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Emiko Udo



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    EP1.09 - Pathology (ID 199)

    • Event: WCLC 2019
    • Type: E-Poster Viewing in the Exhibit Hall
    • Track: Pathology
    • Presentations: 1
    • Now Available
    • Moderators:
    • Coordinates: 9/08/2019, 08:00 - 18:00, Exhibit Hall
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      EP1.09-01 - Suitability of Qubit RNA IQ to Determine the RNA Quality of FFPE Samples in Cancer Genomic Medicine (Now Available) (ID 591)

      08:00 - 18:00  |  Author(s): Emiko Udo

      • Abstract
      • Slides

      Background

      Nucleic acid evaluation of formalin-fixed, paraffin-embedded (FFPE) samples by next-generation sequencing (NGS) is essential in cancer genomic medicine. In this study, our aim was to examine the suitability of the Thermo Fisher Scientific Qubit RNA IQ Assay to evaluate RNA quality by using pigments selectively binding to large or small RNAs, and rapidly measuring fragment percentages with a fluorophotometer.

      Method

      RNA was extracted from FFPE samples (n = 35) prepared in clinical settings. DV200 (low: 30-50%, medium, 50-70%, high: > 70%) and RNA IQ (low-high: 1-10) values, which are recommended as indicators of RNA quality, were determined and the correlation between them was examined. By using NGS analysis to obtain the overall percentage of aligned reads (%) and comparing this to the RNA IQ values (15 samples), the suitability of RNA IQ as a tool for RNA quality evaluation was determined.

      Result

      The correlation coefficient (r) between DV200 and RNA IQ values was 0.72, indicative of a strong correlation. However, a scatter diagram revealed that 4-7 samples used to determine the RNA IQ values accounted for 11.4% of the DV200 values (< 30%) that were not recommended for use as NGS samples. In the scatter diagram showing the overall percentage of aligned reads (%) and the RNA IQ levels, the correlation coefficient between aligned reads (> 50%) and RNA IQ levels > 4 was 0.54, representing a moderate correlation. However, RNA IQ values > 4 accounted for 33.3% (false-positive rate) of the aligned reads (< 50%).

      Conclusion

      NGS analysis demonstrated a high false-positive rate for RNA IQ values. Therefore, further optimization is needed prior to utilizing this method as an indicator of RNA quality for FFPE samples in cancer genomic medicine.

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