112","https://openalex.org/W2170828133","https://openalex.org/W2582743722","https://openalex.org/W4239678514"],"related_works":["https://openalex.org/W1963487910","https://openalex.org/W2010401695","https://openalex.org/W2019912140","https://openalex.org/W2001238177","https://openalex.org/W2387464095","https://openalex.org/W2082810381","https://openalex.org/W1542475324","https://openalex.org/W2157986688","https://openalex.org/W2089535743","https://openalex.org/W2111034253"],"abstract_inverted_index":{"BACKGROUND:":[0],"DNA":[1],"copy":[2,45],"number":[3,33,46,84],"variation":[4,47],"(CNV)":[5],"has":[6,31],"been":[7],"recognized":[8],"as":[9],"an":[10],"important":[11],"source":[12],"of":[13,34,71,77,85,90,100,113,118,148],"genetic":[14],"variation.":[15],"Array":[16],"comparative":[17],"genomic":[18],"hybridization":[19],"(aCGH)":[20],"is":[21,54,93],"commonly":[22],"used":[23],"for":[24,75,146],"CNV":[25,149],"detection,":[26],"but":[27],"the":[28,63,69,83,88,91,94,98,104,144],"microarray":[29],"platform":[30],"a":[32,41,57],"inherent":[35],"limitations.":[36],"RESULTS:":[37],"Here,":[38],"we":[39],"describe":[40],"method":[42,53],"to":[43,126],"detect":[44],"using":[48],"shotgun":[49],"sequencing,":[50],"CNV-seq.":[51],"The":[52],"based":[55],"on":[56],"robust":[58],"statistical":[59],"model":[60],"that":[61,82,108],"describes":[62],"complete":[64],"analysis":[65],"procedure":[66],"and":[67,135],"allows":[68],"computation":[70],"essential":[72],"confidence":[73],"values":[74],"detection":[76],"CNV.":[78],"Our":[79],"results":[80,145],"show":[81,128,143],"reads,":[86],"not":[87],"length":[89],"reads":[92],"key":[95],"factor":[96],"determining":[97],"resolution":[99],"detection.":[101],"This":[102],"favors":[103],"next-generation":[105],"sequencing":[106,120],"methods":[107,121],"rapidly":[109],"produce":[110],"large":[111],"amount":[112],"short":[114],"reads.":[115],"CONCLUSION:":[116],"Simulation":[117],"various":[119],"with":[122],"coverage":[123],"between":[124,131,137,150],"0.1x":[125],"8x":[127],"overall":[129],"specificity":[130],"91.7":[132],"-":[133,139],"99.9%,":[134],"sensitivity":[136],"72.2":[138],"96.5%.":[140],"We":[141],"also":[142],"assessment":[147],"two":[151],"individual":[152],"human":[153],"genomes.":[154]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":21},{"year":2024,"cited_by_count":34},{"year":2023,"cited_by_count":25},{"year":2022,"cited_by_count":31},{"year":2021,"cited_by_count":43},{"year":2020,"cited_by_count":38},{"year":2019,"cited_by_count":48},{"year":2018,"cited_by_count":32},{"year":2017,"cited_by_count":42},{"year":2016,"cited_by_count":44},{"year":2015,"cited_by_count":53},{"year":2014,"cited_by_count":57},{"year":2013,"cited_by_count":41},{"year":2012,"cited_by_count":38}],"updated_date":"2026-08-15T07:11:24.734988","created_date":"2025-10-10T00:00:00"}
