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001     255490
005     20240403131748.0
024 7 _ |a 10.1186/s12859-023-05144-z
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037 _ _ |a DZNE-2023-00291
041 _ _ |a English
082 _ _ |a 610
100 1 _ |a Liebhoff, Anna-Maria
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245 _ _ |a Pathogen detection in RNA-seq data with Pathonoia.
260 _ _ |a Heidelberg
|c 2023
|b Springer
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336 7 _ |a Journal Article
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500 _ _ |a CC BY
520 _ _ |a Bacterial and viral infections may cause or exacerbate various human diseases and to detect microbes in tissue, one method of choice is RNA sequencing. The detection of specific microbes using RNA sequencing offers good sensitivity and specificity, but untargeted approaches suffer from high false positive rates and a lack of sensitivity for lowly abundant organisms.We introduce Pathonoia, an algorithm that detects viruses and bacteria in RNA sequencing data with high precision and recall. Pathonoia first applies an established k-mer based method for species identification and then aggregates this evidence over all reads in a sample. In addition, we provide an easy-to-use analysis framework that highlights potential microbe-host interactions by correlating the microbial to the host gene expression. Pathonoia outperforms state-of-the-art methods in microbial detection specificity, both on in silico and real datasets.Two case studies in human liver and brain show how Pathonoia can support novel hypotheses on microbial infection exacerbating disease. The Python package for Pathonoia sample analysis and a guided analysis Jupyter notebook for bulk RNAseq datasets are available on GitHub.
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650 _ 7 |a Metagenomics
|2 Other
650 _ 7 |a Pathogen detection
|2 Other
650 _ 7 |a RNA sequencing
|2 Other
650 _ 2 |a Humans
|2 MeSH
650 _ 2 |a RNA-Seq
|2 MeSH
650 _ 2 |a Algorithms
|2 MeSH
650 _ 2 |a Sequence Analysis, RNA: methods
|2 MeSH
650 _ 2 |a Base Sequence
|2 MeSH
650 _ 2 |a Bacteria: genetics
|2 MeSH
650 _ 2 |a Metagenomics: methods
|2 MeSH
650 _ 2 |a High-Throughput Nucleotide Sequencing: methods
|2 MeSH
700 1 _ |a Menden, Kevin
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700 1 _ |a Laschtowitz, Alena
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700 1 _ |a Franke, Andre
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700 1 _ |a Schramm, Christoph
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700 1 _ |a Bonn, Stefan
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773 _ _ |a 10.1186/s12859-023-05144-z
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856 4 _ |y OpenAccess
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910 1 _ |a Deutsches Zentrum für Neurodegenerative Erkrankungen
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