Patterns and variations of copy number alterations in acute myeloid leukemia: insights from the LeukAtlas database.

Feb 03, 2025

Experts: Yanxun Su,Zhenxian Han,Yutong Ji,Anqi Liu,Dong Zou,Lina Yan,Dan Liu,Zhang Zhang,Qian-Fei Wang

Recent pan-cancer analysis revealed the global pattern and potential aetiologies of copy number variation signatures in human cancers, particularly those derived from non-hematopoietic tissues. In sharp contrast, the generally low CNV burden in leukemia leaves the CNV landscape and variations largely unexplored, impeding understanding of CNV in leukemia development. Through a comprehensive compilation of public datasets, we constructed LeukAtlas ( https://ngdc.cncb.ac.cn/leukemia ), a user-friendly database encompassing 12,597 CNVs from 1446 AML samples across diverse subtypes and age groups, providing tools for multidimensional CNV analysis. Our analyses suggested the CNV levels significantly varied among AML patients. We discovered two previously unknown CNV patterns in adult AML patients, dominated by segmental LOH and/or minor gain, which have been shown to be associated with chromosomal instability in solid tumors. Additionally, we defined two potential new AML subgroups based on CNVs status, providing new stratification markers within the existing karyotype framework. Representing the most extensive CNV collection in AML, LeukAtlas is a valuable resource for exploring the role of CNVs in the pathogenesis and prognosis stratification of leukemia. Interrogation of this database uncovers novel subclasses with unique CNV profiles and reveals heterogeneous CNV patterns in AML, demonstrating the potential role of chromosomal instability in AML progression.
© 2025. The Author(s), under exclusive licence to Springer Nature Limited.

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ABOUT THE EXPERTS

Yanxun Su,Zhenxian Han,Yutong Ji,Anqi Liu,Dong Zou,Lina Yan,Dan Liu,Zhang Zhang,Qian-Fei Wang

Yanxun Su

China National Center for Bioinformation, 100101, Beijing, China.

Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, China.

University of Chinese Academy of Sciences, 100049, Beijing, China.

Zhenxian Han

China National Center for Bioinformation, 100101, Beijing, China.

Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, China.

National Genomics Data Center, China National Center for Bioinformation, 100101, Beijing, China.

Yutong Ji

China National Center for Bioinformation, 100101, Beijing, China.

Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, China.

University of Chinese Academy of Sciences, 100049, Beijing, China.

Anqi Liu

China National Center for Bioinformation, 100101, Beijing, China.

Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, China.

University of Chinese Academy of Sciences, 100049, Beijing, China.

Dong Zou

China National Center for Bioinformation, 100101, Beijing, China.

Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, China.

National Genomics Data Center, China National Center for Bioinformation, 100101, Beijing, China.

Lina Yan

China National Center for Bioinformation, 100101, Beijing, China.

Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, China.

University of Chinese Academy of Sciences, 100049, Beijing, China.

Dan Liu

China National Center for Bioinformation, 100101, Beijing, China.

Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, China.

University of Chinese Academy of Sciences, 100049, Beijing, China.

Zhang Zhang

China National Center for Bioinformation, 100101, Beijing, China. zhangzhang@big.ac.cn.

Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, China. zhangzhang@big.ac.cn.

University of Chinese Academy of Sciences, 100049, Beijing, China. zhangzhang@big.ac.cn.

National Genomics Data Center, China National Center for Bioinformation, 100101, Beijing, China. zhangzhang@big.ac.cn.

Qian-Fei Wang

China National Center for Bioinformation, 100101, Beijing, China. wangqf@big.ac.cn.

Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, China. wangqf@big.ac.cn.

University of Chinese Academy of Sciences, 100049, Beijing, China. wangqf@big.ac.cn.