TY  - JOUR
AU  - Saßmannshausen, Zoe
AU  - Blank, Lisa Marie
AU  - Solé-Boldo, Llorenç
AU  - Lyko, Frank
AU  - Raddatz, Günter
TI  - estiMAge: development of a DNA methylation clock to estimate the methylation age of single cells.
JO  - Bioinformatics advances
VL  - 5
IS  - 1
SN  - 2635-0041
CY  - Oxford
PB  - Oxford University Press
M1  - DKFZ-2025-00236
SP  - vbaf005
PY  - 2025
N1  - #EA:A130#LA:A130# / DKFZ-ZMBH Alliance
AB  - Since their introduction about 10 years ago, methylation clocks have provided broad insights into the biological age of different species, tissues, and in the context of several diseases or aging. However, their application to single-cell methylation data remains a major challenge, because of the inherent sparsity of such data, as many CpG sites are not covered. A methylation clock applicable on single-cell level could help to further disentangle the processes that drive the ticking of epigenetic clocks.We have developed estiMAge ('estimation of Methylation Age'), a framework that exploits redundancy in methylation data to substitute missing CpGs of trained methylation clocks in single cells. Using Euclidean distance as a measure of similarity, we determine which CpGs covary with the required CpG sites of an epigenetic clock and can be used as surrogates for clock CpGs not covered in single-cell experiments. estiMAge is thus a tool that can be applied to standard epigenetic clocks built on elastic net regression, to achieve bulk and single-cell resolution. We show that estiMAge can accurately predict the ages of young and old hepatocytes and can be used to generate single-cell versions of publicly available epigenetic clocks.The source code and instructions for usage of estiMAge are available at https://github.com/DivEpigenetics/estiMAge.
LB  - PUB:(DE-HGF)16
C6  - pmid:39867532
C2  - pmc:PMC11769677
DO  - DOI:10.1093/bioadv/vbaf005
UR  - https://inrepo02.dkfz.de/record/298229
ER  -