A Cost-Effective Saliva-Based Human Epigenetic Clock Using 10 CpG Sites Identified with the Illumina EPIC 850k Array
<b>Background/Objectives:</b> DNA methylation profiles have emerged as robust biomarkers of ageing, leading to the development of “epigenetic clocks” that estimate biological age. Most established clocks (e.g., Horvath’s 353-CpG pan-tissue clock and Hannum’s 71-CpG blood clock) require d...
Saved in:
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2025-06-01
|
| Series: | DNA |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2673-8856/5/2/28 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849431992627625984 |
|---|---|
| author | Christopher Collins James Brown Henry C. Chung |
| author_facet | Christopher Collins James Brown Henry C. Chung |
| author_sort | Christopher Collins |
| collection | DOAJ |
| description | <b>Background/Objectives:</b> DNA methylation profiles have emerged as robust biomarkers of ageing, leading to the development of “epigenetic clocks” that estimate biological age. Most established clocks (e.g., Horvath’s 353-CpG pan-tissue clock and Hannum’s 71-CpG blood clock) require dozens to hundreds of CpG sites. This study presents a novel saliva-specific epigenetic clock built on 10 sites identified from Illumina MethylationEPIC (850 k) array data. <b>Methods</b>: Saliva DNA methylation was analysed from 3408 individuals (age range 15–89 years, 68% male, 32% female, no diagnosed disease) from the Muhdo Health Ltd. dataset (2022–2024), and 10 CpG sites were selected where methylation levels showed the strongest positive correlations with chronological age (Pearson r = 0.48–0.66, <i>p</i> < 1 × 10−20). These CpGs map to genes involved in developmental and metabolic pathways (including <i>ELOVL2</i>, <i>CHGA</i>, <i>OTUD7A</i>, <i>PRLHR</i>, <i>ZYG11A</i>, and <i>GPR158</i>). A linear combination of the 10 methylation sites was used to calculate a “DNA methylation age”. <b>Results</b>: The 10-CpG clock’s predictions were highly correlated with chronological age (r = 0.80, R2 = 0.64), with a mean absolute error of ~5.5 years. Its performance, while slightly less precise than Horvath’s or Hannum’s multi-CpG clocks, is notable given the minimal marker set. It was observed that all 10 clock CpGs undergo age-related hypermethylation. The biological significance of these loci is discussed, along with the potential health and forensic applications of a saliva-based epigenetic age predictor. <b>Conclusions</b>: This study demonstrates that a saliva-specific epigenetic clock using only 10 CpG sites can capture a substantial portion of age-related DNA methylation changes, providing a cost-effective tool for age estimation. |
| format | Article |
| id | doaj-art-a4be647817c544eab6f31564a4b6475e |
| institution | Kabale University |
| issn | 2673-8856 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | DNA |
| spelling | doaj-art-a4be647817c544eab6f31564a4b6475e2025-08-20T03:27:28ZengMDPI AGDNA2673-88562025-06-01522810.3390/dna5020028A Cost-Effective Saliva-Based Human Epigenetic Clock Using 10 CpG Sites Identified with the Illumina EPIC 850k ArrayChristopher Collins0James Brown1Henry C. Chung2Muhdo Health Ltd., Columba House, Adastral Park, Martlesham Heath, Martlesham, Ipswich IP5 3RE, UKMuhdo Health Ltd., Columba House, Adastral Park, Martlesham Heath, Martlesham, Ipswich IP5 3RE, UKSchool of Sport, Rehabilitation and Exercise Sciences (SRES), University of Essex, Colchester CO4 3WA, UK<b>Background/Objectives:</b> DNA methylation profiles have emerged as robust biomarkers of ageing, leading to the development of “epigenetic clocks” that estimate biological age. Most established clocks (e.g., Horvath’s 353-CpG pan-tissue clock and Hannum’s 71-CpG blood clock) require dozens to hundreds of CpG sites. This study presents a novel saliva-specific epigenetic clock built on 10 sites identified from Illumina MethylationEPIC (850 k) array data. <b>Methods</b>: Saliva DNA methylation was analysed from 3408 individuals (age range 15–89 years, 68% male, 32% female, no diagnosed disease) from the Muhdo Health Ltd. dataset (2022–2024), and 10 CpG sites were selected where methylation levels showed the strongest positive correlations with chronological age (Pearson r = 0.48–0.66, <i>p</i> < 1 × 10−20). These CpGs map to genes involved in developmental and metabolic pathways (including <i>ELOVL2</i>, <i>CHGA</i>, <i>OTUD7A</i>, <i>PRLHR</i>, <i>ZYG11A</i>, and <i>GPR158</i>). A linear combination of the 10 methylation sites was used to calculate a “DNA methylation age”. <b>Results</b>: The 10-CpG clock’s predictions were highly correlated with chronological age (r = 0.80, R2 = 0.64), with a mean absolute error of ~5.5 years. Its performance, while slightly less precise than Horvath’s or Hannum’s multi-CpG clocks, is notable given the minimal marker set. It was observed that all 10 clock CpGs undergo age-related hypermethylation. The biological significance of these loci is discussed, along with the potential health and forensic applications of a saliva-based epigenetic age predictor. <b>Conclusions</b>: This study demonstrates that a saliva-specific epigenetic clock using only 10 CpG sites can capture a substantial portion of age-related DNA methylation changes, providing a cost-effective tool for age estimation.https://www.mdpi.com/2673-8856/5/2/28epigeneticsDNA methylationforensicsageing |
| spellingShingle | Christopher Collins James Brown Henry C. Chung A Cost-Effective Saliva-Based Human Epigenetic Clock Using 10 CpG Sites Identified with the Illumina EPIC 850k Array DNA epigenetics DNA methylation forensics ageing |
| title | A Cost-Effective Saliva-Based Human Epigenetic Clock Using 10 CpG Sites Identified with the Illumina EPIC 850k Array |
| title_full | A Cost-Effective Saliva-Based Human Epigenetic Clock Using 10 CpG Sites Identified with the Illumina EPIC 850k Array |
| title_fullStr | A Cost-Effective Saliva-Based Human Epigenetic Clock Using 10 CpG Sites Identified with the Illumina EPIC 850k Array |
| title_full_unstemmed | A Cost-Effective Saliva-Based Human Epigenetic Clock Using 10 CpG Sites Identified with the Illumina EPIC 850k Array |
| title_short | A Cost-Effective Saliva-Based Human Epigenetic Clock Using 10 CpG Sites Identified with the Illumina EPIC 850k Array |
| title_sort | cost effective saliva based human epigenetic clock using 10 cpg sites identified with the illumina epic 850k array |
| topic | epigenetics DNA methylation forensics ageing |
| url | https://www.mdpi.com/2673-8856/5/2/28 |
| work_keys_str_mv | AT christophercollins acosteffectivesalivabasedhumanepigeneticclockusing10cpgsitesidentifiedwiththeilluminaepic850karray AT jamesbrown acosteffectivesalivabasedhumanepigeneticclockusing10cpgsitesidentifiedwiththeilluminaepic850karray AT henrycchung acosteffectivesalivabasedhumanepigeneticclockusing10cpgsitesidentifiedwiththeilluminaepic850karray AT christophercollins costeffectivesalivabasedhumanepigeneticclockusing10cpgsitesidentifiedwiththeilluminaepic850karray AT jamesbrown costeffectivesalivabasedhumanepigeneticclockusing10cpgsitesidentifiedwiththeilluminaepic850karray AT henrycchung costeffectivesalivabasedhumanepigeneticclockusing10cpgsitesidentifiedwiththeilluminaepic850karray |