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Logo of nihpaAbout Author manuscriptsSubmit a manuscriptNIH Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
 
Mol Cell. Author manuscript; available in PMC Jan 24, 2014.
Published in final edited form as:
PMCID: PMC3780611
NIHMSID: NIHMS418935
Genome-wide Methylation Profiles Reveal Quantitative Views of Human Aging Rates
Gregory Hannum,#1 Justin Guinney,#2 Ling Zhao,3,4,5 Li Zhang,3,4,5,6 Guy Hughes,4,5 SriniVas Sadda,7 Brandy Klotzle,8 Marina Bibikova,8 Jian-Bing Fan,8 Yuan Gao,9 Rob Deconde,1,10 Menzies Chen,1 Indika Rajapakse,11 Stephen Friend,2 Trey Ideker,1,4,10 and Kang Zhang3,4,5
1Department of Bioengineering, University of California, San Diego, CA 92093, USA
2Sage Bionetworks, Seattle, WA 98109, USA
3Molecular Medicine Research Center and Department of Ophthalmology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
4Institute for Genomic Medicine, University of California, San Diego, CA 92093, USA
5Department of Ophthalmology, University of California, San Diego, CA 92093, USA
6Guangzhou iGenomics Co., Ltd, Guangzhou 510300, China
7Doheny Eye Institute, University of Southern California, Los Angeles, CA 90033, USA
8Illumina Incorporation, San Diego, CA 92122, USA
9Lieber Institute, Johns Hopkins University, Baltimore, MD 21205, USA
10Department of Medicine, University of California, San Diego, CA 92093, USA
11Division of Basic Sciences and Biostatistics, Fred Hutchinson Cancer Research Center, Seattle, WA 98110, USA
#Contributed equally.
Correspondence and requests for information should be addressed to T.I. (tideker/at/ucsd.edu) or K.Z. (kzhang/at/ucsd.edu).
To whom correspondence should be addressed. tideker/at/ucsd.edu, kang.zhang/at/gmail.com
The ability to measure human aging from molecular profiles has practical implications in many fields, including disease prevention and treatment, forensics, and extension of life. Although chronological age has been linked to changes in DNA methylation, the methylome has not yet been used to measure and compare human aging rates. Here, we build a quantitative model of aging using measurements at more than 450,000 CpG markers from the whole blood of 656 human individuals, aged 19 to 101. This model measures the rate at which an individual’s methylome ages, which we show is impacted by gender and genetic variants. Furthermore, we show that differences in aging rates help explain epigenetic drift and are reflected in the transcriptome. Our model highlights specific components of the aging process and provides a quantitative read-out for studying the role of methylation in age-related disease.
Not everyone ages in the same manner. It is well known that women tend to live longer than men, and lifestyle choices such as smoking and physical fitness can hasten or delay the aging process (Steven N., 2006; Blair et al., 1989). These observations have led to the search for molecular markers of age which can be used to predict, monitor, and provide insight into age-associated physiological decline and disease. One such marker is telomere length, a molecular trait strongly correlated with age (Harley et al., 1990) which has been shown to have an accelerated rate of decay under environmental stress (Epel et al., 2004; Valdes et al.). Another marker is gene expression, especially for genes that function in metabolic and DNA repair pathways which are predictive of age across a range of different tissue types and organisms (Fraser et al., 2005; Zahn et al., 2007; de Magalhães et al., 2009).
A growing body of research has reported associations between age and the state of the epigenome— the set of modifications to DNA other than changes in the primary nucleotide sequence (Fraga and Esteller, 2007). In particular, DNA methylation associates with chronological age over long time scales (Alisch et al., 2012; Christensen et al., 2009; Bollati et al., 2009; Boks et al., 2009; Rakyan et al., 2010; Bocklandt et al., 2011; Bell et al., 2012) and changes in methylation have been linked to complex age-associated diseases such as metabolic disease (Barres and Zierath, 2011) and cancer (Jones and Laird, 1999; Esteller, 2008). Studies have also observed a phenomenon dubbed “epigenetic drift”, whereby the DNA methylation marks in identical twins increasingly differ as a function of age (Fraga et al., 2005; Boks et al., 2009). Thus, the idea of the epigenome as a fixed imprint is giving way to the model of the epigenome as a dynamic landscape that reflects a variety of chronological changes. The current challenge is to determine whether these changes can be systematically described and modeled to detect different rates of human aging, and to tie these rates to related clinical or environmental variables.
