{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,9]],"date-time":"2026-02-09T07:26:36Z","timestamp":1770621996087,"version":"3.49.0"},"reference-count":56,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2026,1,20]],"date-time":"2026-01-20T00:00:00Z","timestamp":1768867200000},"content-version":"vor","delay-in-days":1480,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["W2512102"],"award-info":[{"award-number":["W2512102"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82371552"],"award-info":[{"award-number":["82371552"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Central South University Research Programme of Advanced Interdisciplinary Study","award":["2023QYJC010"],"award-info":[{"award-number":["2023QYJC010"]}]},{"DOI":"10.13039\/501100004761","name":"Natural Science Foundation of Hunan Province, China","doi-asserted-by":"crossref","award":["2023JJ30975"],"award-info":[{"award-number":["2023JJ30975"]}],"id":[{"id":"10.13039\/501100004761","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>DNA copy number variations (CNVs) exert a profound impact on major genetic disorders in humans. Although multiple sequencing technologies have become the first line of molecular diagnosis for CNVs, existing tools are unable to resolve the pathogenicity of CNVs directly from raw sequencing data.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We developed CNVSeeker, a one-stop and easy-to-use pipeline that provides comprehensive analysis from raw sequencing data to variant interpretation reports, and supports multiple types of sequencing data including short-read data such as whole genome sequencing data and whole exome sequencing data, and long-read sequencing data from Pacific Biosciences HiFi platform or Oxford Nanopore Technologies platform. Through extensive benchmarking, CNVSeeker demonstrated comparable enhancement over the state-of-the-art methods for CNV calling. Moreover, CNVSeeker enables significantly precise variant classification with an accuracy of \u223c87%. By applying CNVSeeker to 1946 individuals with autism spectrum disorder (ASD), a total of 133 ASD-associated CNVs in 122 patients were identified, yielding a diagnostic yield of \u223c6.3%. Additionally, we have also provided a user-friendly webserver for intuitive visualization of results. This study highlights the potential of CNVSeeker to benefit clinicians and geneticists with limited bioinformatic skill by aiding them interpret CNVs directly from various types of raw sequencing data for auxiliary disease diagnosis.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The web server is freely available at https:\/\/genemed.tech\/cnvseeker and the open-source code can be found at https:\/\/github.com\/lovelycatZ\/CNVSeeker.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag034","type":"journal-article","created":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T12:49:11Z","timestamp":1768481351000},"source":"Crossref","is-referenced-by-count":0,"title":["Enhancing interpretation of clinical disease-associated copy number variations from multiple sequencing strategies with CNVSeeker"],"prefix":"10.1093","volume":"42","author":[{"given":"Xudong","family":"Xiang","sequence":"first","affiliation":[{"name":"Department of Geriatrics, National Clinical Research Centre for Geriatric Disorders, Xiangya Hospital & Centre for Medical Genetics, School of Life Sciences, Central South University , Changsha, Hunan 410008,","place":["China"]}]},{"given":"Xinxin","family":"Mao","sequence":"additional","affiliation":[{"name":"Department of Geriatrics, National Clinical Research Centre for Geriatric Disorders, Xiangya Hospital & Centre for Medical Genetics, School of Life Sciences, Central South University , Changsha, Hunan 410008,","place":["China"]}]},{"given":"Tengfei","family":"Luo","sequence":"additional","affiliation":[{"name":"The Central Laboratory of Birth Defects Prevention and Control & Ningbo Key Laboratory of Genomic Medicine and Birth Defects Prevention, The Affiliated Women and Children\u2019s Hospital, Ningbo University , Ningbo 315000,","place":["China"]}]},{"given":"Chenbin","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Geriatrics, National Clinical Research Centre for Geriatric Disorders, Xiangya Hospital & Centre for Medical Genetics, School of Life Sciences, Central South University , Changsha, Hunan 410008,","place":["China"]}]},{"given":"Bozhao","family":"Li","sequence":"additional","affiliation":[{"name":"School of Computer Science and Artificial Intelligence, Hunan University of Technology , Zhuzhou, Hunan 412007,","place":["China"]}]},{"given":"Pei","family":"Yu","sequence":"additional","affiliation":[{"name":"Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University , Changsha, Hunan 410008,","place":["China"]}]},{"given":"Yu","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Geriatrics, National Clinical Research Centre for Geriatric Disorders, Xiangya Hospital & Centre for Medical Genetics, School of Life Sciences, Central South University , Changsha, Hunan 410008,","place":["China"]}]},{"given":"Dai","family":"Wu","sequence":"additional","affiliation":[{"name":"Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University , Changsha, Hunan 410008,","place":["China"]}]},{"given":"Yijing","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Geriatrics, National Clinical Research Centre for Geriatric Disorders, Xiangya Hospital & Centre for Medical Genetics, School of Life Sciences, Central South University , Changsha, Hunan 410008,","place":["China"]},{"name":"Bioinformatics Center, Xiangya Hospital & Furong Laboratory, Central South University , Changsha, Hunan 410008,","place":["China"]}]},{"given":"Qiao","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of Geriatrics, National Clinical Research Centre for Geriatric Disorders, Xiangya Hospital & Centre for Medical Genetics, School of Life Sciences, Central South University , Changsha, Hunan 410008,","place":["China"]},{"name":"Bioinformatics Center, Xiangya Hospital & Furong Laboratory, Central South University , Changsha, Hunan 410008,","place":["China"]}]},{"given":"Yixiao","family":"Zhu","sequence":"additional","affiliation":[{"name":"Department of Geriatrics, National Clinical Research Centre for Geriatric Disorders, Xiangya Hospital & Centre for Medical Genetics, School of Life Sciences, Central South University , Changsha, Hunan 410008,","place":["China"]},{"name":"Bioinformatics Center, Xiangya Hospital & Furong Laboratory, Central South University , Changsha, Hunan 410008,","place":["China"]}]},{"given":"Bin","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Geriatrics, National Clinical Research Centre for Geriatric Disorders, Xiangya Hospital & Centre for Medical Genetics, School of Life Sciences, Central South University , Changsha, Hunan 410008,","place":["China"]},{"name":"Bioinformatics Center, Xiangya Hospital & Furong Laboratory, Central South University , Changsha, Hunan 410008,","place":["China"]},{"name":"Department of Neurology, Xiangya Hospital, Central South University , Changsha, Hunan 410008,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8090-6002","authenticated-orcid":false,"given":"Kun","family":"Xia","sequence":"additional","affiliation":[{"name":"Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University , Changsha, Hunan 410008,","place":["China"]}]},{"given":"Guihu","family":"Zhao","sequence":"additional","affiliation":[{"name":"Department of Geriatrics, National Clinical Research Centre for Geriatric Disorders, Xiangya Hospital & Centre for Medical Genetics, School of Life Sciences, Central South University , Changsha, Hunan 410008,","place":["China"]},{"name":"Bioinformatics Center, Xiangya Hospital & Furong Laboratory, Central South University , Changsha, Hunan 410008,","place":["China"]},{"name":"Department of Neurology, Xiangya Hospital, Central South University , Changsha, Hunan 410008,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3335-9303","authenticated-orcid":false,"given":"Jinchen","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Geriatrics, National Clinical Research Centre for Geriatric Disorders, Xiangya Hospital & Centre for Medical Genetics, School of Life Sciences, Central South University , Changsha, Hunan 410008,","place":["China"]},{"name":"Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University , Changsha, Hunan 410008,","place":["China"]},{"name":"Bioinformatics Center, Xiangya Hospital & Furong Laboratory, Central South University , Changsha, Hunan 410008,","place":["China"]},{"name":"Department of Neurology, Xiangya Hospital, Central South University , Changsha, Hunan 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