Genome-Wide DNA Methylation Profiles in Whole-Blood and Buccal Samples — Cross-Sectional, Longitudinal, and across Platforms

Austin J. Van Asselt; Jeffrey J. Beck; Casey T. Finnicum; Brandon N. Johnson; Noah Kallsen; Jouke Jan Hottenga; Eco J.C. de Geus; Dorret I. Boomsma; Erik A. Ehli; Jenny van Dongen

doi:10.3390/ijms241914640

Genome-Wide DNA Methylation Profiles in Whole-Blood and Buccal Samples — Cross-Sectional, Longitudinal, and across Platforms

Austin J. Van Asselt, Jeffrey J. Beck, Casey T. Finnicum, Brandon N. Johnson, Noah Kallsen, Jouke Jan Hottenga, Eco J.C. de Geus, Dorret I. Boomsma, Erik A. Ehli, Jenny van Dongen^*

^*Corresponding author for this work

Research output: Contribution to Journal › Article › Academic › peer-review

Abstract

The field of DNA methylation research is rapidly evolving, focusing on disease and phenotype changes over time using methylation measurements from diverse tissue sources and multiple array platforms. Consequently, identifying the extent of longitudinal, inter-tissue, and inter-platform variation in DNA methylation is crucial for future advancement. DNA methylation was measured in 375 individuals, with 197 of those having 2 blood sample measurements ~10 years apart. Whole-blood samples were measured on Illumina Infinium 450K and EPIC methylation arrays, and buccal samples from a subset of 58 participants were measured on EPIC array. The data were analyzed with the aims to examine the correlation between methylation levels in longitudinal blood samples in 197 individuals, examine the correlation between methylation levels in the blood and buccal samples in 58 individuals, and examine the correlation between blood methylation profiles assessed on the EPIC and 450K arrays in 83 individuals. We identified 136,833, 7674, and 96,891 CpGs significantly and strongly correlated (>0.50) longitudinally, across blood and buccal samples as well as array platforms, respectively. A total of 3674 of these CpGs were shared across all three sets. Analysis of these shared CpGs identified previously found associations with aging, ancestry, and 7016 mQTLs as well.

Original language	English
Article number	14640
Pages (from-to)	1-16
Number of pages	16
Journal	International Journal of Molecular Sciences
Volume	24
Issue number	19
Early online date	27 Sept 2023
DOIs	https://doi.org/10.3390/ijms241914640
Publication status	Published - Oct 2023

Bibliographical note

Funding Information:
We acknowledge funding from the Amsterdam Public Health Institute (personalized medicine innovation grant); the Avera Institute, Sioux Falls (USA); the National Institutes of Health (NIH R01 HD042157-01A1, MH081802, and Grand Opportunity grants: 1RC2 MH089951 and 1RC2 MH089995); the Netherlands Organization for Scientific Research (NWO): Netherlands Twin Registry Repository: researching the interplay between genome and environment (NWO-Groot 480-15-001/674); Biobanking and Biomolecular Research Infrastructure (BBMRI–NL, NWO 184.033.111); the BBRMI-NL-financed BIOS Consortium (NWO 184.021.007), Genotype/phenotype database for behavior genetic and genetic epidemiological studies (ZonMw Middelgroot 911-09-032); and large-scale infrastructures X-Omics (184.034.019). DIB acknowledges the Royal Netherlands Academy of Science Professor Award (PAH/6635). AJVA acknowledges the University of South Dakota Wesley H. Parke Research Award.

Publisher Copyright:
© 2023 by the authors.

Funding

We acknowledge funding from the Amsterdam Public Health Institute (personalized medicine innovation grant); the Avera Institute, Sioux Falls (USA); the National Institutes of Health (NIH R01 HD042157-01A1, MH081802, and Grand Opportunity grants: 1RC2 MH089951 and 1RC2 MH089995); the Netherlands Organization for Scientific Research (NWO): Netherlands Twin Registry Repository: researching the interplay between genome and environment (NWO-Groot 480-15-001/674); Biobanking and Biomolecular Research Infrastructure (BBMRI–NL, NWO 184.033.111); the BBRMI-NL-financed BIOS Consortium (NWO 184.021.007), Genotype/phenotype database for behavior genetic and genetic epidemiological studies (ZonMw Middelgroot 911-09-032); and large-scale infrastructures X-Omics (184.034.019). DIB acknowledges the Royal Netherlands Academy of Science Professor Award (PAH/6635). AJVA acknowledges the University of South Dakota Wesley H. Parke Research Award.