The mechanisms that drive changes in the aging methylome are not well understood, although they have been attributed to at least two underlying factors (Vijg and Campisi, 2008; Fraga et al., 2005). First, it is possible that environmental exposure will over time activate cellular programs associated with consistent and predictable changes in the epigenome. For example, stress has been shown to alter gene expression patterns through specific changes in DNA methylation (Murgatroyd et al., 2009). Alternatively, spontaneous epigenetic changes may occur with or without environmental stress, leading to fundamentally unpredictable differences in the epigenome between aging individuals. Spontaneous changes may be caused by chemical agents that disrupt DNA methyl groups or through errors in copying methylation states during DNA replication. Both mechanisms lead to differences between the methylomes of aging individuals, suggesting that quantitative measurements of methylome states may identify factors involved with slowed or accelerated rates of aging.
To better understand how the methylome ages and to determine whether human aging rates can be quantified and compared, we initiated a project to perform genome-wide methylomic profiling of a large cohort of individuals spanning a wide age range. Based on these findings, we constructed a predictive model of aging rate which we show is influenced by gender and specific genetic variants. These data help explain epigenetic drift and suggest that age-associated changes in the methylome lead to changes in transcriptional patterns over time. These findings were replicated in a second large cohort.
We obtained methylome-wide profiles of two different cohorts (N1 = 482, N2 = 174) sampled from a mixed population of 426 Caucasian and 230 Hispanic individuals, aged 19 to 101. Samples were taken as whole blood and processed using the Illumina Infinium HumanMethylation450 BeadChip assay (Bibikova et al., 2011), which measures the methylation states of 485,577 CpG markers. Methylation was recorded as a fraction between zero and one, representing the frequency of methylation of a given CpG marker across the population of blood cells taken from a single individual. Conservative quality controls were applied to filter spurious markers and samples (Experimental Procedures). For simplicity, we discarded values for markers on sex chromosomes..Association tests revealed that 70,387 (15%) of the markers had significant associations between methylation fraction and age (Figure 1, FDR < 0.05 by F-Test, Experimental Procedures). We were able to verify at a P < 0.05 significance level 53,670 (76%) of these associations using 40 young and old samples recently published by Heyn et al. (Heyn et al., 2012). More detailed accounts of the individual aging markers and their genomic features are presented in the Supplementary Information (Figure S1, Tables S1, S2). The resulting dataset represents the largest and highest-resolution collection of methylation data produced for the study of aging, providing an unprecedented opportunity to understand the role of epigenetics in the aging process. The complete methylation profiles are available at the Gene Expression Omnibus (GSE40279, http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40279).
Figure 1
Figure 1
Global data on the aging methylome
We built a predictive model of aging on the primary cohort using a penalized multivariate regression method known as Elastic Net (Zou and Hastie, 2005), combined with bootstrap approaches (Experimental Procedures). The model included both methylomic and clinical parameters such as gender and Body Mass Index (BMI) (Figure 2A). The optimal model selected a set of 71 methylation markers which were highly predictive of age (Figure 2A, Table S3). The accuracy of the model was high, with a correlation between age and predicted age of 96% and an error of 3.9 years (Figure 2B). Nearly all markers in the model lay within or near genes with known functions in aging-related conditions including Alzheimer’s disease, cancer, tissue degradation, DNA damage, and oxidative stress. By way of example, two markers lay within the gene somatostatin (SST), a key regulator of endocrine and nervous system function (Yacubova and Komuro, 2002). SST is known to decline with age and has been linked to Alzheimer’s disease (Saito et al., 2005). As a second example, six model markers lay within the transcription factor KLF14, which has been called a ‘master regulator’ of obesity and other metabolic traits (Small et al., 2011). Given the links between aging, longevity, and metabolic activity (Lane et al., 1996; Tatar et al., 2003), it is not surprising that several of our model markers are implicated in obesity and metabolism.
