The DOI matches its Crossref record; 32 of the 32 references it cites were found in a registry or an index.
Allele-specific methylation in the human genome: Implications for genetic studies of complex disease
Open accessAbstract
Across the genome, outside of a small number of known imprinted genes and regions subject to X-inactivation in females, DNA methylation at CpG dinucleotides is often assumed to be complementary across both alleles in a diploid cell. However, recent findings suggest the reality is more complex, with the discovery that allele-specific methylation (ASM) is a common feature across the genome. A key observation is that the majority of ASM is associated with genetic variation in cis, although a noticeable proportion is also non-cis in nature and mediated, for example, by parental origin. ASM appears to be both quantitative, characterized by subtle skewing of DNA methylation between alleles, and heterogeneous, varying across tissues and between individuals. These findings have important implications for complex disease genetics; whilst cis-mediated ASM provides a functional consequence for non-coding genetic variation, heterogeneous and quantitative ASM complicates the identification of disease-associated loci. We propose that non-cis ASM could contribute toward the 'missing heritability' of complex diseases, rendering certain loci hemizygous and masking the direct association between genotype and phenotype. We suggest that the interpretation of results from genomewide association studies can be improved by the incorporation of epi-allelic information, and that in order to fully understand the extent and consequence of ASM in the human genome, a comprehensive sequencing-based analysis of allelic methylation patterns across tissues and individuals is required.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The cited source says what the claim attributes to it.
In the citing paper
“DNA methylation has been shown to frequently occur in an allele-specific manner (He et al., 2015;Meaburn, Schalkwyk, & Mill, 2010;Shoemaker, Deng, Wang, & Zhang, 2010).”
From The applied implications of epigenetics in anxiety, affective and stress-related disorders - A review and synthesis on psychosocial stress, psychotherapy and prevention (2020) · cites this paper as Meaburn, Schalkwyk, & Mill, 2010
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Finding the missing heritability of complex diseases
Manolio, T. A., Collins, F. S., Cox, N. J., Goldstein, D. B., Hindorff, L. A., Hunter, D. J., McCarthy, M. I., Ramos, E. M., Cardon, L. R., Chakravarti, A., et al. (2009) · Nature · doi:10.1038/nature08494 · Cited by 8,336
Influence of life stress on depression: moderation by a polymorphism in the 5-HTT gene
Caspi, A., Sugden, K., Moffitt, T. E., Taylor, A., Craig, I. W., Harrington, H., McClay, J., Mill, J., Martin, J., Braithwaite, A., et al. (2003) · Science · doi:10.1126/science.1083968 · Cited by 8,120
Self-citationRole of genotype in the cycle of violence in maltreated children
Caspi, A., McClay, J., Moffitt, T. E., Mill, J., Martin, J., Craig, I. W., Taylor, A., & Poulton, R. (2002) · Science · doi:10.1126/science.1072290 · Cited by 4,842
Self-citationHuman DNA methylomes at base resolution show widespread epigenomic differences
Lister, R., Pelizzola, M., Dowen, R. H., Hawkins, R. D., Hon, G., Tonti-Filippini, J., Nery, J. R., Lee, L., Ye, Z., Ngo, Q.-M., et al. (2009) · Nature · doi:10.1038/nature08514 · Cited by 4,673
Persistent epigenetic differences associated with prenatal exposure to famine in humans
Heijmans, B. T., Tobi, E. W., Stein, A. D., Putter, H., Blauw, G. J., Susser, E. S., Slagboom, P. E., & Lumey, L. H. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0806560105 · Cited by 3,082
Genomic DNA methylation: the mark and its mediators.
