A Comparative Study of Three Nucleic Acid Integrity Assay Systems
- 1 December 2023
- journal article
- research article
- Published by Mary Ann Liebert Inc in Biopreservation and Biobanking
- Vol. 21 (6), 624-630
- https://doi.org/10.1089/bio.2022.0171
Abstract
Background: The measurement of nucleic acid quality, especially the analysis of integrity, is a key step for many downstream experiments in biomedical research and quality control of biomaterials. General gel electrophoresis is a traditional method for nucleic acid integrity analysis. Currently, more electrophoresis techniques are becoming standardized and automated operations with higher precision. In this study, we have evaluated the comparability and bias of the outcomes from three commercial assay systems. Methods: Seventy-two deoxyribonucleic acid (DNA) and 67 ribonucleic acid (RNA) samples were selected for methodological comparison among different systems. The DNA Quality Number (DQN) and RNA Quality Number (RQN) of BIOptic Qsep400, DNA Quality Score (DQS) and RNA Quality Score (RQS) of PerkinElmer Labchip GX Touch HT were separately compared with the DNA Integrity Number (DIN) and RNA Integrity Number (RINe) of the Agilent 4200 TapeStation according to Clinical and Laboratory Standards Institute (CLSI) guideline (EP09-A3). Results: The biases of the mean estimated between DQN and DIN, DQS and DIN both exceeded the acceptance criteria. The Passing–Bablok regression analysis between DQN and DIN, and the Deming regression analysis between DQS and DIN, showed the biases were both within the acceptance criteria, and the bias between DQN and DIN was smaller. For the comparisons of RQN and RINe, RQS and RINe, the regression analyses revealed the biases were both within the acceptance criteria. The bias of the mean estimated between RQS and RINe was outside of the acceptance criteria. Conclusions: There was a good comparability in nucleic acid integrity detection between BIOptic Qsep400 and PerkinElmer Labchip GX Touch HT with the Agilent 4200 TapeStation. However, the bias and linear correlations require more attention between systems.Keywords
This publication has 12 references indexed in Scilit:
- Recent advances in capillary electrophoresis‐mass spectrometry: Instrumentation, methodology and applicationsElectrophoresis, 2018
- Quality Assurance After a Natural Disaster: Lessons from Hurricane SandyBiopreservation and Biobanking, 2018
- Next-Generation Sequencing of RNA and DNA Isolated from Paired Fresh-Frozen and Formalin-Fixed Paraffin-Embedded Samples of Human Cancer and Normal TissuePLOS ONE, 2014
- Quality Assessment of Biobanked Nucleic Acid Extracts for Downstream Molecular AnalysisBiopreservation and Biobanking, 2012
- Agarose Gel Electrophoresis for the Separation of DNA FragmentsJournal of Visualized Experiments, 2012
- Preanalytical Procedures for DNA Studies: The Experience of the Interinstitutional Multidisciplinary BioBank (BioBIM)Biopreservation and Biobanking, 2011
- NanoDrop Microvolume Quantitation of Nucleic AcidsJournal of Visualized Experiments, 2010
- Capillary Electrophoresis in BioanalysisAnalytical Chemistry, 2008
- The RIN: an RNA integrity number for assigning integrity values to RNA measurementsBMC Molecular Biology, 2006
- Quality control for nucleic acid tests: common ground and special issuesJournal of Clinical Virology, 2001