Cargando…

DNA quality evaluation of formalin-fixed paraffin-embedded heart tissue for DNA methylation array analysis

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 m...

Descripción completa

Detalles Bibliográficos
Autores principales: 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.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9898234/
https://www.ncbi.nlm.nih.gov/pubmed/36737451
http://dx.doi.org/10.1038/s41598-023-29120-y
_version_ 1784882382658076672
author 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.
author_facet 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.
author_sort Dupont, Mikkel E.
collection PubMed
description 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 (r(2) = 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 (r(2) = 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–log(10)(DI) × 0.25.
format Online
Article
Text
id pubmed-9898234
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher Nature Publishing Group UK
record_format MEDLINE/PubMed
spelling pubmed-98982342023-02-05 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. Sci Rep Article 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 (r(2) = 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 (r(2) = 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–log(10)(DI) × 0.25. Nature Publishing Group UK 2023-02-03 /pmc/articles/PMC9898234/ /pubmed/36737451 http://dx.doi.org/10.1038/s41598-023-29120-y Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
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.
DNA quality evaluation of formalin-fixed paraffin-embedded heart tissue for DNA methylation array analysis
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
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9898234/
https://www.ncbi.nlm.nih.gov/pubmed/36737451
http://dx.doi.org/10.1038/s41598-023-29120-y
work_keys_str_mv AT dupontmikkele dnaqualityevaluationofformalinfixedparaffinembeddedhearttissuefordnamethylationarrayanalysis
AT christiansensteffann dnaqualityevaluationofformalinfixedparaffinembeddedhearttissuefordnamethylationarrayanalysis
AT jacobsenstineb dnaqualityevaluationofformalinfixedparaffinembeddedhearttissuefordnamethylationarrayanalysis
AT kampmannmarielouise dnaqualityevaluationofformalinfixedparaffinembeddedhearttissuefordnamethylationarrayanalysis
AT olsenkristineb dnaqualityevaluationofformalinfixedparaffinembeddedhearttissuefordnamethylationarrayanalysis
AT tfelthansenjacob dnaqualityevaluationofformalinfixedparaffinembeddedhearttissuefordnamethylationarrayanalysis
AT bannerjytte dnaqualityevaluationofformalinfixedparaffinembeddedhearttissuefordnamethylationarrayanalysis
AT morlingniels dnaqualityevaluationofformalinfixedparaffinembeddedhearttissuefordnamethylationarrayanalysis
AT andersenjepped dnaqualityevaluationofformalinfixedparaffinembeddedhearttissuefordnamethylationarrayanalysis