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CoolMPS: evaluation of antibody labeling based massively parallel non-coding RNA sequencing

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·2021·Nucleic Acids Research
DOI 10.1093/nar/gkaa1122PMC PMC7826284
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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.

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Metadata

Authors
Li, Y., Fehlmann, T., Borcherding, A., Drmanac, S., Liu, S., Groeger, L., Xu, C., Callow, M., Villarosa, C., Jorjorian, A., Kern, F., Grammes, N., Meese, E., Jiang, H., Drmanac, R., Ludwig, N., & Keller, A.
Affiliations
  • Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
  • Complete Genomics Incorporated, San Jose, CA 95134, USA
  • Department of Human Genetics, Saarland University, 66421 Homburg, Germany
  • MGI, BGI-Shenzhen, Shenzhen 518083, China
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2020-12-08
Volume
49
Issue
2
Pages
e10-e10
ISSN
  • 0305-1048
  • 1362-4962
DOI
10.1093/nar/gkaa1122
PMC
PMC7826284
Cited by
21
References
1
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (vor)
Funders
  • Saarland University
  • Michael J. Fox Foundation for Parkinson's Research (14446)
  • Complete Genomics

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