Genome-wide methylation profiles reveal quantitative views of human aging rates.

PubWeight™: 6.50‹?› | Rank: Top 1%

🔗 View Article (PMC 3780611)

Published in Mol Cell on November 21, 2012

Authors

Gregory Hannum1, Justin Guinney2, Ling Zhao3,4,5, Li Zhang3,4,5,6, Guy Hughes4,5, SriniVas Sadda7, Brandy Klotzle8, Marina Bibikova8, Jian-Bing Fan8, Yuan Gao9, Rob Deconde1,10, Menzies Chen1, Indika Rajapakse11, Stephen Friend2, Trey Ideker1,4,10, Kang Zhang3,4,5

Author Affiliations

1: Department of Bioengineering, University of California, San Diego, CA 92093, USA.
2: Sage Bionetworks, Seattle, WA 98109, USA.
3: Molecular Medicine Research Center and Department of Ophthalmology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.
4: Institute for Genomic Medicine, University of California, San Diego, CA 92093, USA.
5: Department of Ophthalmology, University of California, San Diego, CA 92093, USA.
6: Guangzhou iGenomics Co., Ltd, Guangzhou 510300, China.
7: Doheny Eye Institute, University of Southern California, Los Angeles, CA 90033, USA.
8: Illumina Incorporation, San Diego, CA 92122, USA.
9: Lieber Institute, Johns Hopkins University, Baltimore, MD 21205, USA.
10: Department of Medicine, University of California, San Diego, CA 92093, USA.
11: Division of Basic Sciences and Biostatistics, Fred Hutchinson Cancer Research Center, Seattle, WA 98110, USA.

Associated clinical trials:

Reversing Epigenetic & Other Markers of Senescence by Transfusing Young Plasma To Older Human Subjects (RESET-YOUTH) | NCT03353597

Articles citing this

(truncated to the top 100)

DNA methylation age of human tissues and cell types. Genome Biol (2013) 7.48

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics (2014) 5.93

Accounting for cellular heterogeneity is critical in epigenome-wide association studies. Genome Biol (2014) 3.89

Additional annotation enhances potential for biologically-relevant analysis of the Illumina Infinium HumanMethylation450 BeadChip array. Epigenetics Chromatin (2013) 2.93

Passive and active DNA methylation and the interplay with genetic variation in gene regulation. Elife (2013) 2.70

Obesity accelerates epigenetic aging of human liver. Proc Natl Acad Sci U S A (2014) 2.68

DNA methylation age of blood predicts all-cause mortality in later life. Genome Biol (2015) 2.51

Cancer as a dysregulated epigenome allowing cellular growth advantage at the expense of the host. Nat Rev Cancer (2013) 2.41

Aging of blood can be tracked by DNA methylation changes at just three CpG sites. Genome Biol (2014) 2.40

Human iPSC-based modeling of late-onset disease via progerin-induced aging. Cell Stem Cell (2013) 2.31

The epigenetic clock is correlated with physical and cognitive fitness in the Lothian Birth Cohort 1936. Int J Epidemiol (2015) 1.88

Glycans are a novel biomarker of chronological and biological ages. J Gerontol A Biol Sci Med Sci (2013) 1.77

Cross-sectional and longitudinal changes in DNA methylation with age: an epigenome-wide analysis revealing over 60 novel age-associated CpG sites. Hum Mol Genet (2013) 1.77

Age-associated epigenetic drift: implications, and a case of epigenetic thrift? Hum Mol Genet (2013) 1.76

Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape. Genome Biol (2013) 1.69

Aging and epigenetic drift: a vicious cycle. J Clin Invest (2014) 1.63

Accelerated epigenetic aging in Down syndrome. Aging Cell (2015) 1.61

Blood-based biomarkers of age-associated epigenetic changes in human islets associate with insulin secretion and diabetes. Nat Commun (2016) 1.58

Genetics of healthy aging and longevity. Hum Genet (2013) 1.50

A Molecular Clock Infers Heterogeneous Tissue Age Among Patients with Barrett's Esophagus. PLoS Comput Biol (2016) 1.38

Breastfeeding effects on DNA methylation in the offspring: A systematic literature review. PLoS One (2017) 1.38

Longitudinal, genome-scale analysis of DNA methylation in twins from birth to 18 months of age reveals rapid epigenetic change in early life and pair-specific effects of discordance. Genome Biol (2013) 1.36

Review of processing and analysis methods for DNA methylation array data. Br J Cancer (2013) 1.33

Differential methylation in glucoregulatory genes of offspring born before vs. after maternal gastrointestinal bypass surgery. Proc Natl Acad Sci U S A (2013) 1.28

