DNA quality evaluation of formalin-fixed paraffin-embedded heart tissue for DNA methylation array analysis
Abstract Archived formalin-fixed and paraffin-embedded (FFPE) heart tissue from autopsied individuals represents an important resource for investigating the DNA methylation of heart tissue of deceased individuals. The DNA quality of FFPE tissue from autopsies may be decreased, affecting the DNA meth...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-02-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-29120-y |
| _version_ | 1811171758207664128 |
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| author | Mikkel E. Dupont Steffan N. Christiansen Stine B. Jacobsen Marie-Louise Kampmann Kristine B. Olsen Jacob Tfelt-Hansen Jytte Banner Niels Morling Jeppe D. Andersen |
| author_facet | Mikkel E. Dupont Steffan N. Christiansen Stine B. Jacobsen Marie-Louise Kampmann Kristine B. Olsen Jacob Tfelt-Hansen Jytte Banner Niels Morling Jeppe D. Andersen |
| author_sort | Mikkel E. Dupont |
| collection | DOAJ |
| description | Abstract Archived formalin-fixed and paraffin-embedded (FFPE) heart tissue from autopsied individuals represents an important resource for investigating the DNA methylation of heart tissue of deceased individuals. The DNA quality of FFPE tissue from autopsies may be decreased, affecting the DNA methylation measurements. Therefore, inexpensive screening methods for estimating DNA quality are valuable. We investigated the correlation between the DNA quality of archived FFPE heart tissue examined with the Illumina Infinium HD FFPE QC assay (Infinium QC) and Thermo Fisher’s Quantifiler Trio DNA Quantification kit (QuantifilerTrio), respectively, and the amount of usable DNA methylation data as measured by the probe detection rate (probe DR) obtained with the Illumina Infinium MethylationEPIC array. We observed a high correlation (r2 = 0.75; p < 10−11) between the QuantifilerTrio degradation index, DI, and the amount of usable DNA methylation data analysed with SeSAMe, whereas a much weaker correlation was observed between the Infinium QC and SeSAMe probe DR (r2 = 0.17; p < 0.05). Based on the results, QuantifilerTrio DI seems to predict the proportion of usable DNA methylation data analysed with the Illumina Infinium MethylationEPIC array and SeSAMe by a linear model: SeSAMe probe DR = 0.80–log10(DI) × 0.25. |
| first_indexed | 2024-04-10T17:19:20Z |
| format | Article |
| id | doaj.art-5b83f3aed0224b26aa7f0179883e2bc8 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-04-10T17:19:20Z |
| publishDate | 2023-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-5b83f3aed0224b26aa7f0179883e2bc82023-02-05T12:10:25ZengNature PortfolioScientific Reports2045-23222023-02-011311810.1038/s41598-023-29120-yDNA quality evaluation of formalin-fixed paraffin-embedded heart tissue for DNA methylation array analysisMikkel E. Dupont0Steffan N. Christiansen1Stine B. Jacobsen2Marie-Louise Kampmann3Kristine B. Olsen4Jacob Tfelt-Hansen5Jytte Banner6Niels Morling7Jeppe D. Andersen8Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of CopenhagenSection of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of CopenhagenSection of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of CopenhagenSection of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of CopenhagenSection of Forensic Pathology, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of CopenhagenSection of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of CopenhagenSection of Forensic Pathology, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of CopenhagenSection of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of CopenhagenSection of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of CopenhagenAbstract Archived formalin-fixed and paraffin-embedded (FFPE) heart tissue from autopsied individuals represents an important resource for investigating the DNA methylation of heart tissue of deceased individuals. The DNA quality of FFPE tissue from autopsies may be decreased, affecting the DNA methylation measurements. Therefore, inexpensive screening methods for estimating DNA quality are valuable. We investigated the correlation between the DNA quality of archived FFPE heart tissue examined with the Illumina Infinium HD FFPE QC assay (Infinium QC) and Thermo Fisher’s Quantifiler Trio DNA Quantification kit (QuantifilerTrio), respectively, and the amount of usable DNA methylation data as measured by the probe detection rate (probe DR) obtained with the Illumina Infinium MethylationEPIC array. We observed a high correlation (r2 = 0.75; p < 10−11) between the QuantifilerTrio degradation index, DI, and the amount of usable DNA methylation data analysed with SeSAMe, whereas a much weaker correlation was observed between the Infinium QC and SeSAMe probe DR (r2 = 0.17; p < 0.05). Based on the results, QuantifilerTrio DI seems to predict the proportion of usable DNA methylation data analysed with the Illumina Infinium MethylationEPIC array and SeSAMe by a linear model: SeSAMe probe DR = 0.80–log10(DI) × 0.25.https://doi.org/10.1038/s41598-023-29120-y |
| spellingShingle | Mikkel E. Dupont Steffan N. Christiansen Stine B. Jacobsen Marie-Louise Kampmann Kristine B. Olsen Jacob Tfelt-Hansen Jytte Banner Niels Morling Jeppe D. Andersen DNA quality evaluation of formalin-fixed paraffin-embedded heart tissue for DNA methylation array analysis Scientific Reports |
| title | DNA quality evaluation of formalin-fixed paraffin-embedded heart tissue for DNA methylation array analysis |
| title_full | DNA quality evaluation of formalin-fixed paraffin-embedded heart tissue for DNA methylation array analysis |
| title_fullStr | DNA quality evaluation of formalin-fixed paraffin-embedded heart tissue for DNA methylation array analysis |
| title_full_unstemmed | DNA quality evaluation of formalin-fixed paraffin-embedded heart tissue for DNA methylation array analysis |
| title_short | DNA quality evaluation of formalin-fixed paraffin-embedded heart tissue for DNA methylation array analysis |
| title_sort | dna quality evaluation of formalin fixed paraffin embedded heart tissue for dna methylation array analysis |
| url | https://doi.org/10.1038/s41598-023-29120-y |
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