Klose, R. J., & Bird, A. P. (2006) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2005.12.008 · Cited by 2,501
Cancer-epigenetics comes of age
Jones, P. A., & Laird, P. W. (1999) · Nature Genetics · doi:10.1038/5947 · Cited by 2,358
Phenotypic plasticity and the epigenetics of human disease
Feinberg, A. P. (2007) · Nature · doi:10.1038/nature05919 · Cited by 1,613
Principles and challenges of genome-wide DNA methylation analysis
Laird, P. W. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2732 · Cited by 1,611
Direct detection of DNA methylation during single-molecule, real-time sequencing
Flusberg, B. A., Webster, D. R., Lee, J. H., Travers, K. J., Olivares, E. C., Clark, T. A., Korlach, J., & Turner, S. W. (2010) · Nature Methods · doi:10.1038/nmeth.1459 · Cited by 1,460
Flagged first, then by citations
Cited by
Sorted by citations
Items 101–133 of 133
An Integrative View on the Biopsychology of Stress and Posttraumatic Stress Disorder
Varadarajan, S., Behnke, A., Gumpp, A. M., Mavioğlu, R. N., Fissler, P., & Kolassa, I. (2022) · Springer eBooks · doi:10.1007/978-3-030-97802-0_4 · Cited by 6
Rausch, T., Snajder, R., Léger, A., Simovic-Lorenz, M., Stegle, O., Birney, E., Bonder, M. J., Ernst, A., & Korbel, J. O. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.02.20.480758 · Cited by 7
Steyaert, S., Criekinge, W. V., Paepe, A. D., Denil, S. L. I. J., Mensaert, K., Vandepitte, K., Berghe, W. V., Trooskens, G., & Meyer, T. D. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku847 · Cited by 6
Genetic Variation in the H19 - IGF2 Cluster Might Confer Risk of Developing Impaired Renal Function
Coto, E., Corte, C. D., Tranche, S., Gómez, J., Reguero, J. R., Alonso, B., Iglesias, S., Gil‐Peña, H., Yin, X., & Coto‐Segura, P. (2018) · DNA and Cell Biology · doi:10.1089/dna.2017.4135 · Cited by 6
Алфимова, М. В., Kondratyev, N. V., Golov, A. K., & Голимбет, В. Е. (2018) · Psychiatry Research · doi:10.1016/j.psychres.2018.12.134 · Cited by 6
Grant, A. D., Vail, P., Padi, M., Witkiewicz, A., & Knudsen, E. (2018) · Scientific Reports · doi:10.1038/s41598-019-48967-8 · Cited by 5
Integrative Analysis of Genome-wide Expression and Methylation Data
Wang, K. (2013) · Journal of Biometrics & Biostatistics · doi:10.4172/2155-6180.1000e123 · Cited by 5
Chandradoss, K. R., Chawla, B., Dhuppar, S., Nayak, R., Ramachandran, R., Kurukuti, S., Mazumder, A., & Sandhu, K. S. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.108302 · Cited by 5
Examining the Impact of Imputation Errors on Fine-Mapping Using DNA Methylation QTL as a Model Trait
Chundru, V. K., Marioni, R. E., Prendergast, J. G. D., Vallerga, C. L., Lin, T., Beveridge, A. J., Gratten, J., Hume, D. A., Deary, I. J., Wray, N. R., et al. (2019) · Genetics · doi:10.1534/genetics.118.301861 · Cited by 6
Chung, R., & Kang, C.-Y. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz635 · Cited by 5
Epigenetics of Psychopathology
Smith, A. K., Parets, S. E., & Kim, A. W. (2014) · Springer eBooks · doi:10.1007/978-1-4614-9509-3_10 · Cited by 4
Arya, R., Puppala, S., Farook, V. S., Chittoor, G., Jenkinson, C. P., Blangero, J., Hale, D. E., Duggirala, R., & Almasy, L. A. (2015) · Springer eBooks · doi:10.1007/978-3-662-46306-2_12 · Cited by 4
Exploring allele specific methylation in drug dependence susceptibility
Pineda-Cirera, L., Cabana‐Domínguez, J., Grau‐López, L., Daigre, C., Sánchez‐Mora, C., Palma-Álvarez, R. F., Ramos‐Quiroga, J. A., Marta Ribasés, A., Cormand, B., & Fernàndez‐Castillo, N. (2020) · Journal of Psychiatric Research · doi:10.1016/j.jpsychires.2020.07.044 · Cited by 3
DNA Methylation and Ancestry. The Smoke Starts to Clear
DeMeo, D. L., & Rybicki, B. A. (2013) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201309-1644ed · Cited by 3
A method for identifying allele-specific hydroxymethylation
Yamada, Y. M. A., & Sasaki, S. (2019) · Epigenetics · doi:10.1080/15592294.2019.1664228 · Cited by 2
Widespread methylation quantitative trait loci and their role in schizophrenia riskPreprint
Mandell, K. A. P., Eagles, N. J., Wilton, R. N., Price, A. J., Semick, S. A., Collado‐Torres, L., Tao, R., Han, S., Szalay, A. S., Hyde, T. M., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.09.24.311878 · Cited by 2
