https://www.pnas.org/content/116/43/21350Transcriptomic analysis of human endogenous retroviruses in systemic lupus erythematosus
Endogenous retroviruses (ERVs) are integrated retroviral elements within the human genome. Tokuyama et al. (1) recently published a computational tool, “ERVmap,” to analyze genome-wide, locus-specific expression of human ERVs. The authors found increased expression of 124 ERV loci in patients with systemic lupus erythematosus (SLE), compared to controls, and 0 down-regulated loci. In contrast, our reanalysis of their data using a Bayesian reassignment algorithm, Telescope (2), detected only 23 ERV locations with significant differential expression (DE), including 4 loci with significantly lower expression. We found that the differences between the results could be due to methodological aspects of their analysis, including alignment ambiguity, ERV annotation, and failure to account for sequencing platform as a source of variance (3).