Figure 2
Figure 2
Model predictions and clinical variables
We validated this model on the secondary cohort, consisting of an additional 174 independent samples. These samples were processed in the same manner as the primary cohort, then used to predict age based on the original model (i.e., as trained on the original cohort). The predictions were highly accurate, with a correlation between age and predicted age of 91% and an error of 4.9 years (Figure 2C). The significance of the aging model was also confirmed by the dataset presented in Heyn et al., verifying the age association of 70 of the 71 markers (Heyn et al., 2012). Furthermore, the model was able to fully separate old and young individuals in the Heyn et al. study, even for profiles obtained using bisulfate sequencing rather than the bead-chip technology used in this study (Figure S2).
While the aging model is able to predict the age of most individuals with high accuracy, it is equally valuable as a tool for identifying individual outliers who do not follow the expectation. For example, Figure 2B highlights two individuals whose age is vastly over- or under-predicted based on their methylation data. To examine whether these differences reflect true biological differences in the state of the individual (i.e., versus measurement error or intrinsic variability), we used the aging model to quantify each individual’s apparent methylomic aging rate (AMAR), defined as the ratio of the predicted age, based on methylation data, to the chronological age. We then tested for associations between AMAR and possibly relevant clinical factors, including gender and BMI. Analysis of ethnicity and diabetes status was not possible due to correlations with batch variables (Figure S3). We found that gender, but not BMI had significant contributions to aging rate (F-test, P = 6×10−6, P > 0.05, Experimental Procedures). The methylome of men appeared to age approximately 4% faster than that of women (Figure 2D), even though the overall distributions of age were not significantly different between the men and women in the cohort (P > 0.05, KS-test). Likewise, the validation cohort confirmed the increased aging rate for men (P < 0.05), but was inconclusive for BMI (P > 0.05). This complements a previous finding of an epigenetic signal for BMI that does not change with age (Feinberg et al., 2010).
As genetic associations have been previously reported with human longevity and aging phenotypes (Atzmon et al., 2006; Suh et al., 2008; Willcox et al., 2008; Wheeler et al., 2009), we examined whether the model could distinguish aging rates for individuals with different genetic variants. For this purpose, we obtained whole-exome sequences for 252 of the individuals in our methylome study at 15x coverage. After sequence processing and quality control, these sequences yielded 10,694 common single nucleotide variants across the population (Experimental Procedures). As a negative control, we confirmed that none of the genetic variants were significant predictors of age itself, which is to be expected since the genome sequence is considered to be relatively static over the course of a lifetime. On the other hand, one might expect to find genetic variants that modulate the methylation of age-associated markers, i.e. methylation quantitative-trait loci or meQTLs (Bell et al., 2011). Testing each genetic variant for association with the top age-associated methylation markers, we identified 303 meQTLs (Experimental Procedures, FDR < 0.05, Figure 3A). For validation, we selected 8 genetic variants (corresponding to 14 meQTLs) to test in a validation cohort of 322 individuals from our methylation study. This analysis found that 7 of 8 genetic variants (corresponding to 7 meQTLs) remained highly significant in the validation cohort (FDR < 0.05, Table S4). While all of these variants acted in cis with their meQTLs (within 150 kbp), we confirmed that none directly modified the CpG site or associated probe sequence of the associated methylation marker.
Figure 3
Figure 3
Genetic effects on methylomic aging
The methylation marker cg27193080 was one of those found to be significantly associated with age (P < 10−17), and its methylation fraction was found to be influenced by the Single Nucleotide Polymorphism (SNP) variant rs140692 (P < 10−21) (Figure 3B). This meQTL was particularly interesting as both the SNP and the methylation marker mapped to the gene methyl-CpG binding domain protein 4 (MBD4, with the SNP in an intron and the methylation marker just upstream of the coding region), one of the few known genes encoding a protein that can bind to methylated DNA. This meQTL thus captures a cis-relationship in which rs140692 influences the methylation state of MBD4. That MBD4 plays a role in human aging is supported by previous work linking MBD4 to DNA repair, as well as work showing that mutations and knock-downs of MBD4 lead to increased genomic instability (Bellacosa et al., 1999; Bertoni et al., 2009).
