AmpliconSuite: an end-to-end workflow for analyzing focal amplifications in cancer genomes.

IF 28.3 1区生物学 Q1 BIOCHEMICAL RESEARCH METHODS

Nature Methods Pub Date : 2026-10-16 DOI:10.1038/s41592-026-03264-x

Jens Luebeck, Ted Liefeld, Ivy Tsz-Lo Wong, Edwin Huang, Forrest Kim, Bhargavi Dameracharla, Michael Chan, Rohil Ahuja, Kyra Fetter, Dhruv Khatri, Kaiyuan Zhu, Thorin Tabor, Daniel Schreyer, Gino Prasad, Aditi Gnanasekar, Siavash Raeisi Dehkordi, Simone Spandau, Michał Adamaszek, Rishaan Kenkre, Tushar Agashe, Devika Torvi, Mădălina Giurgiu-Kraljič, Soyeon Kim, Hoon Kim, Peter Bailey, Roel G W Verhaak, Viraj Deshpande, Michael Reich, Paul S Mischel, Jill P Mesirov, Vineet Bafna

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引用次数: 0

Abstract

Here we present AmpliconSuite, a toolkit for focal amplification analysis from cancer whole-genome sequencing that identifies extrachromosomal DNA (ecDNA), breakage-fusion-bridges and other amplification modes. Its ecContext module categorizes ecDNA structures to understand formation mechanisms. Validation across 175 metaphase fluorescence in situ hybridization-probed genes in 72 models demonstrated accurate predictions. Analysis of 6,506 patient pan-cancer samples revealed ecDNA-mediated oncogene co-amplification preferences. To democratize data sharing, we created AmpliconRepository, a community-contributable platform, enabling investigation of results across >15,000 publicly hosted samples.

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AmpliconSuite：端到端的工作流程，用于分析癌症基因组中的病灶扩增。

在这里，我们展示了AmpliconSuite，这是一个用于癌症全基因组测序的病灶扩增分析工具包，可识别染色体外DNA (ecDNA)，断裂融合桥和其他扩增模式。它的ecContext模块对ecDNA结构进行分类，以了解形成机制。在72个模型中对175个中期荧光原位杂交探针基因进行了验证，证明了准确的预测。对6506例泛癌患者样本的分析揭示了ecdna介导的癌基因共扩增偏好。为了实现数据共享的民主化，我们创建了AmpliconRepository，这是一个社区贡献的平台，可以对150 000个公共托管样本的结果进行调查。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Nature Methods 生物-生化研究方法

CiteScore

58.70

自引率

1.70%

发文量

326

审稿时长

1 months

期刊介绍： Nature Methods is a monthly journal that focuses on publishing innovative methods and substantial enhancements to fundamental life sciences research techniques. Geared towards a diverse, interdisciplinary readership of researchers in academia and industry engaged in laboratory work, the journal offers new tools for research and emphasizes the immediate practical significance of the featured work. It publishes primary research papers and reviews recent technical and methodological advancements, with a particular interest in primary methods papers relevant to the biological and biomedical sciences. This includes methods rooted in chemistry with practical applications for studying biological problems.