Abstract
Numerous reports have suggested that infectious agents could play a role in neurodegenerative diseases, but specific etiological agents have not been convincingly demonstrated. To search for candidate agents in an unbiased fashion, we have developed a bioinformatic pipeline that identifies microbial sequences in mammalian RNA-seq data, including sequences with no significant nucleotide similarity hits in GenBank. Effectiveness of the pipeline was tested using publicly available RNA-seq data and in a reconstruction experiment using synthetic data. We then applied this pipeline to a novel RNA-seq dataset generated from a cohort of 120 samples from amyotrophic lateral sclerosis patients and controls, and identified sequences corresponding to known bacteria and viruses, as well as novel virus-like sequences. The presence of these novel virus-like sequences, which were identified in subsets of both patients and controls, were confirmed by quantitative RT-PCR. We believe this pipeline will be a useful tool for the identification of potential etiological agents in the many RNA-seq datasets currently being generated.
Original language | English (US) |
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Article number | jkab141 |
Journal | G3: Genes, Genomes, Genetics |
Volume | 11 |
Issue number | 9 |
DOIs | |
State | Published - 2021 |
Keywords
- ALS
- Microbiome
- RNA-seq
- Transcriptomics
- Virome
ASJC Scopus subject areas
- Molecular Biology
- Genetics
- Genetics(clinical)