Of the seven validated meQTLs, three were identified that had a statistically-significant association not only with age but also with aging rate (AMAR, FDR < 0.05, Figure 3B,C). One is the genetic marker rs2230534, which is a synonymous mutation in the gene NEK4, and has a cis association with the methylation marker cg18404041. The NEK family of kinases plays a key role in cell cycle regulation and cancer (Moniz et al., 2011). The second variant is rs2818384, which is a synonymous mutation in the gene JAKMIP3, and has a cis association with the methylation marker cg05652533. Copy-number variants in JAKMIP3 have been previously associated with glioblastoma (Xiong et al., 2010). The final variant found to influence AMAR is rs42663, which is a missense mutation in the gene GTPBP10, and associates with cg27367526 in the gene STEAP2. STEAP2 is known to play a role in maintenance of iron and copper homeostasis— metals which serve as essential components of the mitochondrial respiratory chain (Ohgami et al., 2006). Studies have shown that perturbations of iron concentrations can induce DNA damage through oxidative stress in mammalian cells (Hartwig and Schlepegrell, 1995; Karthikeyan et al., 2002). These meQTLs represent genetic variants that appear to broadly influence the aging methylome and may be good candidates for further age-associated disease and longevity research.
Our aging model was derived from whole blood, which is advantageous in the design of practical diagnostics and for testing samples collected from other studies. To investigate whether our aging model was representative of other tissues, we obtained DNA methylation profiles for 368 individuals in the control category of The Cancer Genome Atlas (TCGA) (Collins and Barker, 2007), including 83 breast, 183 kidney, 60 lung, and 42 skin samples. An aging model based on both our primary and validation cohorts demonstrated strong predictive power for chronological age in these samples (expected value R = 0.72), although each tissue had a clear linear offset (intercept and slope) from the expectation (Figure 4A). This offset was consistent within a tissue, even across different batches of the TCGA data. We adjusted for each tissue trend using a simple linear model, producing age predictions with an error comparable to that found in blood (Figure 4B). Furthermore, predicted AMARs in each tissue supported the effect of men appearing to age more quickly than women (P < 0.05). Thus, computation of aging rate (AMAR) from blood samples reflects trends that are not specific to blood and may be common throughout many tissues of the human body. Furthermore, this analysis provides evidence that the observed methylomic changes are intrinsic to the methylome and not due primarily to cell heterogeneity, i.e. changing cell-type composition of whole blood with age. In this regard, this study is consistent with a prior analysis of purified CD4+ T-cells and CD14+ monocytes, in which the age-associated epigenetic modifications were found to be similar to the changes observed in whole blood (Rakyan et al, 2010).
Figure 4
Figure 4
Multi-tissue support
To investigate the similarities and differences between the tissues, we built age models de novo for breast, kidney, and lung tissues (Table S5; the skin cohort had too few samples to build a model). Most of the markers in the models differed, though, all of these models and the primary model share the markers cg23606718 and cg16867657. These markers are both annotated to the gene ELOVL2, which has been linked to the photoaging response in human skin (Kim et al., 2010).
The TCGA dataset also contains methylome profiles representing a total of 319 tumors and matched normal tissue samples (breast, kidney, lung, skin). Interestingly, use of our aging model indicated that tumors appear to have aged 40% more than matched normal tissue from the same individual (Wilcox test, P < 10−41, Figure 4C,D). Accelerated tumor aging was apparent regardless of the primary tissue type. We investigated whether this was the result of broad shifts in global methylation levels by examining all 70,387 age-associated markers, of which 44% tend to increase and 56% tend to decrease with age. Methylation fraction values in matched tumor and normal samples supported the finding that tumors coincide with older values for 74% of the markers regardless of the trending direction (Binomial P ~ 0). Furthermore, separate aging models built in the matched normal and tumor samples confirm the apparent aging effect (Figure S4).
