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Parental origin of sequence variants associated with complex diseases
Open accessAbstract
Effects of susceptibility variants may depend on from which parent they are inherited. Although many associations between sequence variants and human traits have been discovered through genome-wide associations, the impact of parental origin has largely been ignored. Here we show that for 38,167 Icelanders genotyped using single nucleotide polymorphism (SNP) chips, the parental origin of most alleles can be determined. For this we used a combination of genealogy and long-range phasing. We then focused on SNPs that associate with diseases and are within 500 kilobases of known imprinted genes. Seven independent SNP associations were examined. Five-one with breast cancer, one with basal-cell carcinoma and three with type 2 diabetes-have parental-origin-specific associations. These variants are located in two genomic regions, 11p15 and 7q32, each harbouring a cluster of imprinted genes. Furthermore, we observed a novel association between the SNP rs2334499 at 11p15 and type 2 diabetes. Here the allele that confers risk when paternally inherited is protective when maternally transmitted. We identified a differentially methylated CTCF-binding site at 11p15 and demonstrated correlation of rs2334499 with decreased methylation of that site.
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“It is now widely believed that many genetic and epigenetic factors are likely to contribute to common complex diseases, including multiple rare SNVs (defined by convention as those that have frequencies < 1%), copy number variations (CNVs), and other forms of structural variation. 3–12”
From Statistical analysis strategies for association studies involving rare variants (2010) · cites this paper as [6]
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Denton, J. S., & Jacobson, D. A. (2011) · Trends in Endocrinology and Metabolism · doi:10.1016/j.tem.2011.09.004 · Cited by 15
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“The first rule-based algorithm for long-range phasing was described by Kong et al , 9,10 and is similar to the method presented later by Hickey et al. 11 Both of these methods detect IBD sharing only in pre-specified genetic regions, identical for all pairs of compared diplotypes, whereas in reality…”
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“One example in which the use of tissue expression data sets not only identified the likely causal transcript, but also uncovered a transcription factor network critical for adipose tissue function is the 7q32 locus, which is one of only two T2D susceptibility loci showing parental-origin-specific association [28].”
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RNA as the substrate for epigenome‐environment interactions
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Haplotype Phasing and Inheritance of Copy Number Variants in Nuclear Families
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“Just as the phase information has been shown to be important in case of SNP variants [29, 30], elucidating the exact distribution of copies of a particular DNA sequence on two sets of chromosomes may prove beneficial in case of CNVs [6, 31].”
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Imumorin, I. G., PETERS, S. O., & Donato, M. D. (2011) · doi:10.1002/9781119949930.ch6 · Cited by 10
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“Several studies have revealed that the maternally transmitted T allele of the rs4731702 SNP is associated with the upregulation of KLF14 gene expression in adipose tissues (16).”
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Haavik, J., Halmøy, A., Hegvik, T., & Johansson, S. (2011) · Future Neurology · doi:10.2217/fnl.11.54 · Cited by 9
“Although some attempts have been made to determine the parental genetic origin of complex diseases [106], most published GWA studies do not separately analyze the maternal genomes, and the maternal programming effects that are discussed in this article will remain undiscovered in conventional”
BackgroundGenome-wide approaches to the etiology of eczema
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“There are good reasons to examine parent-of-origin effects in general, and in studies of language-related traits and disorders in particular: firstly, they may account for some of the so-called “missing heritability” (the difference between disease heritability estimates and the variance explained by significant GWAS…”
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“Because imprinted genes tend to cluster together, it has been efficacious to examine regions within 500kb of imprinted genes to identify parent of origin effects, therefore, these GLRX SNPs might well be within the imprinted cluster [Kong et al., 2009].”
Searching for parent-of-origin effects on cardiometabolic traits in imprinted genomic regions
Granot‐Hershkovitz, E., Wu, P., Karasik, D., Peter, I., Peloso, G. M., Levy, D. A., Vasan, R. S., Cupples, L. A., Liu, C., Meigs, J. B., et al. (2020) · European Journal of Human Genetics · doi:10.1038/s41431-019-0568-1 · Cited by 7
“For example Kong et al. demonstrated POE on type 2 diabetes (T2D) and cancer in Icelandic families showing strengthening of effects for previously reported associations and revealing novel associations with T2D [20].”
