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Clocks summary

2022-12-15

Source: vignettes/clocks.Rmd
clocks.Rmd

 

Chronological Age Clocks

 

Tissue Type Array type CpG sites Preddiction Units methylclock References
Horvath Different Tissues Chronological 27K - 450k 353 0-99 Years Years Horvath Horvath (2013)
Hannum Blood Chronological 450k 71 Years Hannum Hannum et al. (2013)
BNN Skin and blood Chronological 450K - EPIC 391 Years BNN Alfonso and Gonzalez (2020)
Horvath’s skin + blood clock Skin and blood Chronological 450K - EPIC 392 Years skinHorvath Horvath et al. (2018)
PedBE Buccal epithelial cells Chronological 84 0-20 Years Years PedBE McEwen et al. (2019)
Wu’s Blood Chronological 27K - 450k 111 Years Wu Wu et al. (2019)
Best Linear Unbiased Prediction (BLUP) Blood and saliva Chronological 450K - EPIC 319607 Years BLUP Zhang et al. (2019)
Elastic Net (EN) Blood and saliva Chronological 450K - EPIC 514 Years EN Zhang et al. (2019)
Neonatal Epigenetic Estimator of age (NEOage)
PMA - 450K Bucal epithelial cells Chronological 450K 409 Post-Menstrual age Weeks NEOaPMA450K Graw et al. (2021)
PMA - EPIC Bucal epithelial cells Chronological EPIC 522 Post-Menstrual age Weeks NEOaPMAEPIC Graw et al. (2021)
PNA - 450K Bucal epithelial cells Chronological 450K 303 Post-Natal age Weeks NEOaPNA450K Graw et al. (2021)
PNA - EPIC Bucal epithelial cells Chronological EPIC 509 Post-Natal age Weeks NEOaPNAEPIC Graw et al. (2021)

 

Chronological Gestational Age Clocks

 

Tissue Type Array type CpG sites Preddiction Units methylclock References
Knight Coord blood Chronological Gestational 27K - 450k 148 Weeks Knight Knight et al. (2016)
Bohlin Coord blood Chronological Gestational 450K 96 Weeks Bohlin Bohlin et al. (2016)
Mayne Placenta Chronological Gestational 27K - 450k 62 Weeks Mayne Mayne et al. (2017)
EPIC Coord blood Chronological Gestational EPIC 176 Years EPIC Haftorn et al. (2021)
Lee
Robust Placnetal clock (RPC) Placenta Chronological Gestational 450K - EPIC 558 Weeks Lee.RPC Lee et al. (2019)
Control placental clock (CPC) Placenta Chronological Gestational 450K - EPIC 536 Weeks Lee.CPC Lee et al. (2019)
Refined RPC Placenta Chronological Gestational 450K - EPIC 396 Weeks Lee.refRPC Lee et al. (2019)

 

Other Biological Age Clocks

 

Tissue Type Array type CpG sites Preddiction Units methylclock References
Levine Blood Other biological 27K - 450k - EPIC 313 Biological Age Years Levine Levine et al. (2018)
Telomere Length Blood Other biological 450K - EPIC 140 Telomere Length Kb TL Lu et al. (2019)

   

