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肿瘤亚克隆重建评估标准的确立
作者:小柯机器人 发布时间:2020/1/10 14:38:42

加拿大多伦多大学Paul C. Boutros研究团队取得一项新突破。他们建立了评价肿瘤亚克隆重建的标准。2020年1月9日,《自然—生物技术》在线发表了这项成果。

为了解决肿瘤评判系统存在的问题,研究人员系统地评估了重建肿瘤亚克隆的方法。首先,研究人员阐明了亚克隆重建中的主要算法问题,并建立了评估它们的定量指标。然后,研究人员模拟包含所有已知克隆和亚克隆突变类型的真实肿瘤基因组。最后,研究人员以不同的肿瘤读取深度、肿瘤类型和体细胞变异检测为基准对580个肿瘤重建。该分析为建立分析肿瘤异质性的金标准方法提供了基线。

据介绍,肿瘤DNA测序数据可以通过分析基因组异质性以推断进化动力学的计算方法来解释。越来越多的研究已经使用这些方法将癌症的发展与临床进展和对治疗的反应联系起来。尽管在癌症基因组分析中,肿瘤系统发生的推断已迅速成为标准做法,但仍缺乏评估它们准确性的标准。

附:英文原文

Title: A community effort to create standards for evaluating tumor subclonal reconstruction

Author: Adriana Salcedo, Maxime Tarabichi, Shadrielle Melijah G. Espiritu, Amit G. Deshwar, Matei David, Nathan M. Wilson, Stefan Dentro, Jeff A. Wintersinger, Lydia Y. Liu, Minjeong Ko, Srinivasan Sivanandan, Hongjiu Zhang, Kaiyi Zhu, Tai-Hsien Ou Yang, John M. Chilton, Alex Buchanan, Christopher M. Lalansingh, Christine Png, Catalina V. Anghel, Imaad Umar, Bryan Lo, William Zou, Jared T. Simpson, Joshua M. Stuart, Dimitris Anastassiou, Yuanfang Guan, Adam D. Ewing, Kyle Ellrott, David C. Wedge, Quaid Morris, Peter Van Loo, Paul C. Boutros

Issue&Volume: 2020-01-09

Abstract: Tumor DNA sequencing data can be interpreted by computational methods that analyze genomic heterogeneity to infer evolutionary dynamics. A growing number of studies have used these approaches to link cancer evolution with clinical progression and response to therapy. Although the inference of tumor phylogenies is rapidly becoming standard practice in cancer genome analyses, standards for evaluating them are lacking. To address this need, we systematically assess methods for reconstructing tumor subclonality. First, we elucidate the main algorithmic problems in subclonal reconstruction and develop quantitative metrics for evaluating them. Then we simulate realistic tumor genomes that harbor all known clonal and subclonal mutation types and processes. Finally, we benchmark 580 tumor reconstructions, varying tumor read depth, tumor type and somatic variant detection. Our analysis provides a baseline for the establishment of gold-standard methods to analyze tumor heterogeneity.

DOI: 10.1038/s41587-019-0364-z

Source: https://www.nature.com/articles/s41587-019-0364-z

期刊信息

Nature Biotechnology:《自然—生物技术》,创刊于1996年。隶属于施普林格·自然出版集团,最新IF:31.864
官方网址:https://www.nature.com/nbt/
投稿链接:https://mts-nbt.nature.com/cgi-bin/main.plex