{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,4]],"date-time":"2026-11-04T20:41:09Z","timestamp":1793824869133,"version":"4.6.1"},"reference-count":20,"publisher":"Wiley","issue":"1","license":[{"start":{"date-parts":[[2018,11,22]],"date-time":"2018-11-22T00:00:00Z","timestamp":1542844800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003399","name":"Science and Technology Commission of Shanghai Municipality","doi-asserted-by":"publisher","award":["16PJ1406300"],"award-info":[{"award-number":["16PJ1406300"]}],"id":[{"id":"10.13039\/501100003399","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003399","name":"Science and Technology Commission of Shanghai Municipality","doi-asserted-by":"publisher","award":["15410722800"],"award-info":[{"award-number":["15410722800"]}],"id":[{"id":"10.13039\/501100003399","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003399","name":"Science and Technology Commission of Shanghai Municipality","doi-asserted-by":"publisher","award":["16ZR1421700"],"award-info":[{"award-number":["16ZR1421700"]}],"id":[{"id":"10.13039\/501100003399","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Molec Gen &amp;amp; Gen Med"],"published-print":{"date-parts":[[2019,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Background<\/jats:title><jats:p>Targeted gene capture and next\u2010generation sequencing (NGS) has been widely utilized as a robust and cost\u2010effective approach for detecting small variants among a group of disease genes. Copy number variations (CNV) can also be inferred from the read\u2010depth information but the accuracy of CNVs called from panel\u2010based NGS data has not been well evaluated.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Sequencing data were acquired from patients underwent routine clinical targeted panel sequencing testing. Pathogenic CNVs detected from targeted panel sequencing data were evaluated using CNVs generated by two clinical accepted platforms, namely chromosome microarray analysis (CMA) and multiple ligation\u2010dependent probe amplification (MLPA) as benchmarks. CNVkit was used in our study to call CNVs from sequencing data using read\u2010depth information. CMA and MLPA tests were used to confirm and further assess the size and breakpoints of CNVs.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The size of CNVs detected using panel\u2010based NGS data are over 300\u00a0kb. The sizes of CNVs detected are slightly larger (102.3% on average) using the NGS platform than using the CMA platform, and the size accuracy improved as the size of variants increases. The breakpoints of CNVs detected using NGS data are quite close (within 2.3% of margin) to the breakpoints detected by CMA. CNVs on sex chromosomes, however, are less concordant between NGS and CMA platforms.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Copy number variations covering adequate exons on autosomes can be accurately detected using targeted panel sequencing data as using CMA. CNVs detected from sex chromosomes need further evaluation and validation. Except for exon\u2010level deletion\/duplication and CNV on sex chromosome, our data support the use of panel\u2010based NGS data for routine clinical detection of pathogenic CNVs.<\/jats:p><\/jats:sec>","DOI":"10.1002\/mgg3.513","type":"journal-article","created":{"date-parts":[[2018,12,19]],"date-time":"2018-12-19T15:12:24Z","timestamp":1545232344000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":38,"title":["Evaluation of copy number variant detection from panel\u2010based next\u2010generation sequencing data"],"prefix":"10.1002","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4147-5291","authenticated-orcid":false,"given":"Ruen","family":"Yao","sequence":"first","affiliation":[{"name":"Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center Shanghai Jiao Tong University School of Medicine Shanghai China"},{"name":"Institute for Pediatric Translational Medicine, Shanghai Children\u2019s Medical Center Shanghai Jiaotong University School of Medicine Shanghai China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tingting","family":"Yu","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center Shanghai Jiao Tong University School of Medicine Shanghai China"},{"name":"Institute for Pediatric Translational Medicine, Shanghai Children\u2019s Medical Center Shanghai Jiaotong University School of Medicine Shanghai China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanrong","family":"Qing","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center Shanghai Jiao Tong University School of Medicine Shanghai China"},{"name":"Institute for Pediatric Translational Medicine, Shanghai Children\u2019s Medical Center Shanghai Jiaotong University School of Medicine Shanghai China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jian","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center Shanghai Jiao Tong University School of Medicine Shanghai China"},{"name":"Institute for Pediatric Translational Medicine, Shanghai Children\u2019s Medical Center Shanghai Jiaotong University School of Medicine Shanghai China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yiping","family":"Shen","sequence":"additional","affiliation":[{"name":"Division of Genetics and Genomics Boston Children's Hospital, Harvard Medical School Boston Massachusetts"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2018,11,22]]},"reference":[{"key":"e_1_2_7_2_1","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa1311037"},{"key":"e_1_2_7_3_1","doi-asserted-by":"publisher","DOI":"10.1002\/humu.22387"},{"key":"e_1_2_7_4_1","doi-asserted-by":"publisher","DOI":"10.1001\/jamaneurol.2014.1944"},{"key":"e_1_2_7_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2012.08.005"},{"key":"e_1_2_7_6_1","doi-asserted-by":"publisher","DOI":"10.1097\/GIM.0b013e3182217a3a"},{"key":"e_1_2_7_7_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.138115.112"},{"key":"e_1_2_7_8_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp324"},{"key":"e_1_2_7_9_1","doi-asserted-by":"publisher","DOI":"10.1002\/em.21943"},{"key":"e_1_2_7_10_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2010.04.006"},{"key":"e_1_2_7_11_1","doi-asserted-by":"publisher","DOI":"10.1016\/0888-7543(88)90113-9"},{"key":"e_1_2_7_12_1","doi-asserted-by":"publisher","DOI":"10.1002\/pd.4103"},{"key":"e_1_2_7_13_1","doi-asserted-by":"publisher","DOI":"10.1038\/gim.2016.163"},{"key":"e_1_2_7_14_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature05329"},{"key":"e_1_2_7_15_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-15-661"},{"key":"e_1_2_7_16_1","doi-asserted-by":"publisher","DOI":"10.1161\/CIRCGENETICS.116.001573"},{"key":"e_1_2_7_17_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-med-100708-204735"},{"key":"e_1_2_7_18_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1004873"},{"key":"e_1_2_7_19_1","doi-asserted-by":"publisher","DOI":"10.1038\/ejhg.2015.44"},{"key":"e_1_2_7_20_1","doi-asserted-by":"publisher","DOI":"10.1038\/hgv.2014.1"},{"key":"e_1_2_7_21_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.genom.9.081307.164217"}],"container-title":["Molecular Genetics &amp; 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