Major data analysis errors invalidate cancer microbiome findings
| Autor: | Abraham Gihawi, Yuchen Ge, Jennifer Lu, Daniela Puiu, Amanda Xu, Colin S. Cooper, Daniel S. Brewer, Mihaela Pertea, Steven L. Salzberg |
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| Jazyk: | angličtina |
| Rok vydání: | 2023 |
| Předmět: | |
| Zdroj: | mBio, Vol 14, Iss 5 (2023) |
| Druh dokumentu: | article |
| ISSN: | 2150-7511 30353408 |
| DOI: | 10.1128/mbio.01607-23 |
| Popis: | ABSTRACT We re-analyzed the data from a recent large-scale study that reported strong correlations between DNA signatures of microbial organisms and 33 different cancer types and that created machine-learning predictors with near-perfect accuracy at distinguishing among cancers. We found at least two fundamental flaws in the reported data and in the methods: (i) errors in the genome database and the associated computational methods led to millions of false-positive findings of bacterial reads across all samples, largely because most of the sequences identified as bacteria were instead human; and (ii) errors in the transformation of the raw data created an artificial signature, even for microbes with no reads detected, tagging each tumor type with a distinct signal that the machine-learning programs then used to create an apparently accurate classifier. Each of these problems invalidates the results, leading to the conclusion that the microbiome-based classifiers for identifying cancer presented in the study are entirely wrong. These flaws have subsequently affected more than a dozen additional published studies that used the same data and whose results are likely invalid as well. IMPORTANCE Recent reports showing that human cancers have a distinctive microbiome have led to a flurry of papers describing microbial signatures of different cancer types. Many of these reports are based on flawed data that, upon re-analysis, completely overturns the original findings. The re-analysis conducted here shows that most of the microbes originally reported as associated with cancer were not present at all in the samples. The original report of a cancer microbiome and more than a dozen follow-up studies are, therefore, likely to be invalid. |
| Databáze: | Directory of Open Access Journals |
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