期刊
NUCLEIC ACIDS RESEARCH
卷 49, 期 2, 页码 -出版社
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkaa1122
关键词
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资金
- Saarland University
- Michael J. Fox Foundation for Parkinson's Research [14446]
- Complete Genomics
- Michael J. Fox Foundation
Results show that CoolMPS, a new sequencing chemistry, outperformed standard sequencing-by-synthesis in terms of sequencing quality, read mapping percentage, and discovery of novel miRNAs. There was a high correlation between CoolMPS and standard methods, indicating the reliability of CoolMPS for non-coding RNA analysis.
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 sequencingby-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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