DNA quality evaluation of formalin-fixed paraffin-embedded heart tissue for DNA methylation array analysis
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DNA quality evaluation of formalin-fixed paraffin-embedded heart tissue for DNA methylation array analysis. / Dupont, Mikkel E.; Christiansen, Steffan N.; Jacobsen, Stine B.; Kampmann, Marie Louise; Olsen, Kristine B.; Tfelt-Hansen, Jacob; Banner, Jytte; Morling, Niels; Andersen, Jeppe D.
In: Scientific Reports, Vol. 13, No. 1, 2004, 2023.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - DNA quality evaluation of formalin-fixed paraffin-embedded heart tissue for DNA methylation array analysis
AU - Dupont, Mikkel E.
AU - Christiansen, Steffan N.
AU - Jacobsen, Stine B.
AU - Kampmann, Marie Louise
AU - Olsen, Kristine B.
AU - Tfelt-Hansen, Jacob
AU - Banner, Jytte
AU - Morling, Niels
AU - Andersen, Jeppe D.
N1 - Funding Information: We thank Medical Laboratory Technician Anja Ladegaard Jorgensen and Laboratory Technician Nadia Jochumsen for laboratory assistance.
PY - 2023
Y1 - 2023
N2 - 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.
AB - 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.
U2 - 10.1038/s41598-023-29120-y
DO - 10.1038/s41598-023-29120-y
M3 - Journal article
C2 - 36737451
AN - SCOPUS:85147366485
VL - 13
JO - Scientific Reports
JF - Scientific Reports
SN - 2045-2322
IS - 1
M1 - 2004
ER -
ID: 336123076