-
Články
- Časopisy
- Kurzy
- Témy
- Kongresy
- Videa
- Podcasty
Contribution of Large Region Joint Associations to Complex Traits Genetics
It is widely accepted that genetics influences a broad range of human traits and diseases, yet only a few genetic variants are known to determine these traits and their impact is modest. In this report, we made the hypothesis that combining information from a large number of genetic variants would help better explain how they together contribute to traits such as height. To do so, we first had to select a proper method to integrate large numbers of genetic variants in a single test, here named “large region joint association”. Next, we tested our method on height in 3,740 European participants from the Health and Retirement Study. We showed that the contribution of regional associations to variation in height was 17.2%, as compared to the 12.9% explained by known genetic determinants of height. In other words, the joint effect of multiple genetic variants integrated together contributed to a substantial fraction of the genetics of height. These results are significant because they can help identify new genes or genetic regions associated with human traits or diseases. Conversely, these results can be used to better understand genes that we already know are associated. Furthermore, our results provide insights on how traits are genetically determined.
Vyšlo v časopise: Contribution of Large Region Joint Associations to Complex Traits Genetics. PLoS Genet 11(4): e32767. doi:10.1371/journal.pgen.1005103
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1005103Souhrn
It is widely accepted that genetics influences a broad range of human traits and diseases, yet only a few genetic variants are known to determine these traits and their impact is modest. In this report, we made the hypothesis that combining information from a large number of genetic variants would help better explain how they together contribute to traits such as height. To do so, we first had to select a proper method to integrate large numbers of genetic variants in a single test, here named “large region joint association”. Next, we tested our method on height in 3,740 European participants from the Health and Retirement Study. We showed that the contribution of regional associations to variation in height was 17.2%, as compared to the 12.9% explained by known genetic determinants of height. In other words, the joint effect of multiple genetic variants integrated together contributed to a substantial fraction of the genetics of height. These results are significant because they can help identify new genes or genetic regions associated with human traits or diseases. Conversely, these results can be used to better understand genes that we already know are associated. Furthermore, our results provide insights on how traits are genetically determined.
Zdroje
1. Visscher PM, Hill WG, Wray NR (2008) Heritability in the genomics era—concepts and misconceptions. Nature reviews Genetics 9 : 255–266. doi: 10.1038/nrg2322 18319743
2. Yang J, Benyamin B, Mcevoy BP, Gordon S, Henders AK, et al. (2010) Common SNPs explain a large proportion of the heritability for human height. Nature Genetics 42 : 565–569. doi: 10.1038/ng.608 20562875
3. Eichler EE, Flint J, Gibson G, Kong A, Leal SM, et al. (2010) Missing heritability and strategies for finding the underlying causes of complex disease. Nat Rev Genet 11 : 446–450. doi: 10.1038/nrg2809 20479774
4. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Lucia A, et al. (2010) Finding the missing heritability of complex diseases. 461 : 747–753. doi: 10.1038/nature08494 19812666
5. Beyene J, Tritchler D, Asimit JL, Hamid JS (2009) Gene - or region-based analysis of genome-wide association studies. Genet Epidemiol 33 Suppl 1: S105–110. doi: 10.1002/gepi.20481 19924708
6. Gusev A, Bhatia G, Zaitlen N, Vilhjalmsson BJ, Diogo D, et al. (2013) Quantifying missing heritability at known GWAS loci. PLoS Genet 9: e1003993. doi: 10.1371/journal.pgen.1003993 24385918
7. Yang J, Ferreira T, Morris AP, Medland SE, Madden PA, et al. (2012) Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits. Nat Genet 44 : 369–375, S361–363. doi: 10.1038/ng.2213 22426310
