Unknown

Dataset Information

0

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.

SUBMITTER: Melnick M 

PROVIDER: S-EPMC8661426 | biostudies-literature |

REPOSITORIES: biostudies-literature

Similar Datasets

| S-EPMC7745649 | biostudies-literature
| S-EPMC8044432 | biostudies-literature
| S-EPMC3467745 | biostudies-literature
| S-EPMC3051320 | biostudies-literature
| S-EPMC8796424 | biostudies-literature
2024-03-15 | GSE243114 | GEO
| S-EPMC4972086 | biostudies-literature
| S-EPMC5015939 | biostudies-literature
| S-EPMC10578202 | biostudies-literature
| S-EPMC4401249 | biostudies-literature