Zhang, X., & Hocher, B. (2024) · American Journal of Physiology-Cell Physiology · doi:10.1152/ajpcell.00359.2024 · Cited by 8
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“KLF14 is known to be an imprinted gene wherein only the maternal-inherited allele is functional, and interestingly, the gene has been linked to the regulatory processes of placental development and embryogenesis [22,23].”
BackgroundParent-of-origin in individuals with familial neurofibromatosis type 1 and optic pathway gliomas
Johnson, K. J., Fisher, M. J., Listernick, R., North, K. N., Schorry, E. K., Viskochil, D. H., Weinstein, M., Rubin, J. B., & Gutmann, D. H. (2012) · Familial Cancer · doi:10.1007/s10689-012-9549-z · Cited by 8
“population [6].”
BackgroundIndications for Potential Parent-of-Origin Effects within the FTO Gene
Liu, X., Hinney, A., Scholz, M. R., Scherag, A., Tönjes, A., Stümvoll, M., Stadler, P. F., Hebebrand, J., & Böttcher, Y. (2015) · PLoS ONE · doi:10.1371/journal.pone.0119206 · Cited by 8
“For some types of cancer and Type 2 Diabetes (T2D), Kong et al [22] applied phasing algorithms to Icelandic individuals and showed considerable evidence that some genetic variants indeed confer significantly different risk depending strongly on parental origin.”
BackgroundWeinberg, C. R., Shi, M., DeRoo, L. A., Taylor, J. A., Sandler, D. P., & Umbach, D. M. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004174 · Cited by 8
“Such an effect was reported for breast cancer by Kong, et al [10] based on Icelandic family data.”
BackgroundEllberg, C., & Olsson, H. L. (2011) · BMC Cancer · doi:10.1186/1471-2407-11-497 · Cited by 8
“[24] found a region at 11p15 with a paternal inheritance associated with breast cancer, which further supports the possibility of allelic imprinting or a peculiar inheritance involving males with cancer and females developing breast cancer.”
Mozaffari, S. V., Stein, M. M., Magnaye, K. M., Nicolae, D. L., & Ober, C. (2018) · PLoS ONE · doi:10.1371/journal.pone.0203906 · Cited by 8
“One approach to identifying imprinted loci in humans has been to test for parent of origin effects on gene expression and phenotypes in pedigrees [4,12].”
BackgroundUnderstanding CpG Methylation in the Context of Osteoarthritis
Young, D. A., Bui, C., & Barter, M. J. (2012) · Epigenomics · doi:10.2217/epi.12.63 · Cited by 8
Sex-specific transgenerational plasticity I: Maternal and paternal effects on sons and daughtersPreprint
Hellmann, J. K., Bukhari, S. A., Deno, J., & Bell, A. M. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/763862 · Cited by 10
“, eggs versus 227 sperm) and/or parent-of-origin effects (35).”
Genetic Regulation of DNA Methylation Yields Novel Discoveries in GWAS of Colorectal Cancer
Barfield, R., Huyghe, J. R., Lemire, M., Dong, X., Su, Y.-R., Brezina, S., Buchanan, D. D., Figueiredo, J. C., Gallinger, S., Giannakis, M., et al. (2022) · Cancer Epidemiology Biomarkers & Prevention · doi:10.1158/1055-9965.epi-21-0724 · Cited by 6
Mohtashami, Z., Singh, M. K., Neto, F. J. T., Salimiaghdam, N., Hasanpour, H., & Kenney, M. C. (2023) · Antioxidants · doi:10.3390/antiox12020518 · Cited by 9
“Mitochondrial dysfunction is present in glaucoma animal models prior to RGC death [79,80], suggesting a primary effect for mitochondrial abnormalities in glaucoma onset and subsequent progressive loss of vision.”
Partitioning Phenotypic Variance Due to Parent-of-Origin Effects Using Genomic Relatedness Matrices
Laurin, C., Cuéllar-Partida, G., Hemani, G., Smith, G. D., Yang, J., & Evans, D. M. (2017) · Behavior Genetics · doi:10.1007/s10519-017-9880-0 · Cited by 7
“2013), evidence for the existence of POEs in the etiology of complex human traits and diseases is mixed, in part due to the relative paucity of genomic data from families (Kong et al. 2009; Guilmatre and Sharp 2012).”
