Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
- Authors
- Perry, John Rb; Day, Felix; Elks, Cathy E; Sulem, Patrick; Thompson, Deborah J; Ferreira, Teresa; He, Chunyan; Chasman, Daniel I; Esko, TΓ΅nu; Thorleifsson, Gudmar; Albrecht, Eva; Ang, Wei Q; Corre, Tanguy; Cousminer, Diana L; Feenstra, Bjarke; Franceschini, Nora; Ganna, Andrea; Johnson, Andrew D; Kjellqvist, Sanela; Lunetta, Kathryn L; McMahon, George; Nolte, Ilja M; Paternoster, Lavinia; Porcu, Eleonora; Smith, Albert V; Stolk, Lisette; Teumer, Alexander; TΕ‘ernikova, Natalia; Tikkanen, Emmi; Ulivi, Sheila; Wagner, Erin K; Amin, Najaf; Bierut, Laura J; Byrne, Enda M; Hottenga, Jouke-Jan; Koller, Daniel L; Mangino, Massimo; Pers, Tune H; Yerges-Armstrong, Laura M; Zhao, Jing Hua; Andrulis, Irene L; Anton-Culver, Hoda; Atsma, Femke; Bandinelli, Stefania; Beckmann, Matthias W; Benitez, Javier; Blomqvist, Carl; Bojesen, Stig E; Bolla, Manjeet K; Bonanni, Bernardo; Brauch, Hiltrud; Brenner, Hermann; Buring, Julie E; Chang-Claude, Jenny; Chanock, Stephen; Chen, Jinhui; Chenevix-Trench, Georgia; CollΓ©e, J Margriet; Couch, Fergus J; Couper, David; Coveillo, Andrea D; Cox, Angela; Czene, Kamila; D'adamo, Adamo Pio; Smith, George Davey; De Vivo, Immaculata; Demerath, Ellen W; Dennis, Joe; Devilee, Peter; Dieffenbach, Aida K; Dunning, Alison M; Eiriksdottir, Gudny; Eriksson, Johan G; Fasching, Peter A; Ferrucci, Luigi; Flesch-Janys, Dieter; Flyger, Henrik; Foroud, Tatiana; Franke, Lude; Garcia, Melissa E; GarcΓa-Closas, Montserrat; Geller, Frank; de Geus, Eco Ej; Giles, Graham G; Gudbjartsson, Daniel F; Gudnason, Vilmundur; GuΓ©nel, Pascal; Guo, Suiqun; Hall, Per; Hamann, Ute; Haring, Robin; Hartman, Catharina A; Heath, Andrew C; Hofman, Albert; Hooning, Maartje J; Hopper, John L; Hu, Frank B; Hunter, David J; Karasik, David; Kiel, Douglas P; Knight, Julia A; Kosma, Veli-Matti; Kutalik, Zoltan; Lai, Sandra; Lambrechts, Diether; Lindblom, Annika; MΓ€gi, Reedik; Magnusson, Patrik K; Mannermaa, Arto; Martin, Nicholas G; Masson, Gisli; McArdle, Patrick F; McArdle, Wendy L; Melbye, Mads; Michailidou, Kyriaki; Mihailov, Evelin; Milani, Lili; Milne, Roger L; Nevanlinna, Heli; Neven, Patrick; Nohr, Ellen A; Oldehinkel, Albertine J; Oostra, Ben A; Palotie, Aarno; Peacock, Munro; Pedersen, Nancy L; Peterlongo, Paolo; Peto, Julian; Pharoah, Paul Dp; Postma, Dirkje S; Pouta, Anneli; PylkΓ€s, Katri; Radice, Paolo; Ring, Susan; Rivadeneira, Fernando; Robino, Antonietta; Rose, Lynda M; Rudolph, Anja; Salomaa, Veikko; Sanna, Serena; Schlessinger, David; Schmidt, Marjanka K; Southey, Mellissa C; Sovio, Ulla; Stampfer, Meir J; StΓΆckl, Doris; Storniolo, Anna M; Timpson, Nicholas J; Tyrer, Jonathan; Visser, Jenny A; Vollenweider, Peter; VΓΆlzke, Henry; Waeber, Gerard; Waldenberger, Melanie; Wallaschofski, Henri; Wang, Qin; Willemsen, Gonneke; Winqvist, Robert; Wolffenbuttel, Bruce Hr; Wright, Margaret J; Australian Ovarian Cancer Study; GENICA Network; kConFab; LifeLines Cohort Study; InterAct Consortium; Early Growth Genetics (EGG) Consortium; Boomsma, Dorret I; Econs, Michael J; Khaw, Kay-Tee; Loos, Ruth Jf; McCarthy, Mark I; Montgomery, Grant W; Rice, John P; Streeten, Elizabeth A; Thorsteinsdottir, Unnur; van Duijn, Cornelia M; Alizadeh, Behrooz Z; Bergmann, Sven; Boerwinkle, Eric; Boyd, Heather A; Crisponi, Laura; Gasparini, Paolo; Gieger, Christian; Harris, Tamara B; Ingelsson, Erik; JΓ€rvelin, Marjo-Riitta; Kraft, Peter; Lawlor, Debbie; Metspalu, Andres; Pennell, Craig E; Ridker, Paul M; Snieder, Harold; SΓΈrensen, Thorkild Ia; Spector, Tim D; Strachan, David P; Uitterlinden, AndrΓ© G; Wareham, Nicholas J; Widen, Elisabeth; Zygmunt, Marek; Murray, Anna; Easton, Douglas F; Stefansson, Kari; Murabito, Joanne M; Ong, Ken K