DNA methylation and healthy human aging. Aging Cell (2015) 1.27

The cerebellum ages slowly according to the epigenetic clock. Aging (Albany NY) (2015) 1.26

An integrative network algorithm identifies age-associated differential methylation interactome hotspots targeting stem-cell differentiation pathways. Sci Rep (2013) 1.26

DNA methylation age is associated with mortality in a longitudinal Danish twin study. Aging Cell (2015) 1.25

Epigenetic regulation of ageing: linking environmental inputs to genomic stability. Nat Rev Mol Cell Biol (2015) 1.24

A methylome-wide study of aging using massively parallel sequencing of the methyl-CpG-enriched genomic fraction from blood in over 700 subjects. Hum Mol Genet (2013) 1.24

The transcriptional landscape of age in human peripheral blood. Nat Commun (2015) 1.20

Measuring cell-type specific differential methylation in human brain tissue. Genome Biol (2013) 1.19

Reducing the risk of false discovery enabling identification of biologically significant genome-wide methylation status using the HumanMethylation450 array. BMC Genomics (2014) 1.16

Decreased epigenetic age of PBMCs from Italian semi-supercentenarians and their offspring. Aging (Albany NY) (2015) 1.15

Increased epigenetic age and granulocyte counts in the blood of Parkinson's disease patients. Aging (Albany NY) (2015) 1.15

GeMes, clusters of DNA methylation under genetic control, can inform genetic and epigenetic analysis of disease. Am J Hum Genet (2014) 1.15

Aging and DNA methylation. BMC Biol (2015) 1.15

Epigenetic age of the pre-frontal cortex is associated with neuritic plaques, amyloid load, and Alzheimer's disease related cognitive functioning. Aging (Albany NY) (2015) 1.14

Age-related variations in the methylome associated with gene expression in human monocytes and T cells. Nat Commun (2014) 1.13

Genetic and environmental exposures constrain epigenetic drift over the human life course. Genome Res (2014) 1.13

An integrative multi-scale analysis of the dynamic DNA methylation landscape in aging. PLoS Genet (2015) 1.13

Genome-wide age-related changes in DNA methylation and gene expression in human PBMCs. Age (Dordr) (2014) 1.12

DNA methylation biomarkers: cancer and beyond. Genes (Basel) (2014) 1.11

Aging-Induced Stem Cell Mutations as Drivers for Disease and Cancer. Cell Stem Cell (2015) 1.11

Age-related epigenetic drift in the pathogenesis of MDS and AML. Genome Res (2014) 1.08

COHCAP: an integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis. Nucleic Acids Res (2013) 1.08

Genome-wide DNA methylation changes with age in disease-free human skeletal muscle. Aging Cell (2013) 1.08

Buccals are likely to be a more informative surrogate tissue than blood for epigenome-wide association studies. Epigenetics (2013) 1.08

DNA methylation-based measures of biological age: meta-analysis predicting time to death. Aging (Albany NY) (2016) 1.08

Whole-genome fingerprint of the DNA methylome during human B cell differentiation. Nat Genet (2015) 1.07

Acceleration of age-associated methylation patterns in HIV-1-infected adults. PLoS One (2015) 1.07

Epigenetic modulators, modifiers and mediators in cancer aetiology and progression. Nat Rev Genet (2016) 1.07

Epigenetic estimation of age in humpback whales. Mol Ecol Resour (2014) 1.06

Improving cell mixture deconvolution by identifying optimal DNA methylation libraries (IDOL). BMC Bioinformatics (2016) 1.06

Deep biomarkers of human aging: Application of deep neural networks to biomarker development. Aging (Albany NY) (2016) 1.06

Novel region discovery method for Infinium 450K DNA methylation data reveals changes associated with aging in muscle and neuronal pathways. Aging Cell (2013) 1.05

Epigenetic age acceleration predicts cancer, cardiovascular, and all-cause mortality in a German case cohort. Clin Epigenetics (2016) 1.05

Methylome-wide Analysis of Chronic HIV Infection Reveals Five-Year Increase in Biological Age and Epigenetic Targeting of HLA. Mol Cell (2016) 1.03

Ageing-associated changes in the human DNA methylome: genomic locations and effects on gene expression. BMC Genomics (2015) 1.03

Epigenetic aging upon allogeneic transplantation: the hematopoietic niche does not affect age-associated DNA methylation. Leukemia (2014) 1.02

Concordant and discordant DNA methylation signatures of aging in human blood and brain. Epigenetics Chromatin (2015) 1.01

Epigenomics of Alzheimer's disease. Transl Res (2014) 1.01

Distinct DNA methylation patterns of cognitive impairment and trisomy 21 in Down syndrome. BMC Med Genomics (2013) 1.01

DNA methylation, genotype and gene expression: who is driving and who is along for the ride? Genome Biol (2013) 1.00

