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Updated: Sep 2, 2025
Assessment of DNA Contamination in RNA Samples Based on Ribosomal DNA
Published on: January 22, 2018
Genes expressed at low levels raise false discovery rates in RNA samples contaminated with genomic DNA
Xiangnan Li1, Peipei Zhang2, Haijian Wang3
1Ministry of Education Key Laboratory of Contemporary Anthropology and Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China.
Background:
RNA preparations contaminated with genomic DNA (gDNA) are frequently disregarded by RNA-seq studies. Such contamination may generate false results; however, their effect on the outcomes of RNA-seq analyses is unknown. To address this gap in our knowledge, here we added different concentrations of gDNA to total RNA preparations and subjected them to RNA-seq analysis.
Results:
We found that the contaminating gDNA altered the quantification of transcripts at relatively high concentrations. Differentially expressed genes (DEGs) resulting from gDNA contamination may therefore contribute to higher rates of false enrichment of pathways compared with analogous samples lacking numerous DEGs. A strategy was developed to correct gene expression levels in gDNA-contaminated RNA samples, which assessed the magnitude of contamination to improve the reliability of the results.
Conclusions:
Our study indicates that caution must be exercised when interpreting results associated with low-abundance transcripts. The data provided here will likely serve as a valuable resource to evaluate the influence of gDNA contamination on RNA-seq analysis, particularly related to the detection of putative novel gene elements.
