Application of a bioinformatic pipeline to RNA-seq data identifies novel virus-like sequence in human blood
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.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Apr 29, 2021
- Source ID
- 10.1093/g3journal/jkab141
Entities
People
- Björn Oskarsson
- Christopher D. Link
- Joanne Wuu
- Leonard Petrucelli
- Marko Melnick
- Mercedes Prudencio
- Michael Benatar
- Patrick Gonzales
- Robin D. Dowell
- Thomas J Larocca
- Yuping Song
Organizations
- ALS Association
- ALS Recovery Fund
- Colorado State University
- Mayo Clinic
- Muscular Dystrophy Association
- National Institute of Neurological Disorders and Stroke
- National Institutes of Health
- United States Department of Defense
- University of Colorado
- University of Miami