Funders	Funder number
Amsterdam Public Health Institute
Avera Institute
BBMRI	184.033.111, 184.021.007
Biobanking and Biomolecular Research Infrastructure
NWO-Groot	480-15-001/674
Koninklijke Nederlandse Akademie van Wetenschappen	PAH/6635
Sioux Falls
National Institutes of Health	1RC2 MH089951, 1RC2 MH089995, MH081802, R01 HD042157-01A1
National Institutes of Health
ZonMw	Middelgroot 911-09-032
ZonMw
Nederlandse Organisatie voor Wetenschappelijk Onderzoek
large-scale infrastructures X-Omics	184.034.019

Keywords

DNA methylation
epigenetics
Illumina microarrays
longitudinal design
platform comparison
tissue comparison

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https://www.mdpi.com/1422-0067/24/19/14640

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Van Asselt, A. J., Beck, J. J., Finnicum, C. T., Johnson, B. N., Kallsen, N., Hottenga, J. J., de Geus, E. J. C., Boomsma, D. I., Ehli, E. A., & van Dongen, J. (2023). Genome-Wide DNA Methylation Profiles in Whole-Blood and Buccal Samples — Cross-Sectional, Longitudinal, and across Platforms. International Journal of Molecular Sciences, 24(19), 1-16. Article 14640. https://doi.org/10.3390/ijms241914640

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abstract = "The field of DNA methylation research is rapidly evolving, focusing on disease and phenotype changes over time using methylation measurements from diverse tissue sources and multiple array platforms. Consequently, identifying the extent of longitudinal, inter-tissue, and inter-platform variation in DNA methylation is crucial for future advancement. DNA methylation was measured in 375 individuals, with 197 of those having 2 blood sample measurements ~10 years apart. Whole-blood samples were measured on Illumina Infinium 450K and EPIC methylation arrays, and buccal samples from a subset of 58 participants were measured on EPIC array. The data were analyzed with the aims to examine the correlation between methylation levels in longitudinal blood samples in 197 individuals, examine the correlation between methylation levels in the blood and buccal samples in 58 individuals, and examine the correlation between blood methylation profiles assessed on the EPIC and 450K arrays in 83 individuals. We identified 136,833, 7674, and 96,891 CpGs significantly and strongly correlated (>0.50) longitudinally, across blood and buccal samples as well as array platforms, respectively. A total of 3674 of these CpGs were shared across all three sets. Analysis of these shared CpGs identified previously found associations with aging, ancestry, and 7016 mQTLs as well.",

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author = "{Van Asselt}, {Austin J.} and Beck, {Jeffrey J.} and Finnicum, {Casey T.} and Johnson, {Brandon N.} and Noah Kallsen and Hottenga, {Jouke Jan} and {de Geus}, {Eco J.C.} and Boomsma, {Dorret I.} and Ehli, {Erik A.} and {van Dongen}, Jenny",

note = "Funding Information: We acknowledge funding from the Amsterdam Public Health Institute (personalized medicine innovation grant); the Avera Institute, Sioux Falls (USA); the National Institutes of Health (NIH R01 HD042157-01A1, MH081802, and Grand Opportunity grants: 1RC2 MH089951 and 1RC2 MH089995); the Netherlands Organization for Scientific Research (NWO): Netherlands Twin Registry Repository: researching the interplay between genome and environment (NWO-Groot 480-15-001/674); Biobanking and Biomolecular Research Infrastructure (BBMRI–NL, NWO 184.033.111); the BBRMI-NL-financed BIOS Consortium (NWO 184.021.007), Genotype/phenotype database for behavior genetic and genetic epidemiological studies (ZonMw Middelgroot 911-09-032); and large-scale infrastructures X-Omics (184.034.019). DIB acknowledges the Royal Netherlands Academy of Science Professor Award (PAH/6635). AJVA acknowledges the University of South Dakota Wesley H. Parke Research Award. Publisher Copyright: {\textcopyright} 2023 by the authors.",

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Van Asselt, AJ, Beck, JJ, Finnicum, CT, Johnson, BN, Kallsen, N, Hottenga, JJ , de Geus, EJC , Boomsma, DI, Ehli, EA & van Dongen, J 2023, 'Genome-Wide DNA Methylation Profiles in Whole-Blood and Buccal Samples — Cross-Sectional, Longitudinal, and across Platforms', International Journal of Molecular Sciences, vol. 24, no. 19, 14640, pp. 1-16. https://doi.org/10.3390/ijms241914640

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AU - Johnson, Brandon N.

AU - Kallsen, Noah

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AU - de Geus, Eco J.C.

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Genome-Wide DNA Methylation Profiles in Whole-Blood and Buccal Samples — Cross-Sectional, Longitudinal, and across Platforms

Abstract

Bibliographical note

Funding

Keywords

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