Blood-based epigenetic estimators of chronological age in human adults using DNA methylation data from the Illumina MethylationEPIC array
Abstract Background Epigenetic clocks have been recognized for their precise prediction of chronological age, age-related diseases, and all-cause mortality. Existing epigenetic clocks are based on CpGs from the Illumina HumanMethylation450 BeadChip (450 K) which has now been replaced by the latest p...
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BMC
2020-10-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-020-07168-8 |
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| author | Yunsung Lee Kristine L. Haftorn William R. P. Denault Haakon E. Nustad Christian M. Page Robert Lyle Sindre Lee-Ødegård Gunn-Helen Moen Rashmi B. Prasad Leif C. Groop Line Sletner Christine Sommer Maria C. Magnus Håkon K. Gjessing Jennifer R. Harris Per Magnus Siri E. Håberg Astanand Jugessur Jon Bohlin |
| author_facet | Yunsung Lee Kristine L. Haftorn William R. P. Denault Haakon E. Nustad Christian M. Page Robert Lyle Sindre Lee-Ødegård Gunn-Helen Moen Rashmi B. Prasad Leif C. Groop Line Sletner Christine Sommer Maria C. Magnus Håkon K. Gjessing Jennifer R. Harris Per Magnus Siri E. Håberg Astanand Jugessur Jon Bohlin |
| author_sort | Yunsung Lee |
| collection | DOAJ |
| description | Abstract Background Epigenetic clocks have been recognized for their precise prediction of chronological age, age-related diseases, and all-cause mortality. Existing epigenetic clocks are based on CpGs from the Illumina HumanMethylation450 BeadChip (450 K) which has now been replaced by the latest platform, Illumina MethylationEPIC BeadChip (EPIC). Thus, it remains unclear to what extent EPIC contributes to increased precision and accuracy in the prediction of chronological age. Results We developed three blood-based epigenetic clocks for human adults using EPIC-based DNA methylation (DNAm) data from the Norwegian Mother, Father and Child Cohort Study (MoBa) and the Gene Expression Omnibus (GEO) public repository: 1) an Adult Blood-based EPIC Clock (ABEC) trained on DNAm data from MoBa (n = 1592, age-span: 19 to 59 years), 2) an extended ABEC (eABEC) trained on DNAm data from MoBa and GEO (n = 2227, age-span: 18 to 88 years), and 3) a common ABEC (cABEC) trained on the same training set as eABEC but restricted to CpGs common to 450 K and EPIC. Our clocks showed high precision (Pearson correlation between chronological and epigenetic age (r) > 0.94) in independent cohorts, including GSE111165 (n = 15), GSE115278 (n = 108), GSE132203 (n = 795), and the Epigenetics in Pregnancy (EPIPREG) study of the STORK Groruddalen Cohort (n = 470). This high precision is unlikely due to the use of EPIC, but rather due to the large sample size of the training set. Conclusions Our ABECs predicted adults’ chronological age precisely in independent cohorts. As EPIC is now the dominant platform for measuring DNAm, these clocks will be useful in further predictions of chronological age, age-related diseases, and mortality. |
| first_indexed | 2024-12-12T17:38:10Z |
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| id | doaj.art-0615d625d2304aafb5a4fea374fd2938 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-12T17:38:10Z |
| publishDate | 2020-10-01 |
| publisher | BMC |
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| series | BMC Genomics |
| spelling | doaj.art-0615d625d2304aafb5a4fea374fd29382022-12-22T00:17:09ZengBMCBMC Genomics1471-21642020-10-0121111310.1186/s12864-020-07168-8Blood-based epigenetic estimators of chronological age in human adults using DNA methylation data from the Illumina MethylationEPIC arrayYunsung Lee0Kristine L. Haftorn1William R. P. Denault2Haakon E. Nustad3Christian M. Page4Robert Lyle5Sindre Lee-Ødegård6Gunn-Helen Moen7Rashmi B. Prasad8Leif C. Groop9Line Sletner10Christine Sommer11Maria C. Magnus12Håkon K. Gjessing13Jennifer R. Harris14Per Magnus15Siri E. Håberg16Astanand Jugessur17Jon Bohlin18Department of Genetics and Bioinformatics, Norwegian Institute of Public HealthDepartment of Genetics and Bioinformatics, Norwegian Institute of Public HealthDepartment of Genetics and Bioinformatics, Norwegian Institute of Public HealthCentre for Fertility and Health, Norwegian Institute of Public HealthCentre for Fertility and Health, Norwegian Institute of Public HealthCentre for Fertility and Health, Norwegian Institute of Public HealthDepartment of Internal Medicine, Akershus University