Development and application of genomic control methods for genome-wide association studies using non-additive models

PLoS ONE

Volumn 8, Issue 12, 2013, Pages

  Tsepilov, Yakov A ^a,b   Ried, Janina S ^c   Strauch, Konstantin ^c,d   Grallert, Harald ^c   Van Duijn, Cornelia M ^e   Axenovich, Tatiana I ^a,b   Aulchenko, Yurii S ^a,b,f  

^a INSTITUTE OF CYTOLOGY AND GENETICS   (Russian Federation)

^b NOVOSIBIRSK STATE UNIVERSITY   (Russian Federation)

^c INSTITUTE OF EPIDEMIOLOGY   (Germany)

^d UNIVERSITY OF MUNICH   (Germany)

^e ERASMUS MEDICAL CENTER   (Netherlands)

^f UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENE FREQUENCY; GENETIC ASSOCIATION; GENETIC MARKER; GENETIC VARIABILITY; GENOMIC CONTROL; GENOTYPE; INHERITANCE; POPULATION GENETICS; STATISTICAL ANALYSIS; STATISTICAL MODEL;

COMPUTER SIMULATION; DATABASES, GENETIC; GENE FREQUENCY; GENOME; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; GENOTYPE; HUMANS; MODELS, GENETIC;

EID: 84892997367     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0081431     Document Type: Article

References (27)

1. Devlin B, Roeder K (1999) Genomic control for association studies. Biometrics 55: 997-1004.
2. Zheng G, Freidlin B, Li Z, Gastwirth JL (2005) Genomic control for association studies under various genetic models. Biometrics 61: 186-192. (Pubitemid 40380978)
3. Zheng G, Freidlin B, Gastwirth JL (2006) Robust genomic control for association studies. American journal of human genetics 78: 350-356. (Pubitemid 43157574)
4. Zang Y, Zhang H, Yang Y, Zheng G (2007) Robust genomic control and robust delta centralization tests for case-control association studies. Human heredity 63: 187-195. (Pubitemid 46457587)
5. Yan T, Hou B, Yang Y (2009) Correcting for cryptic relatedness by a regression-based genomic control method. BMC genetics 10: 78.
6. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959. (Pubitemid 30397141)
7. Gorroochurn P, Heiman GA, Hodge SE, Greenberg DA (2006) Centralizing the non-central chi-square: A new method to correct for population stratification in genetic case-control association studies. Genetic epidemiology 30: 277-289. doi:10.1002/gepi.20143.
8. Dadd T, Lewis CM, Weale ME (2010) Delta-centralization fails to control for population stratification in genetic association studies. Human heredity 69: 285-294. doi:10.1159/000302720.
9. Oliehoek PA, Windig JJ, van Arendonk JAM, Bijma P (2006) Estimating relatedness between individuals in general populations with a focus on their use in conservation programs. Genetics 173: 483-496. doi:10.1534/genetics.105. 049940. (Pubitemid 43800217)
10. Bittles A (2001) Consanguinity and its relevance to clinical genetics. Clinical genetics 60: 89-98.
11. Bacanu S-A, Devlin B, Roeder K (2002) Association studies for quantitative traits in structured populations. Genetic epidemiology 22: 78-93. (Pubitemid 34019893)
12. Aulchenko YS, Struchalin M V, van Duijn CM (2010) ProbABEL package for genome-wide association analysis of imputed data. BMC bioinformatics 11: 134.
13. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, et al. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nature genetics 38: 904-909. (Pubitemid 44141658)
14. Yu J, Pressoir G, Briggs WH, Vroh Bi I, Yamasaki M, et al. (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nature genetics 38: 203-208. (Pubitemid 43177234)
15. Chen W-M, Abecasis GR (2007) Family-based association tests for genomewide association scans. American journal of human genetics 81: 913-926. (Pubitemid 47580246)
16. Dupuis J, Langenberg C, Prokopenko I, Saxena R, Soranzo N, et al. (2010) New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk. Nature genetics 42: 105-116.
17. De Bakker PIW, Ferreira MAR, Jia X, Neale BM, Raychaudhuri S, et al. (2008) Practical aspects of imputation-driven meta-analysis of genome-wide association studies. Human molecular genetics 17: R122-8.
18. Wellcome Trust Case Control Consortium (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447: 661-678. doi:10.1038/nature05911.
19. Liu J, Xiao Q, Wang Y, Xu Z-M, Yang Q, et al. (2013) Analysis of genome-wide association study-linked loci in Parkinson's disease of Mainland China. Movement disorders: official journal of the Movement Disorder Society. doi:10.1002/mds.25599.
20. Kobayashi D, Nishizawa D, Takasaki Y, Kasai S, Kakizawa T, et al. (2013) Genome-wide association study of sensory disturbances in the inferior alveolar nerve after bilateral sagittal split ramus osteotomy. Molecular pain 9: 34. doi:10.1186/1744-8069-9-34.
21. McLaren PJ, Coulonges C, Ripke S, van den Berg L, Buchbinder S, et al. (2013) Association Study of Common Genetic Variants and HIV-1 Acquisition in 6,300 Infected Cases and 7,200 Controls. PLoS pathogens 9: e1003515. doi:10.1371/journal.ppat.1003515.
22. De Bakker PIW, Raychaudhuri S (2012) Interrogating the major histocompatibility complex with high-throughput genomics. Human molecular genetics 21: R29-36.
23. Aulchenko YS, Ripke S, Isaacs A, van Duijn CM (2007) GenABEL: an R library for genome-wide association analysis. Bioinformatics (Oxford, England) 23: 1294-1296. (Pubitemid 47050548)
24. Liu F, Ikram MA, Janssens ACJW, Schuur M, de Koning I, et al. (2009) A study of the SORL1 gene in Alzheimer's disease and cognitive function. Journal of Alzheimer's disease: JAD 18: 51-64.
25. Aulchenko YS, Ripatti S, Lindqvist I, Boomsma D, Heid IM, et al. (2009) Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. Nature genetics 41: 47-55.
26. Wichmann H-E, Gieger C, Illig T (2005) KORA-gen-resource for population genetics, controls and a broad spectrum of disease phenotypes. Gesundheitswesen (Bundesverband der Ärzte des Öffentlichen Gesundheitsdienstes (Germany)) 67 Suppl 1: S26-30.
27. Kolz M, Johnson T, Sanna S, Teumer A, Vitart V, et al. (2009) Meta-analysis of 28,141 individuals identifies common variants within five new loci that influence uric acid concentrations. PLoS genetics 5: e1000504.