CoolMPS: evaluation of antibody labeling based massively parallel non-coding RNA sequencing. Issue 2 (8th December 2020)

• Record Type: Journal Article
• Authors: Li, Yongping; Fehlmann, Tobias; Borcherding, Adam; Drmanac, Snezana; Liu, Sophie; Groeger, Laura; Xu, Chongjun; Callow, Matthew; Villarosa, Christian; Jorjorian, Alexander; Kern, Fabian; Grammes, Nadja; Meese, Eckart; Jiang, Hui; Drmanac, Radoje; Ludwig, Nicole; Keller, Andreas
• Is Part Of: Nucleic acids research. Volume 49:Issue 2(2021)
• Page Start: e10
• Page End: e10
• Publication Date: 2020-12-08
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkaa1122
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: Results of massive parallel sequencing-by-synthesis vary depending on the sequencing approach. CoolMPS™ is a new sequencing chemistry that incorporates bases by labeled antibodies. To evaluate the performance, we sequenced 240 human non-coding RNA samples (dementia patients and controls) with and without CoolMPS. The Q30 value as indicator of the per base sequencing quality increased from 91.8 to 94%. The higher quality was reached across the whole read length. Likewise, the percentage of reads mapping to the human genome increased from 84.9 to 86.2%. For both technologies, we computed similar distributions between different RNA classes (miRNA, piRNA, tRNA, snoRNA and yRNA) and within the classes. While standard sequencing-by-synthesis allowed to recover more annotated miRNAs, CoolMPS yielded more novel miRNAs. The correlation between the two methods was 0.97. Evaluating the diagnostic performance, we observed lower minimal P -values for CoolMPS (adjusted P -value of 0.0006 versus 0.0004) and larger effect sizes (Cohen's d of 0.878 versus 0.9). Validating 19 miRNAs resulted in a correlation of 0.852 between CoolMPS and reverse transcriptase-quantitative polymerase chain reaction. Comparison to data generated with Illumina technology confirmed a known shift in the overall RNA composition. With CoolMPS we evaluated a novel sequencing-by-synthesis technology showing high performance for the analysis of non-coding RNAs.