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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Many genetic and epigenetic factors, including multiple rare single nucleotide variants, copy number variations, and other structural variation, likely contribute to common complex diseases.
“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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- 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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