- Year
- 2014
- Journal
- Nature
- PMID
- 25231870
- DOI
- 10.1038/nature13545
- PMCID
- PMC4185210
Age at menarche is a marker of timing of puberty in females. It varies widely between individuals, is a heritable trait and is associated with risks for obesity, type 2 diabetes, cardiovascular disease, breast cancer and all-cause mortality. Studies of rare human disorders of puberty and animal models point to a complex hypothalamic-pituitary-hormonal regulation, but the mechanisms that determine pubertal timing and underlie its links to disease risk remain unclear. Here, using genome-wide and custom-genotyping arrays in up to 182,416 women of European descent from 57 studies, we found robust evidence (Pβ<β5βΓβ10(-8)) for 123 signals at 106 genomic loci associated with age at menarche. Many loci were associated with other pubertal traits in both sexes, and there was substantial overlap with genes implicated in body mass index and various diseases, including rare disorders of puberty. Menarche signals were enriched in imprinted regions, with three loci (DLK1-WDR25, MKRN3-MAGEL2 and KCNK9) demonstrating parent-of-origin-specific associations concordant with known parental expression patterns. Pathway analyses implicated nuclear hormone receptors, particularly retinoic acid and Ξ³-aminobutyric acid-B2 receptor signalling, among novel mechanisms that regulate pubertal timing in humans. Our findings suggest a genetic architecture involving at least hundreds of common variants in the coordinated timing of the pubertal transition.
Manhattan and QQ plot of the GWAS for age at menarcheManhattan (main panel) and quantile-quantile (QQ) (embedded) plots illustrating results of the genome-wide association study (GWAS) meta-analysis for age at menarche in up to 182,416 women of European descent. The Manhattan plot presents the association -log10 P-values for each genome-wide SNP (Y-axis) by chromosomal position (X-axis). The red line indicates the threshold for genome-wide statistical significance (P=5Γ10β8). Blue dots represent SNPs whose nearest gene is the same as that of the genome-wide significant signals. The QQ plot illustrates the deviation of association test statistics (blue dots) from the distribution expected under the null hypothesis (red line).
Forest plot of parent-of-origin specific allelic associations at three imprinted menarche lociThe forest plot illustrates the associations of variants in four independent genomic signals for age at menarche that are located in three imprinted gene regions. For each variant, squares (and error bars) indicate the estimated per-allele effect sizes on age at menarche in years (and 95% confidence intervals) from the standard additive models in the combined ReproGen meta-analysis (Black), and separately for the paternally-inherited (Blue) or maternally-inherited allele (Red) in up to 35,377 women from the deCODE study. The association for the menarche locus with the largest effect size at LIN28B is also shown for reference, illustrating the similar magnitude of effect size at the MKRN3 locus when parent-of-origin is taken into account.