If individuals indeed age at different rates, it might be expected that their individual methylomes should diverge over time. This is based on the premise that the methylomes of the very young share certain similarities, and that these similarities diminish as individuals accumulate changes over time. This effect, called epigenetic drift, has been observed in monozygotic twins (Fraga et al., 2005) but few specific hypothesis have been put forth to account for it. To examine epigenetic drift in our samples, we computed the deviance of each methylation marker value as its squared distance from the expected population mean (Figure 5A, Experimental Procedures). Then, in addition to testing for markers whose methylation fraction changes with age (Figures 5B,C), we were able to test for markers whose deviance changes with age (Figures 5D,E) (Breusch and Pagan, 1979). Increasing deviance was a widespread phenomenon—we identified 27,800 markers for which the deviance was significantly associated with age (FDR < 0.05), of which 27,737 (99.8%) represented increased rather than decreased deviance (Figure 5E, Figure S5). For any given individual, especially high or low methylome deviance was a strong predictor of aging rate (R = 0.47, P ~ 0), suggesting that differences in aging rates account for part of methylome heterogeneity and epigenetic drift.
Figure 5
Figure 5
Age associations for methylation fraction and deviance
Another way to examine epigenetic drift is in terms of Shannon Entropy, or loss of information content in the methylome over time (Shannon and Weaver, 1963). An increase in entropy of a CpG marker means that its methylation state becomes less predictable across the population of cells, i.e. its methylation fraction tends towards 50% (Experimental Procedures). Indeed, over all markers associated with a change in methylation fraction in the sample cohort, 70% tended towards a methylation fraction of 50% (Figure 6A, Binomial P ~ 0, Table S2). Consequently, we observed a highly significant increase in methylome entropy over the sample cohort (R = 0.21, P < 10−7). Furthermore, extreme methylome entropy for an individual was highly correlated with accelerated aging rate based on AMAR (R = 0.49, P ~ 0, Figure 6B).
Figure 6
Figure 6
Methylome-wide trends with age
As changes in methylation have been directly linked to changes in gene expression (Sun et al., 2011), we were interested in whether these changes in the aging methylome were mirrored on a functional level in the human transcriptome and reflected differences in aging rates. For this purpose, we obtained and analyzed publicly-available gene expression profiles from the whole blood of 488 individuals spanning an age range of 20 to 75 (Emilsson et al., 2008). We found strong evidence for genes whose expression associates with age (326 genes, FDR < 0.05) and for genes with increasing expression deviance (Binomial P < 10−276, Experimental Procedures). Strikingly, we found that genes with age-associated expression profiles were more likely to have nearby age-associated methylation markers in our data (P < 0.01, Table S6). We used this information to build a model of aging based on the expression of genes that were associated with age in the methylome (Figure 7A, Table S7, Experimental Procedures). This model demonstrated a clear ability to measure aging rate using expression data, reproducing our finding of increased aging rates for men as compared to women (Figure 7B, 11% difference, P < 10−4). The gender effect was not present in a model built using all available genes rather than those associated with age-related changes in the methylome (P > 0.05). Thus, age-associated changes to the methylome are indicative of functional changes in gene expression patterns.
Figure 7
Figure 7
Transcription aging model
In this study we have shown that genome-wide methylation patterns represent a strong and reproducible biomarker of biological aging rate. These patterns enable a quantitative model of the aging methylome which demonstrates high accuracy and an ability to discriminate relevant factors in aging, including gender and genetic variants. Moreover, our ability to apply this model in multiple tissues suggests the possibility of a common molecular clock, regulated in part by changes in the methylome. It remains to be seen whether these changes occur on an intracellular level uniformly across a population of cells, or reflect consistent changes in tissue composition over time.
The ability to predict age from whole blood may permit a wider analysis in longitudinal studies such as the Framingham Study, the Women’s Health Initiative, blood samples collected on neonatal Guthrie cards and other longitudinal studies with rich annotation of biometric and disease traits. Aging trends could emerge from such studies with many potential practical implications, from health assessment and prevention of disease to forensic analysis. Similar to the effect of gender in this study, the identification of additional biometric or environmental factors that influence AMAR, such as smoking, alcohol consumption, or diet, will permit quantitative assessments of their impacts on health and longevity. A useful example would be to periodically assess the rate of aging of an individual using AMAR and determine if diet or environmental factors can accelerate or retard the aging process and diseases such as age related macular degeneration. As models of human aging improve, it is conceivable that biological age, as measured from molecular profiles, might one day supersede chronological age in the clinical evaluation and treatment of patients.