Alfonso, Gerardo, and Juan R Gonzalez. 2020. “Bayesian Neural Networks Improve Methylation Age Estimates.” bioRxiv.
Bohlin, Jon, Siri Eldevik Håberg, Per Magnus, Sarah E Reese, Håkon K Gjessing, Maria Christine Magnus, Christine Louise Parr, CM Page, Stephanie J London, and Wenche Nystad. 2016. “Prediction of Gestational Age Based on Genome-Wide Differentially Methylated Regions.” Genome Biology 17 (1): 207.
Graw, Stefan, Marie Camerota, Brian S Carter, Jennifer Helderman, Julie A Hofheimer, Elisabeth C McGowan, Charles R Neal, et al. 2021. “NEOage Clocks-Epigenetic Clocks to Estimate Post-Menstrual and Postnatal Age in Preterm Infants.” Aging (Albany NY) 13 (20): 23527.
Haftorn, Kristine L, Yunsung Lee, William RP Denault, Christian M Page, Haakon E Nustad, Robert Lyle, Håkon K Gjessing, et al. 2021. “An EPIC Predictor of Gestational Age and Its Application to Newborns Conceived by Assisted Reproductive Technologies.” Clinical Epigenetics 13 (1): 1–13.
Hannum, Gregory, Justin Guinney, Ling Zhao, Li Zhang, Guy Hughes, SriniVas Sadda, Brandy Klotzle, et al. 2013. “Genome-Wide Methylation Profiles Reveal Quantitative Views of Human Aging Rates.” Molecular Cell 49 (2): 359–67.
Horvath, Steve. 2013. “DNA Methylation Age of Human Tissues and Cell Types.” Genome Biology 14 (10): 3156.
Horvath, Steve, Junko Oshima, George M Martin, Ake T Lu, Austin Quach, Howard Cohen, Sarah Felton, et al. 2018. “Epigenetic Clock for Skin and Blood Cells Applied to Hutchinson Gilford Progeria Syndrome and Ex Vivo Studies.” Aging (Albany NY) 10 (7): 1758.
Knight, Anna K, Jeffrey M Craig, Christiane Theda, Marie Bækvad-Hansen, Jonas Bybjerg-Grauholm, Christine S Hansen, Mads V Hollegaard, et al. 2016. “An Epigenetic Clock for Gestational Age at Birth Based on Blood Methylation Data.” Genome Biology 17 (1): 206.
Lee, Yunsung, Sanaa Choufani, Rosanna Weksberg, Samantha L Wilson, Victor Yuan, Amber Burt, Carmen Marsit, et al. 2019. “Placental Epigenetic Clocks: Estimating Gestational Age Using Placental DNA Methylation Levels.” Aging (Albany NY) 11 (12): 4238.
Levine, Morgan E, Ake T Lu, Austin Quach, Brian H Chen, Themistocles L Assimes, Stefania Bandinelli, Lifang Hou, et al. 2018. “An Epigenetic Biomarker of Aging for Lifespan and Healthspan.” Aging (Albany NY) 10 (4): 573.
Lu, Ake T, Anne Seeboth, Pei-Chien Tsai, Dianjianyi Sun, Austin Quach, Alex P Reiner, Charles Kooperberg, et al. 2019. “DNA Methylation-Based Estimator of Telomere Length.” Aging (Albany NY) 11 (16): 5895.
Mayne, Benjamin T, Shalem Y Leemaqz, Alicia K Smith, James Breen, Claire T Roberts, and Tina Bianco-Miotto. 2017. “Accelerated Placental Aging in Early Onset Preeclampsia Pregnancies Identified by DNA Methylation.” Epigenomics 9 (3): 279–89.
McEwen, Lisa M, Kieran J O?Donnell, Megan G McGill, Rachel D Edgar, Meaghan J Jones, Julia L MacIsaac, David Tse Shen Lin, et al. 2019. “The PedBE Clock Accurately Estimates DNA Methylation Age in Pediatric Buccal Cells.” Proceedings of the National Academy of Sciences, 201820843.
Wu, Xiaohui, Weidan Chen, Fangqin Lin, Qingsheng Huang, Jiayong Zhong, Huan Gao, Yanyan Song, and Huiying Liang. 2019. “DNA Methylation Profile Is a Quantitative Measure of Biological Aging in Children.” Aging (Albany NY) 11 (22): 10031.
Zhang, Qian, Costanza L Vallerga, Rosie M Walker, Tian Lin, Anjali K Henders, Grant W Montgomery, Ji He, et al. 2019. “Improved Precision of Epigenetic Clock Estimates Across Tissues and Its Implication for Biological Ageing.” Genome Medicine 11 (1): 1–11.