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| Review of the Literature on Current Changes in the Timing of Pubertal Development and the Incomplete Forms of Early Puberty. | Farello G et al. | β | 2019 | β |
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| Dissection of genetic variation and evidence for pleiotropy in male pattern baldness. | Yap CX et al. | β | 2018 | β |
| Elucidating the genetic architecture of reproductive ageing in the Japanese population. | Horikoshi M et al. | β | 2018 | β |
| Exploring the association of genetic factors with participation in the Avon Longitudinal Study of Parents and Children. | Taylor AE et al. | β | 2018 | β |
| Father Absence and Accelerated Reproductive Development in Non-Hispanic White Women in the United States. | Gaydosh L et al. | β | 2018 | β |
| FineMAV: prioritizing candidate genetic variants driving local adaptations in human populations. | Szpak M et al. | β | 2018 | β |
| FUN-LDA: A Latent Dirichlet Allocation Model for Predicting Tissue-Specific Functional Effects of Noncoding Variation: Methods and Applications. | Backenroth D et al. | β | 2018 | β |
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| Genetically Determined Later Puberty Impacts Lowered Bone Mineral Density in Childhood and Adulthood. | Cousminer DL et al. | β | 2018 | β |
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| Genome sequencing in the clinic: the past, present, and future of genomic medicine. | Prokop JW et al. | β | 2018 | β |
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| Genome-wide survey of parent-of-origin effects on DNA methylation identifies candidate imprinted loci in humans. | Cuellar Partida G et al. | β | 2018 | β |
| Global DNA methylation changes spanning puberty are near predicted estrogen-responsive genes and enriched for genes involved in endocrine and immune processes. | Thompson EE et al. | β | 2018 | β |
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| <i>STAT6</i>, <i>PBX2</i>, and <i>PBRM1</i> Emerge as Predicted Regulators of 452 Differentially Expressed Genes Associated With Puberty in Brahman Heifers. | Nguyen LT et al. | β | 2018 | β |
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| Large-scale meta-analysis highlights the hypothalamic-pituitary-gonadal axis in the genetic regulation of menstrual cycle length. | Laisk T et al. | β | 2018 | β |
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| Partitioning Phenotypic Variance Due to Parent-of-Origin Effects Using Genomic Relatedness Matrices. | Laurin C et al. | β | 2018 | β |
| Phenotype-Specific Enrichment of Mendelian Disorder Genes near GWAS Regions across 62 Complex Traits. | Freund MK et al. | β | 2018 | β |
| Roles of NUCKS1 in Diseases: Susceptibility, Potential Biomarker, and Regulatory Mechanisms. | Huang P et al. | β | 2018 | β |
| Sex-specific glioma genome-wide association study identifies new risk locus at 3p21.31 in females, and finds sex-differences in risk at 8q24.21. | Ostrom QT et al. | β | 2018 | β |
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| Update Breast Cancer 2018 (Part 1) - Primary Breast Cancer and Biomarkers. | Taran FA et al. | β | 2018 | β |
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| Age at Menarche and Risk of Multiple Sclerosis: A Prospective Cohort Study Based on the Danish National Birth Cohort. | Nielsen NM et al. | β | 2017 | β |
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| Association between age at menarche and cardiovascular disease: A systematic review on risk and potential mechanisms. | Luijken J et al. | β | 2017 | β |
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| Characterization of natural variation in North American Atlantic Salmon populations (Salmonidae: <i>Salmo salar</i>) at a locus with a major effect on sea age. | Kusche H et al. | β | 2017 | β |
| Common variants in ZMIZ1 and near NGF confer risk for primary dysmenorrhoea. | Li Z et al. | β | 2017 | β |
| Disentangling puberty: novel neuroendocrine pathways and mechanisms for the control of mammalian puberty. | AvendaΓ±o MS et al. | β | 2017 | β |
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| Diversity in non-repetitive human sequences not found in the reference genome. | Kehr B et al. | β | 2017 | β |
| Evidence for Very Recent Positive Selection in Mongolians. | Nakayama K et al. | β | 2017 | β |