BackgroundInfluentialNudel, R., Zetterberg, R., Hemager, N., Christiani, C. J., Ohland, J., Burton, B. K., Greve, A. N., Spang, K. S., Ellersgaard, D., Gantriis, D. L., et al. (2022) · Behavioral and Brain Functions · doi:10.1186/s12993-022-00198-0 · Cited by 7
“POEs have been implicated in many studies of complex traits and diseases [24].”
BackgroundElliott, H. R., Walia, G. K., Duggirala, A., Groom, A., Reddy, S., Chandak, G. R., Gupta, V., Laakso, M., Dekker, J. M., Walker, M., et al. (2013) · journal of Diabetes Research and Clinical Metabolism · doi:10.7243/2050-0866-2-6 · Cited by 6
“Additionally, underlying genetic variation also plays a role in determining patterns of DNA methylation [7-11].”
BackgroundGenetics of Type 2 diabetes in Asian Indians
Radha, V., Kanthimathi, S., & Mohan, V. (2011) · Diabetes Management · doi:10.2217/dmt.11.14 · Cited by 7
Sun, X., Sui, W., Wang, X., Hou, X., Ou, M., Dai, Y., & Xiang, Y. (2016) · Molecular Medicine Reports · doi:10.3892/mmr.2016.5014 · Cited by 8
Transmission of Type 2 diabetes to sons and daughters: the D.E.S.I.R. cohort
Balkau, B., Roussel, R., Wagner, S., Tichet, J., Froguel, P., Fagherazzi, G., Bonnet, F., & for the D.E.S.I.R. Study Group (2017) · Diabetic Medicine · doi:10.1111/dme.13446 · Cited by 7
Imprinted genes in myeloid lineage commitment in normal and malignant hematopoiesis
Benetatos, L., & Vartholomatos, G. (2015) · Leukemia · doi:10.1038/leu.2015.47 · Cited by 7
Kahn, H. S., Stein, A. D., & Lumey, L. H. (2010) · Journal of Developmental Origins of Health and Disease · doi:10.1017/s2040174410000474 · Cited by 7
“Perhaps a gene can have opposite effects on the risk of diabetes if its origin is paternal rather than maternal.(39) Apart from this imprinting phenomenon, genetic variants associated with reduced insulin sensitivity may be fewer in number, less prevalent or have more modest effects on the insulin sensitivity phenotyp…”
BackgroundA Unified Framework Integrating Parent-of-Origin Effects for Association Study
Xiao, F., Ma, J., & Amos, C. I. (2013) · PLoS ONE · doi:10.1371/journal.pone.0072208 · Cited by 7
“identified several variants of known imprinted genes showing significant effects on development of breast cancer, carcinoma and type II diabetes [7].”
BackgroundMolecular Genetics of Metabolic Syndrome
Chang, Y., Yu, Y., & Chuang, L. (2013) · Wiley eBooks · doi:10.1002/9780470015902.a0024320 · Cited by 7
Realizing the full potential of Our Future Health through data linkage and trans-biobank efforts
Straub, V. J., Benónísdóttir, S., Kong, A., & Mills, M. C. (2025) · Nature Genetics · doi:10.1038/s41588-025-02327-7 · Cited by 6
Self-citationBaumann, P., Schriever, S. C., Kullmann, S., Zimprich, A., Peter, A., Gailus‐Durner, V., Fuchs, H., de Angelis, M. H., Wurst, W., Tschöp, M. H., et al. (2020) · Brain and Behavior · doi:10.1002/brb3.1928 · Cited by 6
“The increased preference for sweet high caloric food in Dusp8 minor allele adds to earlier work on the association of SNP rs2334499 minor allele with the overall type 2 diabetes risk (Kong et al., 2009; Morris et al., 2012) or the increased hypothalamic insulin resistance (Schriever et al., 2020).”
