期刊
G3-GENES GENOMES GENETICS
卷 11, 期 9, 页码 -出版社
OXFORD UNIV PRESS INC
DOI: 10.1093/g3journal/jkab141
关键词
ALS; transcriptomics; RNA-seq; microbiome; virome
资金
- NIH [NS063964]
- ALS Association (ALSA) [WA1096, 16-IIP-253]
- NINDS [R35NS097273, P01NS084974]
- Mayo Clinic Foundation
- Neuroscience Focused Research Team Mayo Clinic grant
- Association of Frontotemporal Dementia (AFTD)
- Alzheimer's Association-AD Strategic Fund
- Muscular Dystrophy Association [172123]
- ALS Recovery Fund
- Kimmelman Estate
- Department of Defense (Chem-Bio Diagnostics program) [HDTRA-1-18-10032]
This study developed a bioinformatic pipeline to identify potential etiological agents in RNA-seq data, successfully confirming the presence of known and novel viral sequences through testing and application in practical cases.
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.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据