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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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BackgroundA sequence variant at 4p16.3 confers susceptibility to urinary bladder cancer
Kiemeney, L. A. L. M., Sulem, P., Besenbacher, S., Vermeulen, S. H. H. M., Sigurðsson, Á., Þorleifsson, G., Gudbjartsson, D. F., Stacey, S., Guðmundsson, J., Zanon, C., et al. (2010) · Nature Genetics · doi:10.1038/ng.558 · Cited by 190
Self-citationSteinthórsdóttir, V., McGinnis, R. E., Williams, N., Stefánsdóttir, L., Þorleifsson, G., Shooter, S., Fadista, J., Sigurdsson, J. K., Auro, K. M., Berezina, G., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19733-6 · Cited by 201
Self-citationA hybrid approach for the automated finishing of bacterial genomes
Bashir, A., Klammer, A. A., Robins, W. P., Chin, C.-S., Webster, D. R., Paxinos, E. E., Hsu, D., Ashby, M., Wang, S., Peluso, P. S., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2288 · Cited by 186
“Third-generation single-molecule, real-time (SMRT) sequencing technology from Pacific Biosciences (PacBio) 36 produces sequencing reads by either reading a continuous sequence from the molecular template or by reading a discontinuous, but linearly ordered, set of reads from the template in a…”
MethodThe role of imprinted genes in humans
Ishida, M., & Moore, G. E. (2012) · Molecular Aspects of Medicine · doi:10.1016/j.mam.2012.06.009 · Cited by 185
Nead, K. T., Sharp, S. J., Thompson, D. J., Painter, J. N., Savage, D. B., Semple, R. K., Barker, A., Perry, J. R. B., Attia, J., Dunning, A. M., et al. (2015) · JNCI Journal of the National Cancer Institute · doi:10.1093/jnci/djv178 · Cited by 189
Loss-of-function variants in ATM confer risk of gastric cancer
Helgason, H., Rafnar, Þ., Ólafsdóttir, H. S., Jonasson, J. G., Sigurðsson, Á., Stacey, S., Jónasdóttir, A., Tryggvadóttír, L., Alexiusdottir, K. K., Haraldsson, Á., et al. (2015) · Nature Genetics · doi:10.1038/ng.3342 · Cited by 180
Self-citationGrarup, N., Sulem, P., Sandholt, C. H., Þorleifsson, G., Ahluwalia, T. S., Steinthórsdóttir, V., Bjarnason, H., Gudbjartsson, D. F., Magnússon, Ó. Þ., Sparsø, T., et al. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003530 · Cited by 177
“In Iceland, a large population-based resource has been generated applying WGS and highly accurate imputation of the sequence information into a large fraction of the population [20,21].”
MethodSelf-citationCommentary: The seven plagues of epigenetic epidemiology
Heijmans, B. T., & Mill, J. (2012) · International Journal of Epidemiology · doi:10.1093/ije/dyr225 · Cited by 208
Genetics of type 2 diabetes: pathophysiologic and clinical relevance
Herder, C., & Roden, M. (2010) · European Journal of Clinical Investigation · doi:10.1111/j.1365-2362.2010.02454.x · Cited by 187
Common and rare variants associated with kidney stones and biochemical traits
Oddsson, Á., Sulem, P., Helgason, H., Edvardsson, V. O., Þorleifsson, G., Sveinbjörnsson, G., Haraldsdottir, E., Eyjolfsson, G. I., Sigurðardóttir, Ó., Ólafsson, Í., et al. (2015) · Nature Communications · doi:10.1038/ncomms8975 · Cited by 173
Self-citationde Miguel-Yanes, J. M., Shrader, P. J., Pencina, M. J., Fox, C. S., Manning, A. K., Grant, R. W., Dupuis, J., Florez, J. C., D’Agostino, R. B., Cupples, L. A., et al. (2010) · Diabetes Care · doi:10.2337/dc10-1265 · Cited by 172
Relatedness disequilibrium regression estimates heritability without environmental bias
Young, A. I., Frigge, M. L., Gudbjartsson, D. F., Thorleifsson, G., Bjornsdottir, G., Sulem, P., Masson, G., Thorsteinsdottir, U., Stefansson, K., & Kong, A. (2018) · Nature Genetics · doi:10.1038/s41588-018-0178-9 · Cited by 173
Self-citationAhlqvist, E., Ahluwalia, T. S., & Groop, L. (2011) · Clinical Chemistry · doi:10.1373/clinchem.2010.157016 · Cited by 166
Styrkársdóttir, U., Lund, S. H., Þorleifsson, G., Zink, F., Stefánsson, Ó. A., Sigurdsson, J. K., Juliusson, K., Bjarnadóttir, K., Sigurbjörnsdóttir, S., Jonsson, S., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0247-0 · Cited by 174
Self-citationGenetic Screening for the Risk of Type 2 Diabetes
Lyssenko, V., & Laakso, M. (2013) · Diabetes Care · doi:10.2337/dcs13-2009 · Cited by 181
“Hypermethylation of the maternal allele of KCNQ1 results in monoallelic activity of the neighboring maternally expressed protein-coding genes and is associatedwith the risk of type 2 diabetes (51).”
