DNA methylation age and the epigenetic clock

Steve Horvath (shorvath at mednet.ucla.edu)

 

Abstract

Using 82 Illumina DNA methylation array data sets (n=7844) involving 51 healthy tissues and cell types, I developed a multi-tissue predictor of age which allows one to estimate the DNA methylation (DNAm) age of most tissues and cell types. DNAm age has the following properties: a) it is close to zero for embryonic and induced pluripotent stem (iPS) cells, b) it correlates with cell passage number, c) it gives rise to a highly heritable measure of age acceleration, and d) it is applicable to chimpanzee tissues.

http:/genomebiology.com/2013/14/10/R115

 

Frequently asked questions (FAQs): faq.htm

 

Updated results:

1) cancer tissue: Oct 27, 2013

2) Figure 3E correction2

DNAm age calculator

DNAm age calculator webpage (below) contains information on how to calculate DNA methylation (DNAm) age based on data measured using the Illumina Infinium platform (e.g. 450K or 27K data).

The age calculator automatically outputs the estimated DNAm age. After uploading the data, the function will return an Excel file whose rows report the estimated DNAm age of each subject and additional information.

Access Online Age Calculator: https://dnamage.genetics.ucla.edu/

 

Alternatively Access Online Age Calculator which is only temporarily available.

DNA methylation data

Example data based on the Illumina DNA Infinium platform

MethylationDataExample55.csv

Tutorial for the online age calculator

A tutorial that describes how to calculate DNAm age based on Illumina DNA Infinium 27K or 450K data is available here:

TUTORIALonlineCalculator.docx or TUTORIALonlineCalculator.pdf

 

Save these files into the directory where your DNA meth data are located.

To run this tutorial, also download the following example data sets:

MethylationDataExample55.csv

SampleAnnotationExample55.csv

R Tutorials

The following R software tutorial shows how to calculate DNAm age based on Illumina DNA Infinium 27K or 450K data is available. These R scripts carry out normalization steps and show how to estimate DNAm age.

 

Tutorial 1: Analysis of data set 55.

Word document: TUTORIAL1.docx

PDF file: TUTORIAL1.pdf

 

1) probeAnnotation21kdatMethUsed.csv

2) datMiniAnnotation27k.csv

3) AdditionalFile3.csv

4) StepwiseAnalysis.txt

5) NORMALIZATION.R

Save these files into the directory where your DNA meth data are located.

To run this tutorial, also download the following example data sets:

6) MethylationDataExample55.csv

7) SampleAnnotationExample55.csv

 

Citing the software

Acknowledgments

Please email Steve Horvath with questions (shorvath at mednet.ucla.edu), subject heading: DNAmAge.

NIH 5R01AG042511-02

SH gratefully acknowledges the many researchers who made their DNA-methylation datasets publically available and responded to his email requests. Special thanks to Gene Expression Omnibus, ArrayExpress, and The Cancer Genome Atlas.


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