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Reproducibility of the Infinium methylationEPIC BeadChip assay using low DNA amounts

The Infinium MethylationEPIC BeadChip (EPIC) is a reliable method for measuring the DNA methylation of more than 850,000 CpG positions. In clinical and forensic settings, it is critical to be able to work with low DNA amounts without risking reduced reproducibility. We evaluated the EPIC for a range...

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Autores principales: Christiansen, Steffan Noe, Andersen, Jeppe Dyrberg, Kampmann, Marie-Louise, Liu, Jing, Andersen, Mikkel Meyer, Tfelt-Hansen, Jacob, Morling, Niels
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Taylor & Francis 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9621037/
https://www.ncbi.nlm.nih.gov/pubmed/35356867
http://dx.doi.org/10.1080/15592294.2022.2051861
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author Christiansen, Steffan Noe
Andersen, Jeppe Dyrberg
Kampmann, Marie-Louise
Liu, Jing
Andersen, Mikkel Meyer
Tfelt-Hansen, Jacob
Morling, Niels
author_facet Christiansen, Steffan Noe
Andersen, Jeppe Dyrberg
Kampmann, Marie-Louise
Liu, Jing
Andersen, Mikkel Meyer
Tfelt-Hansen, Jacob
Morling, Niels
author_sort Christiansen, Steffan Noe
collection PubMed
description The Infinium MethylationEPIC BeadChip (EPIC) is a reliable method for measuring the DNA methylation of more than 850,000 CpG positions. In clinical and forensic settings, it is critical to be able to work with low DNA amounts without risking reduced reproducibility. We evaluated the EPIC for a range of DNA amounts using two-fold serial dilutions investigated on two different days. While the β-value distributions were generally unaffected by decreasing DNA amounts, the median squared Pearson’s correlation coefficient (R(2)) of between-days β-value comparisons decreased from 0.994 (500 ng DNA) to 0.957 (16 ng DNA). The median standard deviation of the β-values was 0.005 and up to 0.017 (median of medians: 0.014) for β-values around 0.6–0.7. With decreasing amounts of DNA from 500 ng to 16 ng, the percentage of probes with standard deviations ≤ 0.1 decreased from 99.9% to 99.4%. This study showed that high reproducibility results are obtained with DNA amounts in the range 125–500 ng DNA, while DNA amounts equal to 63 ng or below gave less reproducible results.
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spelling pubmed-96210372022-11-01 Reproducibility of the Infinium methylationEPIC BeadChip assay using low DNA amounts Christiansen, Steffan Noe Andersen, Jeppe Dyrberg Kampmann, Marie-Louise Liu, Jing Andersen, Mikkel Meyer Tfelt-Hansen, Jacob Morling, Niels Epigenetics Research Paper The Infinium MethylationEPIC BeadChip (EPIC) is a reliable method for measuring the DNA methylation of more than 850,000 CpG positions. In clinical and forensic settings, it is critical to be able to work with low DNA amounts without risking reduced reproducibility. We evaluated the EPIC for a range of DNA amounts using two-fold serial dilutions investigated on two different days. While the β-value distributions were generally unaffected by decreasing DNA amounts, the median squared Pearson’s correlation coefficient (R(2)) of between-days β-value comparisons decreased from 0.994 (500 ng DNA) to 0.957 (16 ng DNA). The median standard deviation of the β-values was 0.005 and up to 0.017 (median of medians: 0.014) for β-values around 0.6–0.7. With decreasing amounts of DNA from 500 ng to 16 ng, the percentage of probes with standard deviations ≤ 0.1 decreased from 99.9% to 99.4%. This study showed that high reproducibility results are obtained with DNA amounts in the range 125–500 ng DNA, while DNA amounts equal to 63 ng or below gave less reproducible results. Taylor & Francis 2022-03-31 /pmc/articles/PMC9621037/ /pubmed/35356867 http://dx.doi.org/10.1080/15592294.2022.2051861 Text en © 2022 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group. https://creativecommons.org/licenses/by-nc-nd/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives License (http://creativecommons.org/licenses/by-nc-nd/4.0/ (https://creativecommons.org/licenses/by-nc-nd/4.0/) ), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited, and is not altered, transformed, or built upon in any way.
spellingShingle Research Paper
Christiansen, Steffan Noe
Andersen, Jeppe Dyrberg
Kampmann, Marie-Louise
Liu, Jing
Andersen, Mikkel Meyer
Tfelt-Hansen, Jacob
Morling, Niels
Reproducibility of the Infinium methylationEPIC BeadChip assay using low DNA amounts
title Reproducibility of the Infinium methylationEPIC BeadChip assay using low DNA amounts
title_full Reproducibility of the Infinium methylationEPIC BeadChip assay using low DNA amounts
title_fullStr Reproducibility of the Infinium methylationEPIC BeadChip assay using low DNA amounts
title_full_unstemmed Reproducibility of the Infinium methylationEPIC BeadChip assay using low DNA amounts
title_short Reproducibility of the Infinium methylationEPIC BeadChip assay using low DNA amounts
title_sort reproducibility of the infinium methylationepic beadchip assay using low dna amounts
topic Research Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9621037/
https://www.ncbi.nlm.nih.gov/pubmed/35356867
http://dx.doi.org/10.1080/15592294.2022.2051861
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