SlideCNA: spatial copy number alteration detection from Slide-seq-like spatial transcriptomics data

Diane Zhang

doi:10.1186/s13059-025-03573-y

2025-05-02

Orit Rozenblatt–Rosen

DOI：10.1186/s13059-025-03573-y

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摘要

En 中文

实体瘤在遗传、分子和细胞组成上具有空间异质性，但最近的时空图谱研究大多分别绘制了肿瘤中的遗传和RNA变异。为利用RNA识别拷贝数改变（CNAs）的潜力，我们开发了SlideCNA，一种从稀疏时空转录组学数据中提取CNA信号的计算工具，其分辨率接近单细胞水平。SlideCNA采用表达感知时空分箱方法以克服稀疏性限制，同时保持空间信号以恢复CNA模式。我们在模拟和真实的（转移性）乳腺癌Slide-seq数据上测试了SlideCNA，并展示了其用于空间亚克隆检测的潜力。

Keyword:

Spatial transcriptomics

Slide-seq

Single-cell RNA-seq

Copy number alterations

Cancer

Tumor microenvironment

Clonality

期刊

Genome Biology

IF:

9.4

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6.4K

被引数:

7.3W

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Ludwig Maximilians Univ Munchen

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Brigham and Women's Hospital

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