BackgroundDominguez-Salas, P., Cox, S. E., Prentice, A. M., Hennig, B. J., & Moore, S. E. (2012) · Proceedings of the Nutrition Society · doi:10.1017/s0029665111003338 · Cited by 163
“The most convincing evidence has been observed in relation to carcinogenesis((40,41)), but there is also growing evidence that epigenetic dysregulation affects other life-course diseases such as CVD((42)), type 2 diabetes((43)) and obesity((44)).”
Nickels, S., Truong, T., Hein, R., Purrington, K. S., Buck, K., Behrens, S., Eilber, U., Schmidt, M. E., Häberle, L., Vrieling, A., et al. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003284 · Cited by 172
“The SNP lies close to the H19/IGF2 imprinted region, and the association of breast cancer with rs3817198 has been reported to be restricted to the paternally inherited allele [11].”
BackgroundRare and Common Genetic Events in Type 2 Diabetes: What Should Biologists Know?
Bonnefond, A., & Froguel, P. (2015) · Cell Metabolism · doi:10.1016/j.cmet.2014.12.020 · Cited by 174
Styrkársdóttir, U., Þorleifsson, G., Helgadottir, H. T., Bömer, N., Metrustry, S., Bierma‐Zeinstra, S., Strijbosch, A. M., Εvangelou, Ε., Hart, D. J., Beekman, M., et al. (2014) · Nature Genetics · doi:10.1038/ng.2957 · Cited by 158
Self-citationGenetics of diabetes – Are we missing the genes or the disease?
Groop, L., & Pociot, F. (2013) · Molecular and Cellular Endocrinology · doi:10.1016/j.mce.2013.04.002 · Cited by 168
Rafnar, Þ., Vermeulen, S. H. H. M., Sulem, P., Þorleifsson, G., Aben, K. K. H., Witjes, J. A., Grotenhuis, A. J., Verhaegh, G. W. C. T., de Kaa, C. A. H., Besenbacher, S., et al. (2011) · Human Molecular Genetics · doi:10.1093/hmg/ddr303 · Cited by 152
“The imputation method used for the Icelandic data set has been described previously (42).”