Origins of aberrant DNA methylation in acute myeloid leukemia. Leukemia (2013) 1.00

Validation of DNA methylation profiling in formalin-fixed paraffin-embedded samples using the Infinium HumanMethylation450 Microarray. Epigenetics (2014) 1.00

From inflammaging to healthy aging by dietary lifestyle choices: is epigenetics the key to personalized nutrition? Clin Epigenetics (2015) 0.98

Grasping nettles: cellular heterogeneity and other confounders in epigenome-wide association studies. Hum Mol Genet (2014) 0.97

An epigenetic clock analysis of race/ethnicity, sex, and coronary heart disease. Genome Biol (2016) 0.97

An epigenetic clock for gestational age at birth based on blood methylation data. Genome Biol (2016) 0.97

Accelerated DNA methylation age: Associations with PTSD and neural integrity. Psychoneuroendocrinology (2015) 0.97

DNA methylation levels at individual age-associated CpG sites can be indicative for life expectancy. Aging (Albany NY) (2016) 0.97

Removing unwanted variation in a differential methylation analysis of Illumina HumanMethylation450 array data. Nucleic Acids Res (2015) 0.96

H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells. Genome Res (2014) 0.96

Prenatal and early life influences on epigenetic age in children: a study of mother-offspring pairs from two cohort studies. Hum Mol Genet (2015) 0.96

Longitudinal analysis of DNA methylation associated with birth weight and gestational age. Hum Mol Genet (2015) 0.96

Methylation of the SLC6a2 gene promoter in major depression and panic disorder. PLoS One (2013) 0.96

Epimutations mimic genomic mutations of DNMT3A in acute myeloid leukemia. Leukemia (2013) 0.96

Lifetime stress accelerates epigenetic aging in an urban, African American cohort: relevance of glucocorticoid signaling. Genome Biol (2015) 0.96

Omics technologies and the study of human ageing. Nat Rev Genet (2013) 0.95

Human leukocyte telomere length is associated with DNA methylation levels in multiple subtelomeric and imprinted loci. Sci Rep (2014) 0.94

Regulatory link between DNA methylation and active demethylation in Arabidopsis. Proc Natl Acad Sci U S A (2015) 0.94

Age-related DNA methylation in normal breast tissue and its relationship with invasive breast tumor methylation. Epigenetics (2013) 0.94

The senescent methylome and its relationship with cancer, ageing and germline genetic variation in humans. Genome Biol (2015) 0.94

Distinctive topology of age-associated epigenetic drift in the human interactome. Proc Natl Acad Sci U S A (2013) 0.94

Influence of environmental exposure on human epigenetic regulation. J Exp Biol (2015) 0.93

Self-control forecasts better psychosocial outcomes but faster epigenetic aging in low-SES youth. Proc Natl Acad Sci U S A (2015) 0.93

Epigenetic Aging Signatures Are Coherently Modified in Cancer. PLoS Genet (2015) 0.92

Aging: progressive decline in fitness due to the rising deleteriome adjusted by genetic, environmental, and stochastic processes. Aging Cell (2016) 0.91

Replicative senescence is associated with nuclear reorganization and with DNA methylation at specific transcription factor binding sites. Clin Epigenetics (2015) 0.91

Phagocyte dysfunction, tissue aging and degeneration. Ageing Res Rev (2013) 0.91

Discordance of DNA methylation variance between two accessible human tissues. Sci Rep (2015) 0.91

Epigenetic clock analyses of cellular senescence and ageing. Oncotarget (2016) 0.90

A novel multi-tissue RNA diagnostic of healthy ageing relates to cognitive health status. Genome Biol (2015) 0.90

Menopause accelerates biological aging. Proc Natl Acad Sci U S A (2016) 0.89

Age and sun exposure-related widespread genomic blocks of hypomethylation in nonmalignant skin. Genome Biol (2015) 0.88

A meta-analysis on age-associated changes in blood DNA methylation: results from an original analysis pipeline for Infinium 450k data. Aging (Albany NY) (2015) 0.88

Trimethylation of Lys36 on H3 restricts gene expression change during aging and impacts life span. Genes Dev (2015) 0.87

Associations between maternal risk factors of adverse pregnancy and birth outcomes and the offspring epigenetic clock of gestational age at birth. Clin Epigenetics (2017) 0.87

Age-related profiling of DNA methylation in CD8+ T cells reveals changes in immune response and transcriptional regulator genes. Sci Rep (2015) 0.86

Articles cited by this

Bioconductor: open software development for computational biology and bioinformatics. Genome Biol (2004) 143.19

SOAP: short oligonucleotide alignment program. Bioinformatics (2008) 68.13

Regularization Paths for Generalized Linear Models via Coordinate Descent. J Stat Softw (2010) 38.65

