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来自"癌症基因组图谱"项目的全基因组测序样本中微生物含量的全面分析

Yuchen Ge^1,2, Jennifer Lu^1,3, Daniela Puiu^1,2

¹Center for Computational Biology, Johns Hopkins University, Baltimore, Maryland, United States.

bioRxiv : the preprint server for biology

|July 29, 2024

概括

技术错误导致癌症基因组图谱 (TCGA) 数据中错误识别了微生物. 这项研究重新分析了TCGA全基因组测序数据,发现微生物的数量比以前报告的要少,并确定了许多污染物.

科学领域:

微生物学微生物学
生物信息学是一种生物信息学.
基因组学就是基因组学.

背景情况:

最近的研究报告了人类瘤中特定的微生物物种.
这些发现表明微生物对癌症类型具有高度特异性.
人们对癌症基因组图谱 (TCGA) 数据中微生物检测的准确性表示担忧.

研究的目的:

重新分析TCGA全基因组测序 (WGS) 数据,检测25种癌症类型中的微生物存在.
通过使用最新的方法,验证或反驳以前关于癌症中微生物物种的报道.
为未来关于瘤微生物组的研究提供可靠的数据集.

主要方法:

对5,734个TCGA WGS数据集进行了扩展分析.
利用最新的计算工具和微生物数据库.
与最近两项关于癌症相关微生物的主要研究进行了比较.

主要成果:

证实了以前的发现,TCGA数据中的微生物存在量明显低于报告的水平.
确定了许多以前报告的微生物物种作为污染物或不存在.
在25种癌症类型中检测到比预期的要小得多的微生物特征.

结论:

之前的分析中出现的技术错误使得癌症中微生物的发病率上升.
在TCGA数据中检测到的瘤微生物组,不如以前声称的丰富和特异性.
从TCGA样本中读取微生物计数的公共数据集被发布,以帮助未来的研究和防止数据的误解.

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