BackgroundInfluentialImprinted Genes Impact Upon Beta Cell Function in the Current (and Potentially Next) Generation
Villanueva-Hayes, C., & Millership, S. J. (2021) · Frontiers in Endocrinology · doi:10.3389/fendo.2021.660532 · Cited by 6
Primak, A. L., Дмитриевич, Б. К., Rubina, K. A., Станиславович, Д. С., Neyfeld, E. A., Illarionova, M. E., Semina, E. V., Sheleg, D., Va, T., & Karagyaur, M. N. (2024) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2024.1361764 · Cited by 7
Parent-of-origin effects on schizophrenia-relevant behaviours of type III neuregulin 1 mutant mice
Shang, K., Talmage, D. A., & Karl, T. (2017) · Behavioural Brain Research · doi:10.1016/j.bbr.2017.05.057 · Cited by 6
Epigenetics in Exercise Science and Sports Medicine
Zimmer, P., Schenk, A., & Bloch, W. (2016) · Elsevier eBooks · doi:10.1016/b978-0-12-803239-8.00029-6 · Cited by 6
Roofeh, D., Tumuluru, D., Shilpakar, S., & Nimgaonkar, V. L. (2013) · International Journal of Mental Health · doi:10.2753/imh0020-7411420101 · Cited by 6
“Imprinting has also been proposed for diabetes mellitus [73].”
Head, S. T., Leslie, E. J., Cutler, D. J., & Epstein, M. P. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btad199 · Cited by 5
“For example, Kong et al. (2009) inferred parental origin of alleles when parental genotype data are not available by first phasing Icelandic probands.”
BackgroundMethodkConFab Investigators, Barnes, D. R., Australian Ovarian Cancer Study Group, Barrowdale, D., Beesley, J., Chen, X., James, P. A., Hopper, J. L., Goldgar, D. E., Chenevix‐Trench, G., et al. (2013) · British Journal of Cancer · doi:10.1038/bjc.2013.277 · Cited by 5
Metadata
- Authors
- DIAGRAM Consortium, Kong, A., Steinthorsdottir, V., Masson, G., Thorleifsson, G., Sulem, P., Besenbacher, S., Jonasdottir, A., Sigurdsson, A., Kristinsson, K. T., Jonasdottir, A., Frigge, M. L., Gylfason, A., Olason, P. I., Gudjonsson, S. A., Sverrisson, S., Stacey, S. N., Sigurgeirsson, B., Benediktsdottir, K. R., Sigurdsson, H., Jonsson, T., Benediktsson, R., Olafsson, J. H., Johannsson, O. T., Hreidarsson, A. B., Sigurdsson, G., Ferguson-Smith, A. C., Gudbjartsson, D. F., Thorsteinsdottir, U., & Stefansson, K.
- Affiliations
- deCODE Genetics (Iceland) (IS)
- National University Hospital of Iceland (IS)
- Corresponding author
- Kong, Augustine
- ORCID
- Venue
- Nature
- Published
- 2009-12
- Volume
- 462
- Issue
- 7275
- Pages
- 868-874
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3746295
- OpenAlex
- W2156431476
- Cited by
- 553
- References
- 23
- Citations by year
- 2026: 3 · 2025: 12 · 2024: 16 · 2023: 8 · 2022: 18 · 2021: 24 · 2020: 24 · 2019: 22 · 2018: 28 · 2017: 32 · 2016: 32 · 2015: 55 · 2014: 43 · 2013: 57 · 2012: 49
- FWCI
- 34.22
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Research Explorer (The University of Manchester) (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Site cant be reached (submittedVersion)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, other-oa)
- Open Research (University of Surrey) (submittedVersion)
- Hirsla (Landspítali University Hospital) (submittedVersion, other-oa)
- Newcastle University ePrints (Newcastle Univesity)
- Funders
- Wellcome Trust (077016, 090532)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01DK029867)
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (K08AR055688)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Syndromes and Imprinting
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Keywords
- parental origin, genomic imprinting, imprinted genes, genetic variants, type 2 diabetes, breast cancer, basal cell carcinoma, 11p15, CTCF binding sites, DNA methylation, genealogy, TCF7L2, complex diseases
- MeSH terms
- CCCTC-Binding Factor, Alleles, Binding Sites, Breast Neoplasms, Basal Cell Carcinoma, Chromosomes, Human, Pair 11, Chromosomes, Human, Pair 7, Diabetes Mellitus, Type 2, Fathers, Female, Haplotypes, Humans, Iceland, Male, Mothers, Pedigree, Repressor Proteins, Genome, Human, Genomic Imprinting, DNA Methylation, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide
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