{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,19]],"date-time":"2026-04-19T01:14:00Z","timestamp":1776561240573,"version":"3.51.2"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2025,3,4]],"date-time":"2025-03-04T00:00:00Z","timestamp":1741046400000},"content-version":"vor","delay-in-days":3,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Zhejiang lab Development of Novel Functional Proteins Based on Databases and Artificial Intelligence","award":["No.117005-AC2106\/002"],"award-info":[{"award-number":["No.117005-AC2106\/002"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["No. 31871332"],"award-info":[{"award-number":["No. 31871332"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Copy number alterations (CNAs) are an important type of genomic variation which play a crucial role in the initiation and progression of cancer. With the explosion of single-cell RNA sequencing (scRNA-seq), several computational methods have been developed to infer CNAs from scRNA-seq studies. However, to date, no independent studies have comprehensively benchmarked their performance. Herein, we evaluated five state-of-the-art methods based on their performance in tumor versus normal cell classification; CNAs profile accuracy, tumor subclone inference, and aneuploidy identification in non-malignant cells. Our results showed that Numbat outperformed others across most evaluation criteria, while CopyKAT excelled in scenarios when expression matrix alone was used as input. In specific tasks, SCEVAN showed the best performance in clonal breakpoint detection and Numbat showed high sensitivity in copy number neutral LOH (cnLOH) detection. Additionally, we investigated how referencing settings, inclusion of tumor microenvironment cells, tumor type, and tumor purity impact the performance of these tools. This study provides a valuable guideline for researchers in selecting the appropriate methods for their datasets.<\/jats:p>","DOI":"10.1093\/bib\/bbaf076","type":"journal-article","created":{"date-parts":[[2025,2,11]],"date-time":"2025-02-11T23:18:40Z","timestamp":1739315920000},"source":"Crossref","is-referenced-by-count":8,"title":["Benchmarking copy number aberrations inference tools using single-cell multi-omics datasets"],"prefix":"10.1093","volume":"26","author":[{"given":"Minfang","family":"Song","sequence":"first","affiliation":[{"name":"Research Center for Life Sciences Computing, Zhejiang Lab , Kechuang Avenue, Zhongtai Sub-District, Yuhang District, Hangzhou, Zhejiang 311121 ,","place":["China"]},{"name":"School of Life Science and Technology, ShanghaiTech University , Haike Road, Pudong New District, Shanghai 201210 ,","place":["China"]},{"name":"Shanghai Clinical Research and Trial Center , Keyuan Road, Pudong New District, Shanghai , 201210,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shuai","family":"Ma","sequence":"additional","affiliation":[{"name":"School of Life Science and Technology, ShanghaiTech University , Haike Road, Pudong New District, Shanghai 201210 ,","place":["China"]},{"name":"Shanghai Clinical Research and Trial Center , Keyuan Road, Pudong New District, Shanghai , 201210,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gong","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Life Science and Technology, ShanghaiTech University , Haike Road, Pudong New District, Shanghai 201210 ,","place":["China"]},{"name":"Shanghai Clinical Research and Trial Center , Keyuan Road, Pudong New District, Shanghai , 201210,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yukun","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Life Science and Technology, ShanghaiTech University , Haike Road, Pudong New District, Shanghai 201210 ,","place":["China"]},{"name":"Shanghai Clinical Research and Trial Center , Keyuan Road, Pudong New District, Shanghai , 201210,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhenzhen","family":"Yang","sequence":"additional","affiliation":[{"name":"Yazhouwan National Laboratory , Yazhou Bay Science and Technology City, Yazhou District, Sanya, Hainan Province 572025 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bin","family":"Xie","sequence":"additional","affiliation":[{"name":"Research Center for Life Sciences Computing, Zhejiang Lab , Kechuang Avenue, Zhongtai Sub-District, Yuhang District, Hangzhou, Zhejiang 311121 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tongkun","family":"Guo","sequence":"additional","affiliation":[{"name":"Research Center for Life Sciences Computing, Zhejiang Lab , Kechuang Avenue, Zhongtai Sub-District, Yuhang District, Hangzhou, Zhejiang 311121 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xingxu","family":"Huang","sequence":"additional","affiliation":[{"name":"Research Center for Life Sciences Computing, Zhejiang Lab , Kechuang Avenue, Zhongtai Sub-District, Yuhang District, Hangzhou, Zhejiang 311121 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2104-6828","authenticated-orcid":false,"given":"Liye","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Life Science and Technology, ShanghaiTech University , Haike Road, Pudong New District, Shanghai 201210 ,","place":["China"]},{"name":"Shanghai Clinical Research and Trial Center , Keyuan Road, Pudong New District, Shanghai , 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