8. Lappalainen T, Montgomery SB, Nica AC, Dermitzakis ET (2011) Epistatic selection between coding and regulatory variation in human evolution and disease. American journal of human genetics 89 : 459–463. doi: 10.1016/j.ajhg.2011.08.004 21907014
9. Cheung VG, Spielman RS (2009) Genetics of human gene expression: mapping DNA variants that influence gene expression. 10 : 595–604. doi: 10.1038/nrg2630 19636342
10. Consortium TEP (2012) An integrated encyclopedia of DNA elements in the human genome. 489 : 57–74. doi: 10.1038/nature11247 22955616
11. Ionita-Laza I, Lee S, Makarov V, Buxbaum JD, Lin X (2013) Sequence kernel association tests for the combined effect of rare and common variants. Am J Hum Genet 92 : 841–853. doi: 10.1016/j.ajhg.2013.04.015 23684009
12. Tregouet DA, Konig IR, Erdmann J, Munteanu A, Braund PS, et al. (2009) Genome-wide haplotype association study identifies the SLC22A3-LPAL2-LPA gene cluster as a risk locus for coronary artery disease. Nat Genet 41 : 283–285. doi: 10.1038/ng.314 19198611
13. Ehret GB, Lamparter D, Hoggart CJ, Genetic Investigation of Anthropometric Traits C, Whittaker JC, et al. (2012) A multi-SNP locus-association method reveals a substantial fraction of the missing heritability. Am J Hum Genet 91 : 863–871. doi: 10.1016/j.ajhg.2012.09.013 23122585
14. Visscher PM (2008) Sizing up human height variation. Nature genetics 40 : 489–490. doi: 10.1038/ng0508-489 18443579
15. Berndt SI, Gustafsson S, Magi R, Ganna A, Wheeler E, et al. (2013) Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture. Nat Genet 45 : 501–512. doi: 10.1038/ng.2606 23563607
16. Genomes Project C, Abecasis GR, Auton A, Brooks LD, DePristo MA, et al. (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491 : 56–65. doi: 10.1038/nature11632 23128226
17. Lango Allen H, Estrada K, Lettre G, Berndt SI, Weedon MN, et al. (2010) Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature 467 : 832–838. doi: 10.1038/nature09410 20881960
18. Speliotes EK, Willer CJ, Berndt SI, Monda KL, Thorleifsson G, et al. (2010) Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. Nat Genet 42 : 937–948. doi: 10.1038/ng.686 20935630
19. Global Lipids Genetics C, Willer CJ, Schmidt EM, Sengupta S, Peloso GM, et al. (2013) Discovery and refinement of loci associated with lipid levels. Nat Genet 45 : 1274–1283. doi: 10.1038/ng.2797 24097068
20. Dehghan A, Dupuis J, Barbalic M, Bis JC, Eiriksdottir G, et al. (2011) Meta-analysis of genome-wide association studies in >80 000 subjects identifies multiple loci for C-reactive protein levels. Circulation 123 : 731–738. doi: 10.1161/CIRCULATIONAHA.110.948570 21300955
21. International Schizophrenia C, Purcell SM, Wray NR, Stone JL, Visscher PM, et al. (2009) Common polygenic variation contributes to risk of schizophrenia and bipolar disorder. Nature 460 : 748–752. doi: 10.1038/nature08185 19571811
22. Speed D, Hemani G, Johnson MR, Balding DJ (2012) Improved heritability estimation from genome-wide SNPs. Am J Hum Genet 91 : 1011–1021. doi: 10.1016/j.ajhg.2012.10.010 23217325
23. Patterson N, Price AL, Reich D (2006) Population structure and eigenanalysis. PLoS Genet 2: e190. 17194218
24. Zou F, Lee S, Knowles MR, Wright FA (2010) Quantification of population structure using correlated SNPs by shrinkage principal components. Hum Hered 70 : 9–22. doi: 10.1159/000288706 20413978
25. Wu MC, Lee S, Cai T, Li Y, Boehnke M, et al. (2011) Rare-variant association testing for sequencing data with the sequence kernel association test. American journal of human genetics 89 : 82–93. doi: 10.1016/j.ajhg.2011.05.029 21737059
26. Presence of multiple independent effects in risk loci of common complex human diseases. Am J Hum Genet 91 : 185–192. doi: 10.1016/j.ajhg.2012.05.020 22770979
27. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81 : 559–575. 17701901
28. Erdfelder E, Faul F, Buchner A (1996) GPOWER: A general power analysis program. Behavior Research Methods, Instruments, Computers 28 : 1–11.
29. Duchesne P, Lafaye De Micheaux P (2010) Computing the distribution of quadratic forms: Further comparisons between the Liu—Tang—Zhang approximation and exact methods. Computational Statistics Data Analysis 54 : 858–862.
30. Davies RB (1980) Algorithm AS 155: The Distribution of a Linear Combination of χ2 Random Variables. Journal of the Royal Statistical Society Series C (Applied Statistics) 29 : 323–333.
