MEDALT：通过单细胞拷贝数系谱追踪发现基因。

IF 12.3 1区生物学 Q1 Agricultural and Biological Sciences

Genome Biology Pub Date : 2021-02-23 DOI:10.1186/s13059-021-02291-5

Fang Wang, Qihan Wang, Vakul Mohanty, Shaoheng Liang, Jinzhuang Dou, Jincheng Han, Darlan Conterno Minussi, Ruli Gao, Li Ding, Nicholas Navin, Ken Chen

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引用次数: 0

摘要

我们提出了一种最小事件距离非整倍体世系树（MEDALT）算法，该算法可根据单细胞拷贝数（SCCN）特征推断细胞群的进化历史，还提出了一种名为世系分化分析（LSA）的统计例程，该例程有助于从SCCN世系树中发现与适配性相关的改变和基因。在重建拷贝数系谱方面，MEDALT似乎比系统发生学方法更准确。从 20 名三阴性乳腺癌患者的数据中，我们的方法有效地优先发现了对乳腺癌细胞适应性至关重要的基因，并预测了患者的生存期，包括那些与趋同进化有关的基因。我们研究的源代码可在 https://github.com/KChen-lab/MEDALT 上获取。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

MEDALT: single-cell copy number lineage tracing enabling gene discovery.

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MEDALT: single-cell copy number lineage tracing enabling gene discovery.

We present a Minimal Event Distance Aneuploidy Lineage Tree (MEDALT) algorithm that infers the evolution history of a cell population based on single-cell copy number (SCCN) profiles, and a statistical routine named lineage speciation analysis (LSA), whichty facilitates discovery of fitness-associated alterations and genes from SCCN lineage trees. MEDALT appears more accurate than phylogenetics approaches in reconstructing copy number lineage. From data from 20 triple-negative breast cancer patients, our approaches effectively prioritize genes that are essential for breast cancer cell fitness and predict patient survival, including those implicating convergent evolution.The source code of our study is available at https://github.com/KChen-lab/MEDALT .

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来源期刊

Genome Biology BIOTECHNOLOGY & APPLIED MICROBIOLOGY-GENETICS & HEREDITY

CiteScore

25.50

自引率

3.30%

发文量

审稿时长

14 weeks

期刊介绍： Genome Biology is a leading research journal that focuses on the study of biology and biomedicine from a genomic and post-genomic standpoint. The journal consistently publishes outstanding research across various areas within these fields. With an impressive impact factor of 12.3 (2022), Genome Biology has earned its place as the 3rd highest-ranked research journal in the Genetics and Heredity category, according to Thomson Reuters. Additionally, it is ranked 2nd among research journals in the Biotechnology and Applied Microbiology category. It is important to note that Genome Biology is the top-ranking open access journal in this category. In summary, Genome Biology sets a high standard for scientific publications in the field, showcasing cutting-edge research and earning recognition among its peers.