Comprehensive analysis of microbial content in whole-genome sequencing samples from The Cancer Genome Atlas project

IF 14.6 1区 医学 Q1 CELL BIOLOGY
Yuchen Ge, Jennifer Lu, Daniela Puiu, Mahler Revsine, Steven L. Salzberg
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引用次数: 0

Abstract

In recent years, a growing number of publications have reported the presence of microbial species in human tumors and mixtures of microbes that appear to be highly specific to different cancer types. Our recent reanalysis of data from three cancer types revealed that technical errors have caused erroneous reports of numerous microbial species found in sequencing data from The Cancer Genome Atlas (TCGA) project. Here, we have expanded our analysis to cover all 5734 whole-genome sequencing (WGS) datasets currently available from TCGA, covering 25 distinct types of cancer. We analyzed the microbial content using updated computational methods and databases and compared our results to those from two major recent studies that focused on bacteria, viruses, and fungi in cancer. Our results expand upon and reinforce our recent findings, which show that the presence of microbes is far smaller than had been previously reported and that many species identified in TCGA data might not be present at all. As part of this expanded analysis and to help others avoid being misled by flawed data, we have released a dataset that contains detailed read counts for bacteria, viruses, archaea, and fungi detected in all 5734 TCGA samples, which can serve as a public reference for future investigations.
癌症基因组图谱项目全基因组测序样品中微生物含量的综合分析
近年来,越来越多的出版物报道了人类肿瘤中存在的微生物物种和微生物混合物,这些微生物物种似乎对不同类型的癌症具有高度特异性。我们最近对三种癌症类型数据的重新分析显示,技术错误导致了癌症基因组图谱(TCGA)项目测序数据中发现的许多微生物物种的错误报告。在这里,我们扩展了我们的分析,涵盖了TCGA目前提供的所有5734个全基因组测序(WGS)数据集,涵盖了25种不同类型的癌症。我们使用更新的计算方法和数据库分析了微生物含量,并将我们的结果与最近两项主要研究的结果进行了比较,这两项研究的重点是癌症中的细菌、病毒和真菌。我们的研究结果扩展并加强了我们最近的发现,这些发现表明微生物的存在远比以前报道的要小,而且TCGA数据中发现的许多物种可能根本不存在。作为扩展分析的一部分,并帮助其他人避免被有缺陷的数据误导,我们发布了一个数据集,其中包含所有5734个TCGA样本中检测到的细菌,病毒,古菌和真菌的详细读取计数,可作为未来调查的公共参考。
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来源期刊
Science Translational Medicine
Science Translational Medicine CELL BIOLOGY-MEDICINE, RESEARCH & EXPERIMENTAL
CiteScore
26.70
自引率
1.20%
发文量
309
审稿时长
1.7 months
期刊介绍: Science Translational Medicine is an online journal that focuses on publishing research at the intersection of science, engineering, and medicine. The goal of the journal is to promote human health by providing a platform for researchers from various disciplines to communicate their latest advancements in biomedical, translational, and clinical research. The journal aims to address the slow translation of scientific knowledge into effective treatments and health measures. It publishes articles that fill the knowledge gaps between preclinical research and medical applications, with a focus on accelerating the translation of knowledge into new ways of preventing, diagnosing, and treating human diseases. The scope of Science Translational Medicine includes various areas such as cardiovascular disease, immunology/vaccines, metabolism/diabetes/obesity, neuroscience/neurology/psychiatry, cancer, infectious diseases, policy, behavior, bioengineering, chemical genomics/drug discovery, imaging, applied physical sciences, medical nanotechnology, drug delivery, biomarkers, gene therapy/regenerative medicine, toxicology and pharmacokinetics, data mining, cell culture, animal and human studies, medical informatics, and other interdisciplinary approaches to medicine. The target audience of the journal includes researchers and management in academia, government, and the biotechnology and pharmaceutical industries. It is also relevant to physician scientists, regulators, policy makers, investors, business developers, and funding agencies.
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