Sample collection and test procedures
This study was approved by the institutional review boards of the University of California, San Diego, the University of Southern California and West China Hospital. All participants signed informed consent statements prior to participation. Blood was drawn from a vein in the patient’s arm into blood collection tubes containing the anticoagulant acid citrate dextrose. Genomic DNA was extracted from the whole blood using a Qiagen FlexiGene DNA Kit and stored at −20 degrees Celsius. Methylation fraction values for the autosomal chromosomes were measured using the Illumina Infinium HumanMethylation450 BeadChip (Bibikova et al., 2011). This procedure uses bisulfate-treated DNA and two site-specific probes for each marker, which bind to the associated methylated and un-methylated sequences. The intensity of the methylated probe relative to the total probe intensity for each site represents the fractional level of methylation at that site in the sample. These values were adjusted for internal controls using Illumina’s Genome Studio software. Methylation fraction values with a detection p-value greater than 0.01 were set to ‘missing’. One patient sample and 830 markers were removed as they had greater than 5% missing values. The remaining missing values were imputed with the KNN approach (10 nearest markers) using the R “impute” package (Troyanskaya et al., 2001). We performed exome sequencing on 258 of these samples, using a solution hybrid selection method to capture DNA followed by parallel sequencing on an Illumina HiSeq platform. Genotype calls were made using the SOAP program (Li et al., 2008). Calls with a quality score less than twenty were set as missing. Only variants which had fewer than 10% missing calls, were within Hardy-Weinberg equilibrium (P <= 10−4), and of a common frequency (> 5%) were retained (10,694). Individuals with less than 20% missing calls (252) were retained. Additional genotyping was done with multiplex PCR followed by MALDI-TOF mass spectrometry analysis using the iPLEX/MassARRAY/Typer platform.
Methylation quality control
We used principal component (PC) analysis to identify and remove outlier samples. We converted each sample into a z-score statistic, based on the squared distance of its 1st PC from the population mean. The z-statistic was converted to a false-discovery rate using the Gaussian cumulative distribution and the Benjamini-Hochberg procedure (Benjamini and Hochberg, 1995). Samples falling below an FDR of 0.2 were designated at outliers and removed. This filtering procedure was performed iteratively until no samples were determined to be an outlier. A total of 24 samples were removed in this manner.
Association testing
Association tests for trends in methylation fraction and deviance were performed using nested linear models and the F-test. As methylation levels may be sensitive to a number of factors, we included several covariates, including gender, BMI, diabetes status, ethnicity, and batch. Tests for whole-methylome changes in deviance were computed using the binomial test, based on the number of markers with a positive rather than negative coefficient. Markers were annotated as having support from the TCGA data if the coefficient of aging was the same sign and the significance was better than P < 0.05.
Annotation enrichment
Methylation marker annotations for CpG islands and GO terms were obtained from the IlluminaHumanMethylation450k.db database from Bioconductor (Gentleman et al., 2004). Annotation enrichment tests were performed using the two-sided Fisher’s exact test.
Aging model
The diagnostic model of age was made using a multivariate linear model approach based on the Elastic Net algorithm implemented in the R package ‘glmnet’ (Jerome Friedman, Trevor Hastie, 2010). This approach is a combination of traditional Lasso and ridge regression methods, emphasizing model sparsity while appropriately balancing the contributions of correlated variables. It is ideal for building linear models in situations where the number of variables (markers) greatly outweighs the number of samples. Optimal regularization parameters were estimated using ten-fold cross-validation. We employed bootstrap analysis, sampling the dataset with replacement 500 times and building a model for each bootstrap cohort. We included in the final model only markers that were present in more than half of all bootstraps. The covariates gender, BMI, diabetes status, ethnicity, and batch were included in the model and were exempted from penalization (regularization). P-values are based on a least-squares model built using the same terms and drop-one F-tests. As BMI was strongly associated with age, the term was first adjusted for age before computing significance in the model. AMAR was computed using the aging model, but without the variables gender, BMI, and diabetes status. The coefficients were not changed. AMAR was then taken as an individual’s predicted age divided by her or his actual age.
