{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,25]],"date-time":"2025-11-25T23:31:20Z","timestamp":1764113480370,"version":"3.46.0"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2025,10,25]],"date-time":"2025-10-25T00:00:00Z","timestamp":1761350400000},"content-version":"vor","delay-in-days":0,"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":["72293581","72274152","62402376"],"award-info":[{"award-number":["72293581","72274152","62402376"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Shallow whole-genome sequencing (sWGS), a rapid and cost-effective sequencing technology, has gradually been widely adopted for CNV analyses. However, with genome\u2011wide coverage of only 0.1\u20135\u00d7, sWGS data display a pronounced zero\u2011inflation phenomenon\u2014a large fraction of loci has zero sequencing reads. Zero inflation causes read counts to fluctuate by several\u2011fold between adjacent windows. As a result, random upward blips in coverage can be misinterpreted as copy\u2011number gains (false positives), and true deletions often become indistinguishable from pervasive zero\u2011coverage noise. In addition, existing CNV detection tools developed for sWGS data often struggle to adapt across different CNV sizes. These combined effects severely constrain the accuracy of CNV inference.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>To address above challenges, we propose ZIPcnv, a novel CNV detection tool specifically designed for sWGS data. First, we apply a segment sliding window to smooth the raw read depth signal, which transforms the original zero-inflated statistical characteristics into approximately normal distribution characteristics. We then design a statistical process model that robustly detects persistent shifts under high background noise using a cumulative sum strategy, classifying genomic regions into candidate and non-candidate CNV regions. Finally, dynamic sliding windows are used for one-pass detection of CNVs of varying lengths, with window size adapting to the CNV region size. We evaluated the performance of ZIPcnv on simulated data and 190 real whole-genome sequencing samples. Experimental results show that ZIPcnv consistently outperforms currently popular CNV detection tools.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and Implementation<\/jats:title>\n                    <jats:p>The ZIPcnv source code is freely available at https:\/\/github.com\/Nevermore233\/ZIPcnv.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf592","type":"journal-article","created":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T12:25:23Z","timestamp":1761222323000},"source":"Crossref","is-referenced-by-count":0,"title":["ZIPcnv: accurate and efficient inference of copy number variations from shallow whole-genome sequencing"],"prefix":"10.1093","volume":"41","author":[{"given":"Zhengfa","family":"Xue","sequence":"first","affiliation":[{"name":"School of Computer Science and Technology, Faculty of Electronics and Information Engineering, Xi\u2019an Jiaotong University , Xi\u2019an, Shaanxi 710049,","place":["China"]},{"name":"Shaanxi Engineering Research Center of Medical and Health Big Data, Xi\u2019an Jiaotong University , Xi\u2019an, Shaanxi 710049,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9089-3126","authenticated-orcid":false,"given":"Jingyu","family":"Zeng","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genome and Multi-omics Technologies, BGI Research, Beishan Industrial Zone , Shenzhen 518083,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xuwen","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Respiratory Medicine, The Second Affiliated Hospital of Xi\u2019an Jiaotong University , Xi\u2019an, Shaanxi 710003,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiajing","family":"Yuan","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Faculty of Electronics and Information Engineering, Xi\u2019an Jiaotong University , Xi\u2019an, Shaanxi 710049,","place":["China"]},{"name":"Shaanxi Engineering Research Center of Medical and Health Big Data, Xi\u2019an Jiaotong University , Xi\u2019an, Shaanxi 710049,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4875-3488","authenticated-orcid":false,"given":"Tianci","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Faculty of Electronics and Information Engineering, Xi\u2019an Jiaotong University , Xi\u2019an, Shaanxi 710049,","place":["China"]},{"name":"Shaanxi Engineering Research Center of Medical and Health Big Data, Xi\u2019an Jiaotong University , Xi\u2019an, Shaanxi 710049,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xin","family":"Lai","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Faculty of Electronics and Information Engineering, Xi\u2019an Jiaotong University , Xi\u2019an, Shaanxi 710049,","place":["China"]},{"name":"Shaanxi Engineering Research Center of Medical and Health Big Data, Xi\u2019an Jiaotong University , Xi\u2019an, Shaanxi 710049,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lin","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genome and Multi-omics Technologies, BGI Research, Beishan Industrial Zone , Shenzhen 518083,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yu","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genome and Multi-omics Technologies, BGI Research, Beishan Industrial Zone , Shenzhen 518083,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huanhuan","family":"Zhu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genome and Multi-omics Technologies, BGI Research, Beishan Industrial Zone , Shenzhen 518083,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7554-4975","authenticated-orcid":false,"given":"Xin","family":"Jin","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genome and Multi-omics Technologies, BGI Research, Beishan Industrial Zone , Shenzhen 518083,","place":["China"]},{"name":"The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology , Guangzhou 510006,","place":["China"]},{"name":"Shenzhen Key Laboratory of Transomics Biotechnologies, BGI Research, Beishan Industrial Zone, Yantian District , Shenzhen 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