MethodSelf-citationA combined long-range phasing and long haplotype imputation method to impute phase for SNP genotypes
Hickey, J. M., Kinghorn, B. P., Tier, B., Wilson, J. F., Dunstan, N., & van der Werf, J. H. J. (2011) · Genetics Selection Evolution · doi:10.1186/1297-9686-43-12 · Cited by 147
“Knowing the phase of marker genotype data can be useful in genome-wide association studies (GWAS), because it makes it possible to use analysis frameworks that account for identity by descent (IBD) or parent of origin of alleles [1] and it can lead to a large increase in data quantities via genotype or sequence imputa…”
BackgroundThe emerging genetics of type 2 diabetes
Bonnefond, A., Froguel, P., & Vaxillaire, M. (2010) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2010.06.004 · Cited by 153
Schmidt, E. B., Dhaouadi, I., Gaziano, I., Oliverio, M., Klemm, P., Awazawa, M., Mitterer, G., Fernández‐Rebollo, E., Pradas-Juni, M., Wagner, W., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-05933-8 · Cited by 145
Common and low-frequency variants associated with genome-wide recombination rate
Kong, A., Þorleifsson, G., Frigge, M. L., Másson, G., Gudbjartsson, D. F., Villemoes, R., Magnúsdóttir, E., Olafsdottir, S. B., Þorsteinsdóttir, U., & Stefánsson, K. (2013) · Nature Genetics · doi:10.1038/ng.2833 · Cited by 138
Self-citationPhased Whole-Genome Genetic Risk in a Family Quartet Using a Major Allele Reference Sequence
Dewey, F. E., Chen, R., Cordero, S. P., Ormond, K. E., Caleshu, C. A., Karczewski, K. J., Whirl‐Carrillo, M., Wheeler, M. T., Dudley, J. T., Byrnes, J., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002280 · Cited by 141
“Furthermore, several common SNPs have been associated with disease risk, most notably diabetes mellitus 2, in a sex specific manner, such that maternal origin confers direct association with risk of disease and paternal origin confers indirect association with disease risk [35].”
BackgroundA rare IL33 loss-of-function mutation reduces blood eosinophil counts and protects from asthma
Smith, D. E., Helgason, H., Sulem, P., Björnsdóttir, U. S., Lim, A. C., Sveinbjörnsson, G., Hasegawa, H., Brown, M. E., Ketchem, R. R., Gavala, M. L., et al. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1006659 · Cited by 140
“150,656 Icelanders who had been genotyped with various Illumina SNP chips and their genotypes phased using long-range phasing chip-genotyped individuals using long-range phasing [44].”
MethodSelf-citationChoufani, S., Shapiro, J. S., Susiarjo, M., Butcher, D. T., Grafodatskaya, D., Lou, Y., Ferreira, J. C., Pinto, D., Scherer, S. W., Shaffer, L. G., et al. (2011) · Genome Research · doi:10.1101/gr.111922.110 · Cited by 139
Allele-specific methylation in the human genome: Implications for genetic studies of complex disease
Meaburn, E. L., Schalkwyk, L. C., & Mill, J. (2010) · Epigenetics · doi:10.4161/epi.5.7.12960 · Cited by 132
Helgason, H., Sulem, P., Duvvari, M. R., Luo, H., Þorleifsson, G., Stefánsson, H., Jónsdóttir, I., Másson, G., Gudbjartsson, D. F., Walters, G. B., et al. (2013) · Nature Genetics · doi:10.1038/ng.2740 · Cited by 141
Self-citationA missense variant in PTPN22 is a risk factor for drug-induced liver injury
Cirulli, E. T., Nicoletti, P., Abramson, K., Andrade, R. J., Bjornsson, E. S., Chalasani, N., Fontana, R. J., Hallberg, P., Li, Y. J., Lucena, M. I., et al. (2019) · Gastroenterology · doi:10.1053/j.gastro.2019.01.034 · Cited by 137
Chen, X., Li, S., YANG, Y., Yang, X., Liu, Y., LIU, Y., HU, W., Li, J., & WANG, X. (2012) · Journal of Thrombosis and Haemostasis · doi:10.1111/j.1538-7836.2012.04815.x · Cited by 136
DNA methylation and epigenetic control of cellular differentiation
Khavari, D. A., Sen, G. L., & Rinn, J. L. (2010) · Cell Cycle · doi:10.4161/cc.9.19.13385 · Cited by 135
Pollak, N. M., Hoffman, M., Goldberg, I. J., & Drosatos, K. (2018) · JACC Basic to Translational Science · doi:10.1016/j.jacbts.2017.09.001 · Cited by 145
Parental Obesity and Risk of Autism Spectrum Disorder
Surén, P., Gunnes, N., Roth, C., Bresnahan, M. A., Hornig, M., Hirtz, D., Lie, K. K., Lipkin, W. I., Magnus, P. M., Reichborn-Kjennerud, T., et al. (2014) · PEDIATRICS · doi:10.1542/peds.2013-3664 · Cited by 137
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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