水母：时空肿瘤演化与克隆动态的整合可视化

Jellyfish: integrative visualization of spatio-temporal tumor evolution and clonal dynamics.

作者信息

Lavikka Kari, Maarala Altti Ilari, Oikkonen Jaana, Hautaniemi Sampsa

机构信息

Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki 00014, Finland.

出版信息

Bioinformatics. 2025 Mar 4;41(3). doi: 10.1093/bioinformatics/btaf091.

DOI:10.1093/bioinformatics/btaf091

PMID:39999015

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11897425/

Abstract

SUMMARY

Spatial and temporal intra-tumor heterogeneity drives tumor evolution and therapy resistance. Existing visualization tools often fail to capture both dimensions simultaneously. To address this, we developed Jellyfish, a tool that integrates phylogenetic and sample trees into a single plot, providing a holistic view of tumor evolution and capturing both spatial and temporal evolution. Available as a JavaScript library and R package, Jellyfish generates interactive visualizations from tumor phylogeny and clonal composition data. We demonstrate its ability to visualize complex subclonal dynamics using data from ovarian high-grade serous carcinoma.

AVAILABILITY AND IMPLEMENTATION

Jellyfish is freely available with MIT license at https://github.com/HautaniemiLab/jellyfish (JavaScript library) and https://github.com/HautaniemiLab/jellyfisher (R package).

摘要

肿瘤内的时空异质性驱动肿瘤进化和治疗抗性。现有的可视化工具常常无法同时捕捉这两个维度。为了解决这个问题，我们开发了Jellyfish，这是一种将系统发育树和样本树整合到单个图中的工具，提供肿瘤进化的整体视图，并捕捉时空进化。Jellyfish作为一个JavaScript库和R包可用，它从肿瘤系统发育和克隆组成数据生成交互式可视化。我们使用来自卵巢高级别浆液性癌的数据展示了其可视化复杂亚克隆动态的能力。