Štítky
Genetika Reprodukčná medicína
Článek Retraction: Astakine 2—the Dark Knight Linking Melatonin to Circadian Regulation in CrustaceansČlánek Adventures in WonderlandČlánek Genomic Location of the Major Ribosomal Protein Gene Locus Determines Global Growth and InfectivityČlánek Spatial Fluctuations in Expression of the Heterocyst Differentiation Regulatory Gene in FilamentsČlánek Genome-Wide Negative Feedback Drives Transgenerational DNA Methylation Dynamics in ArabidopsisČlánek Systematic Dissection of the Sequence Determinants of Gene 3’ End Mediated Expression ControlČlánek The Chromatin Remodeler CHD8 Is Required for Activation of Progesterone Receptor-Dependent EnhancersČlánek Selection against Heteroplasmy Explains the Evolution of Uniparental Inheritance of MitochondriaČlánek The DNA Helicase Recql4 Is Required for Normal Osteoblast Expansion and Osteosarcoma FormationČlánek Dual-Specificity Anti-sigma Factor Reinforces Control of Cell-Type Specific Gene Expression in
Článok vyšiel v časopisePLOS Genetics
Najčítanejšie tento týždeň
2015 Číslo 4- Gynekologové a odborníci na reprodukční medicínu se sejdou na prvním virtuálním summitu
- Je „freeze-all“ pro všechny? Odborníci na fertilitu diskutovali na virtuálním summitu
-
Všetky články tohto čísla
- Retraction: Astakine 2—the Dark Knight Linking Melatonin to Circadian Regulation in Crustaceans
- Adventures in Wonderland
- Experimental Swap of 's Assortative Mating Preferences Demonstrates Key Role of X-Chromosome Divergence Island in Incipient Sympatric Speciation
- Chromosome Replacement and Deletion Lead to Clonal Polymorphism of Berry Color in Grapevine
- The Protein Quality Control Machinery Regulates Its Misassembled Proteasome Subunits
- Genome-Wide Association Study Identifies as a Critical Gene for Susceptibility to Noise-Induced Hearing Loss
- Genomic Location of the Major Ribosomal Protein Gene Locus Determines Global Growth and Infectivity
- Viable Neuronopathic Gaucher Disease Model in Medaka () Displays Axonal Accumulation of Alpha-Synuclein
- Multi-locus Analysis of Genomic Time Series Data from Experimental Evolution
- The Genetic Legacy of the Expansion of Turkic-Speaking Nomads across Eurasia
- Lack of GDAP1 Induces Neuronal Calcium and Mitochondrial Defects in a Knockout Mouse Model of Charcot-Marie-Tooth Neuropathy
- The Pif1 Helicase, a Negative Regulator of Telomerase, Acts Preferentially at Long Telomeres
- Inhibiting K63 Polyubiquitination Abolishes No-Go Type Stalled Translation Surveillance in
- SYD-1C, UNC-40 (DCC) and SAX-3 (Robo) Function Interdependently to Promote Axon Guidance by Regulating the MIG-2 GTPase
- Spatial Fluctuations in Expression of the Heterocyst Differentiation Regulatory Gene in Filaments
- Synergistic and Independent Actions of Multiple Terminal Nucleotidyl Transferases in the 3’ Tailing of Small RNAs in Arabidopsis
- Host Genetic Variation Influences Gene Expression Response to Rhinovirus Infection
- Contribution of Large Region Joint Associations to Complex Traits Genetics
- Volatility of Mutator Phenotypes at Single Cell Resolution
- Proteolysis of Virulence Regulator ToxR Is Associated with Entry of into a Dormant State
- Genome-Wide Negative Feedback Drives Transgenerational DNA Methylation Dynamics in Arabidopsis
- A Multi-layered Protein Network Stabilizes the FtsZ-ring and Modulates Constriction Dynamics
- Systematic Dissection of the Sequence Determinants of Gene 3’ End Mediated Expression Control
- Genome Sequencing of the Perciform Fish Provides Insights into Molecular and Genetic Mechanisms of Stress Adaptation
- Natural Variant E610G Is a Semi-dominant Suppressor of IAP-Induced RNA Processing Defects
- The Alkaline Response Pathway: Identification of a Novel Rim Pathway Activator
- Transgenerational Inheritance of Diet-Induced Genome Rearrangements in Drosophila
- A Single Nucleotide Polymorphism Uncovers a Novel Function for the Transcription Factor Ace2 during Hyphal Development
- DNA Damage Response and Spindle Assembly Checkpoint Function throughout the Cell Cycle to Ensure Genomic Integrity
- The Functional Interplay Between the t(9;22)-Associated Fusion Proteins BCR/ABL and ABL/BCR in Philadelphia Chromosome-Positive Acute Lymphatic Leukemia
- Extreme Recombination Frequencies Shape Genome Variation and Evolution in the Honeybee,
- Beyond Glycolysis: GAPDHs Are Multi-functional Enzymes Involved in Regulation of ROS, Autophagy, and Plant Immune Responses
- Comprehensive Profiling of Amino Acid Response Uncovers Unique Methionine-Deprived Response Dependent on Intact Creatine Biosynthesis