HospitalInstitute of Clinical Medicine, Faculty of Medicine, University of OsloDepartment of Clinical Sciences, Clinical Research Centre, Lund UniversityDepartment of Clinical Sciences, Clinical Research Centre, Lund UniversityDepartment of Pediatric and Adolescents Medicine, Akershus University HospitalDepartment of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University HospitalCentre for Fertility and Health, Norwegian Institute of Public HealthCentre for Fertility and Health, Norwegian Institute of Public HealthDepartment of Genetics and Bioinformatics, Norwegian Institute of Public HealthCentre for Fertility and Health, Norwegian Institute of Public HealthCentre for Fertility and Health, Norwegian Institute of Public HealthDepartment of Genetics and Bioinformatics, Norwegian Institute of Public HealthCentre for Fertility and Health, Norwegian Institute of Public HealthAbstract Background Epigenetic clocks have been recognized for their precise prediction of chronological age, age-related diseases, and all-cause mortality. Existing epigenetic clocks are based on CpGs from the Illumina HumanMethylation450 BeadChip (450 K) which has now been replaced by the latest platform, Illumina MethylationEPIC BeadChip (EPIC). Thus, it remains unclear to what extent EPIC contributes to increased precision and accuracy in the prediction of chronological age. Results We developed three blood-based epigenetic clocks for human adults using EPIC-based DNA methylation (DNAm) data from the Norwegian Mother, Father and Child Cohort Study (MoBa) and the Gene Expression Omnibus (GEO) public repository: 1) an Adult Blood-based EPIC Clock (ABEC) trained on DNAm data from MoBa (n = 1592, age-span: 19 to 59 years), 2) an extended ABEC (eABEC) trained on DNAm data from MoBa and GEO (n = 2227, age-span: 18 to 88 years), and 3) a common ABEC (cABEC) trained on the same training set as eABEC but restricted to CpGs common to 450 K and EPIC. Our clocks showed high precision (Pearson correlation between chronological and epigenetic age (r) > 0.94) in independent cohorts, including GSE111165 (n = 15), GSE115278 (n = 108), GSE132203 (n = 795), and the Epigenetics in Pregnancy (EPIPREG) study of the STORK Groruddalen Cohort (n = 470). This high precision is unlikely due to the use of EPIC, but rather due to the large sample size of the training set. Conclusions Our ABECs predicted adults’ chronological age precisely in independent cohorts. As EPIC is now the dominant platform for measuring DNAm, these clocks will be useful in further predictions of chronological age, age-related diseases, and mortality.http://link.springer.com/article/10.1186/s12864-020-07168-8DNA methylationEpigenetic ageChronological ageIllumina MethylationEPIC BeadChipMoBa |
| spellingShingle | Yunsung Lee Kristine L. Haftorn William R. P. Denault Haakon E. Nustad Christian M. Page Robert Lyle Sindre Lee-Ødegård Gunn-Helen Moen Rashmi B. Prasad Leif C. Groop Line Sletner Christine Sommer Maria C. Magnus Håkon K. Gjessing Jennifer R. Harris Per Magnus Siri E. Håberg Astanand Jugessur Jon Bohlin Blood-based epigenetic estimators of chronological age in human adults using DNA methylation data from the Illumina MethylationEPIC array BMC Genomics DNA methylation Epigenetic age Chronological age Illumina MethylationEPIC BeadChip MoBa |
| title | Blood-based epigenetic estimators of chronological age in human adults using DNA methylation data from the Illumina MethylationEPIC array |
| title_full | Blood-based epigenetic estimators of chronological age in human adults using DNA methylation data from the Illumina MethylationEPIC array |
| title_fullStr | Blood-based epigenetic estimators of chronological age in human adults using DNA methylation data from the Illumina MethylationEPIC array |
| title_full_unstemmed | Blood-based epigenetic estimators of chronological age in human adults using DNA methylation data from the Illumina MethylationEPIC array |
| title_short | Blood-based epigenetic estimators of chronological age in human adults using DNA methylation data from the Illumina MethylationEPIC array |
| title_sort | blood based epigenetic estimators of chronological age in human adults using dna methylation data from the illumina methylationepic array |
| topic | DNA methylation Epigenetic age Chronological age Illumina MethylationEPIC BeadChip MoBa |
| url | http://link.springer.com/article/10.1186/s12864-020-07168-8 |
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