Contribution of Large Region Joint Associations to Complex Traits Genetics

PLoS Genetics

Volumn 11, Issue 4, 2015, Pages

  Paré, Guillaume ^a,b,c   Asma, Senay ^b   Deng, Wei Q ^d  

^a MCMASTER UNIVERSITY   (Canada)

^b HAMILTON HEALTH SCIENCES   (Canada)

^c MCMASTER UNIVERSITY   (Canada)

^d UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

C REACTIVE PROTEIN; HIGH DENSITY LIPOPROTEIN CHOLESTEROL; LOW DENSITY LIPOPROTEIN CHOLESTEROL;

ARTICLE; BODY MASS; GENE LOCUS; GENETIC ASSOCIATION; GENETIC LINKAGE; GENETIC TRAIT; GENETIC VARIABILITY; HAPLOTYPE; HERITABILITY; HUMAN; LARGE REGION JOINT ASSOCIATION; PHENOTYPIC VARIATION; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; BIOLOGICAL MODEL; FEMALE; GENETICS; HUMAN CHROMOSOME; MALE; PHENOTYPE; QUANTITATIVE TRAIT LOCUS;

BODY MASS INDEX; C-REACTIVE PROTEIN; CHOLESTEROL, LDL; CHROMOSOMES, HUMAN; FEMALE; HUMANS; MALE; MODELS, GENETIC; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI;

EID: 84930336953     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1005103     Document Type: Article

References (30)

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, Whittaker JC, Genetic Investigation of Anthropometric Traits C, 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. Abecasis GR, Auton A, Brooks LD, DePristo MA, Genomes Project C, 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. Willer CJ, Schmidt EM, Sengupta S, Peloso GM, Global Lipids Genetics C, 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. Purcell SM, Wray NR, Stone JL, Visscher PM, International Schizophrenia C, 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.