Background Quality control of samples in biobanks has a critical role in ensuring high quality data that is generated in downstream analyses. At the same time, quality control criteria need to be suitable for the specific situation. A cost-effective solution to creating and verifying quality control criteria would be to retrospectively analyse pre-existing data in biobanks. This study aimed at applying this approach to improve quality control criteria for genomic DNA samples used for microarray-based genotyping. Methods The results of post-genotyping data quality control of 34,626 samples were combined with pre-existing spectrophotometric and sample-processing related quality control data from the biobank, as well as retrospectively generated agarose gel electrophoresis results to identify most relevant quality control criteria that could have predicted the genotyping data quality control results of different samples. Results This analysis revealed a significant link between genotyping data quality control failure and the degradation of DNA samples observed in agarose gel electrophoresis. Spectrophotometrically measured A260/A230 ratios were also shown to be predictive of potential DNA degradation issues. Significant increases in DNA concentrations and A260/A280 ratios for samples were shown to be potentially predictive of DNA degradation in specific samples. An additional effect of sample positions on sample release plates and genotyping arrays on genotyping failure rates was identified. Discussion Using sample related data in a biobank plus some quick and inexpensive testing of a subgroup of samples allowed to identify quality issues during handling and processing of samples prior to analysis. The effect of sample positions could potentially be linked to sample evaporation from sample release plates and better sealing of sample release plates during processing could possibly be used to reduce this effect. Conclusion In conclusion, the retrospective quality control and analysis of pre-existing data was shown to be a viable method in improving quality control criteria for DNA samples.
| Datum der Bewilligung | 2019 |
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| Originalsprache | Englisch |
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| Gradverleihende Hochschule | - Medizinische Universität Graz
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| Betreuer/-in | Berthold Huppertz (Betreuer*in) |
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DNA quality control metrics for samples used for genotyping arrays
Smit, S. (Autor/-in). 2019
Studienabschlussarbeit: Abschlussarbeit