- Windpipe Controls Intestinal Homeostasis by Regulating JAK/STAT Pathway via Promoting Receptor Endocytosis and Lysosomal Degradation
- Ataxin-2 Regulates Translation in a New BAC-SCA2 Transgenic Mouse Model
- Cross-Population Joint Analysis of eQTLs: Fine Mapping and Functional Annotation
- The Power of Gene-Based Rare Variant Methods to Detect Disease-Associated Variation and Test Hypotheses About Complex Disease
- The Chromatin Remodeler CHD8 Is Required for Activation of Progesterone Receptor-Dependent Enhancers
- Competition between VanU Repressor and VanR Activator Leads to Rheostatic Control of Vancomycin Resistance Operon Expression
- A Missense Change in the Gene Links Aberrant Autophagy to a Neurodegenerative Vacuolar Storage Disease
- Simultaneous Discovery, Estimation and Prediction Analysis of Complex Traits Using a Bayesian Mixture Model
- Selection against Heteroplasmy Explains the Evolution of Uniparental Inheritance of Mitochondria
- Genome-Destabilizing Effects Associated with Top1 Loss or Accumulation of Top1 Cleavage Complexes in Yeast
- Imputation-Based Population Genetics Analysis of Malaria Parasites
- Heterozygosity for a Hypomorphic Polβ Mutation Reduces the Expansion Frequency in a Mouse Model of the Fragile X-Related Disorders
- Neto-Mediated Intracellular Interactions Shape Postsynaptic Composition at the Neuromuscular Junction
- Ndd1 Turnover by SCF Is Inhibited by the DNA Damage Checkpoint in
- Frameshift Variant Associated with Novel Hoof Specific Phenotype in Connemara Ponies
- The DNA Helicase Recql4 Is Required for Normal Osteoblast Expansion and Osteosarcoma Formation
- Spastin Binds to Lipid Droplets and Affects Lipid Metabolism
- Maintenance of Glia in the Optic Lamina Is Mediated by EGFR Signaling by Photoreceptors in Adult Drosophila
- Auxin Influx Carriers Control Vascular Patterning and Xylem Differentiation in
- Dual-Specificity Anti-sigma Factor Reinforces Control of Cell-Type Specific Gene Expression in
- The Lowe Syndrome Protein OCRL1 Is Required for Endocytosis in the Zebrafish Pronephric Tubule
- Postnatal Loss of Hap1 Reduces Hippocampal Neurogenesis and Causes Adult Depressive-Like Behavior in Mice
- CAPER Is Vital for Energy and Redox Homeostasis by Integrating Glucose-Induced Mitochondrial Functions via ERR-α-Gabpa and Stress-Induced Adaptive Responses via NF-κB-cMYC
- Distinct and Cooperative Activities of HESO1 and URT1 Nucleotidyl Transferases in MicroRNA Turnover in
- The Evolutionary Origination and Diversification of a Dimorphic Gene Regulatory Network through Parallel Innovations in and
- MAPK Signaling Pathway Alters Expression of Midgut ALP and ABCC Genes and Causes Resistance to Cry1Ac Toxin in Diamondback Moth
- Spatio-temporal Remodeling of Functional Membrane Microdomains Organizes the Signaling Networks of a Bacterium
- Asymmetric Transcript Discovery by RNA-seq in . Blastomeres Identifies , a Gene Important for Anterior Morphogenesis
- A Stress-Induced Small RNA Modulates Alpha-Rhizobial Cell Cycle Progression
- Systematic Profiling of Poly(A)+ Transcripts Modulated by Core 3’ End Processing and Splicing Factors Reveals Regulatory Rules of Alternative Cleavage and Polyadenylation
- The UPR Branch IRE1- in Plants Plays an Essential Role in Viral Infection and Is Complementary to the Only UPR Pathway in Yeast
- A Non-canonical RNA Silencing Pathway Promotes mRNA Degradation in Basal Fungi
- Co-chaperone p23 Regulates . Lifespan in Response to Temperature
- Re-replication of a Centromere Induces Chromosomal Instability and Aneuploidy
- Shade Avoidance Components and Pathways in Adult Plants Revealed by Phenotypic Profiling
- Lipid-Induced Epigenomic Changes in Human Macrophages Identify a Coronary Artery Disease-Associated Variant that Regulates Expression through Altered C/EBP-Beta Binding
- PLOS Genetics
- Archív čísel
- Aktuálne číslo
- Informácie o časopise
Najčítanejšie v tomto čísle- Lack of GDAP1 Induces Neuronal Calcium and Mitochondrial Defects in a Knockout Mouse Model of Charcot-Marie-Tooth Neuropathy
- Proteolysis of Virulence Regulator ToxR Is Associated with Entry of into a Dormant State
- Frameshift Variant Associated with Novel Hoof Specific Phenotype in Connemara Ponies
- Ataxin-2 Regulates Translation in a New BAC-SCA2 Transgenic Mouse Model
Prihlásenie#ADS_BOTTOM_SCRIPTS#Zabudnuté hesloZadajte e-mailovú adresu, s ktorou ste vytvárali účet. Budú Vám na ňu zasielané informácie k nastaveniu nového hesla.
- Časopisy