Telomeres shorten during ageing of human fibroblasts. Nature (1990) 23.97

Genetics of gene expression and its effect on disease. Nature (2008) 21.35

Missing value estimation methods for DNA microarrays. Bioinformatics (2001) 20.84

Epigenetics in cancer. N Engl J Med (2008) 17.36

Epigenetic differences arise during the lifetime of monozygotic twins. Proc Natl Acad Sci U S A (2005) 15.46

Physical fitness and all-cause mortality. A prospective study of healthy men and women. JAMA (1989) 14.34

Accelerated telomere shortening in response to life stress. Proc Natl Acad Sci U S A (2004) 12.89

Cancer epigenetics comes of age. Nat Genet (1999) 12.63

High density DNA methylation array with single CpG site resolution. Genomics (2011) 10.35

Obesity, cigarette smoking, and telomere length in women. Lancet (2005) 8.59

The endocrine regulation of aging by insulin-like signals. Science (2003) 8.10

Aging and environmental exposures alter tissue-specific DNA methylation dependent upon CpG island context. PLoS Genet (2009) 7.07

DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol (2011) 6.48

FOXO3A genotype is strongly associated with human longevity. Proc Natl Acad Sci U S A (2008) 5.71

Functionally significant insulin-like growth factor I receptor mutations in centenarians. Proc Natl Acad Sci U S A (2008) 5.14

Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains. Genome Res (2010) 5.08

Mapping the cancer genome. Pinpointing the genes involved in cancer will help chart a new course across the complex landscape of human malignancies. Sci Am (2007) 4.66

Dynamic DNA methylation programs persistent adverse effects of early-life stress. Nat Neurosci (2009) 4.53

Distinct DNA methylomes of newborns and centenarians. Proc Natl Acad Sci U S A (2012) 4.26

Epigenome-wide scans identify differentially methylated regions for age and age-related phenotypes in a healthy ageing population. PLoS Genet (2012) 4.05

Decline in genomic DNA methylation through aging in a cohort of elderly subjects. Mech Ageing Dev (2008) 3.93

Personalized epigenomic signatures that are stable over time and covary with body mass index. Sci Transl Med (2010) 3.81

Meta-analysis of age-related gene expression profiles identifies common signatures of aging. Bioinformatics (2009) 3.50

Epigenetic predictor of age. PLoS One (2011) 3.46

Epigenetics and aging: the targets and the marks. Trends Genet (2007) 3.44

The relationship of DNA methylation with age, gender and genotype in twins and healthy controls. PLoS One (2009) 3.41

Puzzles, promises and a cure for ageing. Nature (2008) 3.23

AGEMAP: a gene expression database for aging in mice. PLoS Genet (2007) 3.22

Identification of an imprinted master trans regulator at the KLF14 locus related to multiple metabolic phenotypes. Nat Genet (2011) 3.20

Lipoprotein genotype and conserved pathway for exceptional longevity in humans. PLoS Biol (2006) 3.12

Why women live longer than men: sex differences in longevity. Gend Med (2006) 3.00

Age-associated DNA methylation in pediatric populations. Genome Res (2012) 2.53

The Steap proteins are metalloreductases. Blood (2006) 2.37

Calorie restriction lowers body temperature in rhesus monkeys, consistent with a postulated anti-aging mechanism in rodents. Proc Natl Acad Sci U S A (1996) 2.23

Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing. PLoS One (2011) 2.16

MED1, a novel human methyl-CpG-binding endonuclease, interacts with DNA mismatch repair protein MLH1. Proc Natl Acad Sci U S A (1999) 1.99

Aging and gene expression in the primate brain. PLoS Biol (2005) 1.76

Somatostatin regulates brain amyloid beta peptide Abeta42 through modulation of proteolytic degradation. Nat Med (2005) 1.49

Nek family of kinases in cell cycle, checkpoint control and cancer. Cell Div (2011) 1.37

The mitochondrial protein frataxin prevents nuclear damage. Hum Mol Genet (2002) 1.33

Sequential use of transcriptional profiling, expression quantitative trait mapping, and gene association implicates MMP20 in human kidney aging. PLoS Genet (2009) 1.30

Stage-specific control of neuronal migration by somatostatin. Nature (2002) 1.20

Skin aging and photoaging alter fatty acids composition, including 11,14,17-eicosatrienoic acid, in the epidermis of human skin. J Korean Med Sci (2010) 1.08

Enhanced gene repair mediated by methyl-CpG-modified single-stranded oligonucleotides. Nucleic Acids Res (2009) 1.05

Induction of oxidative DNA damage by ferric iron in mammalian cells. Carcinogenesis (1995) 0.88