Region-Based Association Analysis of Human Quantitative Traits in Related Individuals

PLoS ONE

Volumn 8, Issue 6, 2013, Pages

  Belonogova, Nadezhda M ^a   Svishcheva, Gulnara R ^a   van Duijn, Cornelia M ^b   Aulchenko, Yurii S ^a   Axenovich, Tatiana I ^a  

^a INSTITUTE OF CYTOLOGY AND GENETICS   (Russian Federation)

^b ERASMUS MEDICAL CENTER   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

HIGH DENSITY LIPOPROTEIN; LOW DENSITY LIPOPROTEIN; TRIACYLGLYCEROL;

ARTICLE; BODY HEIGHT; BODY MASS; CHOLESTEROL BLOOD LEVEL; COMPUTER PROGRAM; GENETIC ASSOCIATION; HUMAN; KERNEL METHOD; PHENOTYPE; QUANTITATIVE TRAIT; REGIONAL BASED ASSOCIATION ANALYSIS; REGRESSION ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; HUMANS; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI;

EID: 84879170573     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0065395     Document Type: Article

References (34)

1. Aulchenko YS, Struchalin MV, Belonogova NM, Axenovich TI, Weedon MN, et al. (2009) Predicting human height by Victorian and genomic methods. Eur J Hum Genet 17: 1070-1075.
2. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, et al. (2009) Finding the missing heritability of complex diseases. Nature 461: 747-753.
3. Vineis P, Pearce N, (2010) Missing heritability in genome-wide association study research. Nat Rev Genet 11: 589 doi: 10.1038/nrg2809-c2.
4. So HC, Gui AH, Cherny SS, Sham PC, (2011) Evaluating the heritability explained by known susceptibility variants: a survey of ten complex diseases. Genet Epidemiol 35: 310-317.
5. Li B, Leal SM, (2008) Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. Am J Hum Genet 83: 311-321.
6. 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.
7. 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-S110.
8. Madsen BE, Browning SR, (2009) A groupwise association test for rare mutations using a weighted sum statistic. PLoS Genet 5: e1000384.
9. Morris AP, Zeggini E, (2010) An evaluation of statistical approaches to rare variant analysis in genetic association studies. Genet Epidemiol 34: 188-193.
10. Price AL, Kryukov GV, de Bakker PIW, Purcell SM, Staples J, et al. (2010) Pooled association tests for rare variants in exon-resequencing studies. Am J Hum Genet 86: 832-838.
11. Neale BM, Rivas MA, Voight BF, Altshuler D, Devlin B, et al. (2011) Testing for an Unusual Distribution of Rare Variants. PLoS Genet 7: 161-165.
12. Liu D, Lin X, Ghosh D, (2007) Semiparametric regression of multidimensional genetic pathway data: least-squares kernel machines and linear mixed models. Biometrics 63: 1079-1088.
13. Liu D, Ghosh D, Lin X, (2008) Estimation and testing for the effect of a genetic pathway on a disease outcome using logistic kernel machine regression via logistic mixed models. BMC Bioinformatics 9: 292 doi: 10.1186/1471-2105-9-292.
14. Kwee LC, Liu D, Lin X, Ghosh D, Epstein MP, (2008) A powerful and flexible multilocus association test for quantitative traits. Am J Hum Genet 82: 386-397.
15. Wu MC, Kraft P, Epstein MP, Taylor DM, Chanock SJ, et al. (2010) Powerful SNP-set analysis for case-control genome-wide association studies. Am J Hum Genet 86: 929-942.
16. 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. Am J Hum Genet 89: 82-93.
17. Li L, Zheng W, Lee JS, Zhang X, Ferguson J, et al. (2011) Collapsing-based and kernel-based single-gene analyses applied to Genetic Analysis Workshop 17 mini-exome data. BMC Proc 5 (Suppl 9):: S117.
18. Lee S, Wu MC, Lin X, (2012) Optimal tests for rare variant effects in sequencing association studies. Biostatistics 13: 762-775.
19. Schifano ED, Epstein MP, Bielak LF, Jhun MA, Kardia SL, et al. (2012) SNP set association analysis for familial data. Genet Epidemiol doi: []10.1002/gepi.21676. [Epub ahead of print].
20. Chen WM, Abecasis GR, (2007) Family-based association tests for genomewide association scans. Am J Hum Genet 81: 913-926.
21. Gianola D, van Kaam JB, (2008) Reproducing kernel hilbert spaces regression methods for genomic assisted prediction of quantitative traits. Genetics 178: 2289-2303.
22. Abney M, Ober C, McPeek MS, (2002) Quantitative-trait homozygosity and association mapping and empirical genomewide significance in large, complex pedigrees: fasting serum-insulin level in the Hutterites. Am J Hum Genet 70: 920-34.
23. Amin N, van Duijn CM, Aulchenko YS, (2007) A genomic background based method for association analysis in related individuals. PLoS One 2: e1274.
24. Svishcheva GR, Axenovich TI, Belonogova NM, van Duijn CM, Aulchenko YS, (2012) Rapid variance components-based method for whole-genome association analysis. Nat Genet 44: 1166-1170.
25. Almasy L, Dyer TD, Peralta JM, Kent JW Jr, Charlesworth JC, et al. (2011) Genetic Analysis Workshop 17 mini-exome simulation. BMC Proc 5 (Suppl 9):: S2.
26. Pardo LM, MacKay I, Oostra B, van Duijn CM, Aulchenko YS, (2005) The effect of genetic drift in a young genetically isolated population. Ann Hum Genet 69: 288-295.
27. Perola M, (2011) Genome-wide association approaches for identifying loci for human height genes. Best Pract Res Clin Endocrinol Metab 25: 19-23.
28. Aulchenko YS, de Koning DJ, Haley C, (2007) Genomewide rapid association using mixed model and regression: A fast and simple method for genomewide pedigree-based quantitative trait loci association analysis. Genetics 177: 577-585.
29. Devlin B, Roeder K, (1999) Genomic control for association studies. Biometrics 55: 997-1004.
30. Zhang D, Lin X, (2003) Hypothesis testing in semiparametric additive mixed models. Biostatistics 4: 57-74.
31. Gao Q, He Y, Yuan Z, Zhao J, Zhang B, et al. (2011) Gene- or region-based association study via kernel principal component analysis. BMC Genet 12: 75 doi: 10.1186/1471-2156-12-75.
32. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, et al. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38: 904-909.
33. Zhang Q, Chung D, Kraja A, Borecki II, Province MA, (2011) Methods for adjusting population structure and familial relatedness in association test for collective effect of multiple rare variants on quantitative traits. BMC Proc 5 (Suppl 9):: S35.
34. Zhu H, Li L, Zhou H, (2012) Nonlinear dimension reduction with Wright-Fisher kernel for genotype aggregation and association mapping. Bioinformatics 28: i375-i381.