Copy number alterations (CNAs) 是人类癌症中基因改变的主要来源，对癌症进展起着重要作用。然而，我们仍然缺乏关于 CNA 的突变过程和特征的全面理解。在这里，我们开发了一种机制不可知的方法，基于不同的片段属性对 CNA 进行分类，这些属性反映了致突变过程的后果，可以从不同类型的数据中提取，包括全基因组测序（WGS）和单核苷酸多态性（SNP）芯片。从2778个全癌症分析的 WGS 样本中提取了14个 CNA 特征，随后使用 10 851个癌症基因组图谱 SNP 芯片数据集进行进一步验证。通过这项研究，揭示了一些新型 CNA 的模式。一些 CNA 特征的活动始终预测癌症患者的预后。本研究提供了一种理解癌症中 CNA 特征的库，可能对癌症的预后、演变和病因产生影响。© 作者 2023。本文由牛津大学出版社发表。

Copy number alterations (CNAs) are a predominant source of genetic alterations in human cancer and play an important role in cancer progression. However comprehensive understanding of the mutational processes and signatures of CNA is still lacking. Here we developed a mechanism-agnostic method to categorize CNA based on various fragment properties, which reflect the consequences of mutagenic processes and can be extracted from different types of data, including whole genome sequencing (WGS) and single nucleotide polymorphism (SNP) array. The 14 signatures of CNA have been extracted from 2778 pan-cancer analysis of whole genomes WGS samples, and further validated with 10 851 the cancer genome atlas SNP array dataset. Novel patterns of CNA have been revealed through this study. The activities of some CNA signatures consistently predict cancer patients' prognosis. This study provides a repertoire for understanding the signatures of CNA in cancer, with potential implications for cancer prognosis, evolution and etiology.© The Author(s) 2023. Published by Oxford University Press.