Dyslexia and Related Communication Disorders
Friend, A., Pennington, B. F., Smith, S. D., & Gilger, J. W. (2013) · Elsevier eBooks · doi:10.1016/b978-0-12-383834-6.00113-0 · Cited by 1
Alterations in DNA Methylation and Hydroxymethylation Due to Parental Care in Rhesus Macaques
Provençal, N., Massart, R., Nemoda, Z., & Suomi, S. J. (2016) · Epigenetics and human health · doi:10.1007/978-3-319-24493-8_7 · Cited by 1
Mislabeled learning for psychiatric disorder detectionPreprint
Li, D., Liu, W., & Han, H. (2022) · medRxiv · doi:10.1101/2022.08.11.22278675 · Cited by 1
Genetic Variants Associated with DNA methylation
Wang, F., Zhang, M., Wen, Y. H., & Zhang, S. J. (2015) · Cancer Genetics and Epigenetics · doi:10.5376/cge.2015.03.0007
The HLA Complex Group 9 Gene Modification Study in Major Psychosis
Pal, M. (2015) · TSpace (University of Toronto)
Liu, L., Lü, M., Gu, X. J., Ma, X., Feng, J., Cao, Y., Gong, W., Zhao, Q., & Qiang, F. (2020) · Journal of Cancer · doi:10.7150/jca.40089
Klengel, T., & Rein, T. (2016) · Epigenetics and human health · doi:10.1007/978-3-319-29901-3_1
Pelizzola, M. (2017) · doi:10.1002/9781118540770.ch2
asms: finding allele-specific methylation in human genomes without phasing
Raineri, E., Marco, M. Á. E., Casals, E., & Esteve‐Codina, A. (2026) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqag072
Elfiky, A. M. I., Smits, H. M., van der Wal, M., Dekkers, C., Boesjes, C. M., Drylewicz, J., de Bruin-Weller, M. S., & van Wijk, F. (2026) · Clinical & Experimental Allergy · doi:10.1111/cea.70397
Li, Q., Gai, Y., Li, Z., Wang, Z., Li, X., Wen, W., & Zhao, C. (2025) · Molecular Neurobiology · doi:10.1007/s12035-025-05469-1
Ye, J., Huang, Z., Li, Q., Li, Z., Lan, Y., Wang, Z., Ni, C., Wu, X., Jiang, T., Li, Y., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26652330
Ye, J., Huang, Z., Li, Q., Li, Z., Lan, Y., Wang, Z., Ni, C., Wu, X., Jiang, T., Li, Y., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26652333
Kubota, A., Kobayashi, H., & Tajima, A. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.04.01.715790
Étude de la méthylation des gènes STAT3, IL2RA et CDH1 dans la maladie de Crohn iléale
Abdalla, S. (2023) · theses.fr (ABES) · doi:10.70675/933404e2z16c4z4b5bz87dfze0af93efba89
Advances in Visualizing Cytosine Methylation and Allele‐Specific Epigenetic States in Tissue Context
Kitazawa, S., Haraguchi, R., & Kitazawa, R. (2026) · Pathology International · doi:10.1111/pin.70133
Lefebvre, M., Cleris, A., Parmentier, M., Loo, P. V., Detours, V., & Tarabichi, M. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.09.02.748867
Metadata
- Authors
- Meaburn, E. L., Schalkwyk, L. C., & Mill, J.
- Affiliations
- King's College London (GB)
- Corresponding author
- Mill, Jonathan
- Venue
- Epigenetics
- Publisher
- Informa UK Limited
- Published
- 2010-10
- Volume
- 5
- Issue
- 7
- Pages
- 578-582
- ISSN
- 1559-2294 (ISSN-L)
- 1559-2308
- PMC
- PMC3052843
- OpenAlex
- W2008091117
- Cited by
- 132
- References
- 32
- Citations by year
- 2026: 5 · 2025: 4 · 2024: 3 · 2023: 4 · 2022: 5 · 2021: 5 · 2020: 9 · 2019: 9 · 2018: 6 · 2017: 14 · 2016: 8 · 2015: 12 · 2014: 9 · 2013: 11 · 2012: 14
- FWCI
- 1.09
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by-nc
- Locations
- Epigenetics (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Open Access at Essex (University of Essex) (acceptedVersion)
- BIROn (Birkbeck, University of London) (submittedVersion)
- Research Portal (King's College London) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Syndromes and Imprinting
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- allele-specific methylation, DNA methylation, CpG, parental origin, missing heritability, complex disease genetics, genome-wide association study, epigenetic inheritance, tissue heterogeneity
- MeSH terms
- Alleles, Disease, Environment, Female, Genetic Complementation Test, Genotype, Humans, Models, Biological, Genetic Variation, Genome, Human, DNA Methylation, Genetic Predisposition to Disease, X Chromosome Inactivation, Genome-Wide Association Study
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