Genetic variant associations
Each genetic variant was tested for association in an additive model with the top aging associated methylation markers using nested linear models and the F-test. We included covariates for gender, BMI, diabetes status, ethnicity, and batch. Variant positions were based on the human reference build GRCh37 and gene annotations were based on chromosomal proximity within 20kbp.
Computing methylation deviance
Methylation deviance was computed using the following approach: First, we removed the methylation trends due to all given variables, including age, gender, and BMI by fitting a linear model for each marker and acting only on the residuals. Next, we identified and removed highly non-normal markers based on the Shapiro-Wilk test (P < 10−5). To allow for naturally occurring extreme deviations in the normality test, we first estimated the outliers of each marker based on a Grubb’s statistic, choosing the inclusion threshold based on the Benjamini-Hochberg FDR (Benjamini and Hochberg, 1995). If any samples had an FDR less than 0.4, we ignored them and repeated the outlier detection until no outliers were detected. Finally, the deviance of each remaining marker was computed as the square of its adjusted methylation value.
Entropy analysis
Entropy statistics were computed on methylation data adjusted for covariates and filtered for normality (see computing methylation deviance). We computed the normalized Shannon entropy (Shannon and Weaver, 1963) of an individual’s methylome according to the formula:
equation M1
where MFi is the methylation fraction of the ith methylation marker and N is the number of markers.
Mapping CpG islands
Genomic positions and marker annotations for 27,176 CpG islands were obtained from the IlluminaHumanMethylation450k.db database from Bioconductor (Gentleman et al., 2004). We obtained the positions for markers within each island with at least four markers (25,028), as well as the nearest 100 markers upstream and downstream. These positions were then combined with the marker value of interest (i.e. methylation fraction, aging coefficient, deviance) to produce a genomic map for each island and the surrounding region. After normalizing each map to the center of the island, we averaged the values at each relative genomic point across all islands to produce a common map.
Highlights
  • Human aging rates can be quantified from the methylome
  • Aging rates are affected by both gender and genetics
  • Different aging rates account for part of epigenetic drift
  • Methylome aging rates correspond with patterns of transcription
Supplementary Material
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Acknowledgements
We thank Janusz Dutkowski, Kumar Sharma and Mariano Alvarez for critical discussions and Daniel O’Conner for reviewing the manuscript. L.Zhao, L. Z and K.Z. were supported by grants from National Basic Research Program of China (973 Program, 2013CB967504), NSFC (Grant 81130017), NEI/NIH grants EY014428, EY018660, EY019270, EY021374, VA Merit Award, the Research to Prevent Blindness, and the Burroughs Wellcome Fund Clinical Scientist Award in Translational Research. G.Ha., M.C., and T.I. are supported by NIH grants P50GM085764 and R01E5014811. This work is a product of the Sage Federation, a consortium of research labs whose goal is to encourage greater openness and sharing of biomedical data and analyses.
Footnotes
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Accession Numbers The complete methylation profiles have been deposited in NCBI’s Gene Expression Omnibus under accession number GSE40279.
Supplemental Information Supplemental information includes 7 tables and 5 figures and can be found with this article online at ###.
Author Contributions L.Zhao, L.Zhang, G.Hu., S.S, and Y.G. collected and processed samples with guidance from K.Z.; B.K., M.B. and J.F. performed the methylation assays; L.Zhao, L.Zhang and K. Z. performed exome sequencing and genotyping; G.Ha. and J.G. performed the principal statistical analyses with guidance from T.I., R.D., M.C., and S.F. I.R. discussed the entropy metric. G.Ha., J.G., T.I., Y.G., and K.Z. wrote the manuscript.
Author Information B.K, M.B, and J.F. work for Illumina Inc.