Yuchen Ge, Jennifer Lu, Daniela Puiu, Mahler Revsine, Steven L. Salzberg
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Comprehensive analysis of microbial content in whole-genome sequencing samples from The Cancer Genome Atlas project
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.
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.