| Gene expression profiling of puberty-associated genes reveals abundant tissue and sex-specific changes across postnatal development. | Hou H et al. | β | 2017 | β |
| Genetic Associations with Gestational Duration and Spontaneous Preterm Birth. | Zhang G et al. | β | 2017 | β |
| Genetic determinants of adiponectin regulation revealed by pregnancy. | Hivert MF et al. | β | 2017 | β |
| Genetic Polymorphism of NUCKS1 Is Associated With the Susceptibility of Adolescent Idiopathic Scoliosis. | Xu L et al. | β | 2017 | β |
| Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations. | Kim-Hellmuth S et al. | β | 2017 | β |
| Genetic Variation of Follicle-Stimulating Hormone Action Is Associated With Age at Testicular Growth in Boys. | Busch AS et al. | β | 2017 | β |
| Genetic variations, reproductive aging, and breast cancer risk in African American and European American women: The Women's Circle of Health Study. | Coignet MV et al. | β | 2017 | β |
| Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk. | Day FR et al. | β | 2017 | β |
| Identification and evaluation of lncRNA and mRNA integrative modules in human peripheral blood mononuclear cells. | Mo XB et al. | β | 2017 | β |
| Integrating Gene Expression with Summary Association Statistics to Identify Genes Associated with 30 Complex Traits. | Mancuso N et al. | β | 2017 | β |
| LD Hub: a centralized database and web interface to perform LD score regression that maximizes the potential of summary level GWAS data for SNP heritability and genetic correlation analysis. | Zheng J et al. | β | 2017 | β |
| Linkage disequilibrium-dependent architecture of human complex traits shows action of negative selection. | Gazal S et al. | β | 2017 | β |
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| Meta-analysis identifies novel risk loci and yields systematic insights into the biology of male-pattern baldness. | Heilmann-Heimbach S et al. | β | 2017 | β |
| Mining the topography and dynamics of the 4D Nucleome to identify novel CNS drug pathways. | Higgins GA et al. | β | 2017 | β |
| Nakalanga Syndrome: Clinical Characteristics, Potential Causes, and Its Relationship with Recently Described Nodding Syndrome. | FΓΆger K et al. | β | 2017 | β |
| Paternally Inherited DLK1 Deletion Associated With Familial Central Precocious Puberty. | Dauber A et al. | β | 2017 | β |
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| An Ancient Fecundability-Associated Polymorphism Switches a Repressor into an Enhancer of Endometrial TAP2 Expression. | Mika KM et al. | β | 2016 | β |
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| A two-phase procedure for non-normal quantitative trait genetic association study. | Zhang W et al. | β | 2016 | β |
| Breast cancer risk variants at 6q25 display different phenotype associations and regulate ESR1, RMND1 and CCDC170. | Dunning AM et al. | β | 2016 | β |
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| DNA methylation of LINE-1 and Alu repetitive elements in relation to sex hormones and pubertal timing in Mexican-American children. | Huen K et al. | β | 2016 | β |
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| Further evidence for a parent-of-origin effect at the NOP9 locus on language-related phenotypes. | Pettigrew KA et al. | β | 2016 | β |
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| Genetic evidence for natural selection in humans in the contemporary United States. | Beauchamp JP | β | 2016 | β |
| Genetic evidence that lower circulating FSH levels lengthen menstrual cycle, increase age at menopause and impact female reproductive health. | Ruth KS et al. | β | 2016 | β |
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| Genome-wide association study identifies common and low-frequency variants at the AMH gene locus that strongly predict serum AMH levels in males. | Perry JR et al. | β | 2016 | β |
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| Identification of Common Genetic Variants Influencing Spontaneous Dizygotic Twinning and Female Fertility. | Mbarek H et al. | β | 2016 | β |
| MANAGEMENT OF ENDOCRINE DISEASE: Reversible hypogonadotropic hypogonadism. | Dwyer AA et al. | β | 2016 | β |
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| Targeted resequencing of the pericentromere of chromosome 2 linked to constitutional delay of growth and puberty. | Cousminer DL et al. | β | 2015 | β |
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