An improved score test for genetic association studies

Genetic Epidemiology

Volumn 35, Issue 5, 2011, Pages 350-359

  Sha, Qiuying ^a   Zhang, Zhaogong ^a,b   Zhang, Shuanglin ^a  

^a MICHIGAN TECHNOLOGICAL UNIVERSITY   (United States)

^b HEILONGJIANG UNIVERSITY   (China)

Author keywords

Association studies; Genome wide association; Improved score test; Score test

Indexed keywords

ALLELE; AMYOTROPHIC LATERAL SCLEROSIS; ARTICLE; CONTROLLED STUDY; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENOTYPE; HAPLOTYPE; HUMAN; MAJOR CLINICAL STUDY; POPULATION; SCORE TEST; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL PARAMETERS;

ALLELES; AMYOTROPHIC LATERAL SCLEROSIS; CASE-CONTROL STUDIES; COMPUTER SIMULATION; DATABASES, GENETIC; GENE FREQUENCY; GENETIC MARKERS; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HAPLOTYPES; HUMANS; LINEAR MODELS; MODELS, GENETIC; MODELS, STATISTICAL;

EID: 79958147356     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.20583     Document Type: Article

References (36)

1. Ardlie KG, Kruglyak L, Seielstad M. 2002. Patterns of linkage disequilibrium in the human genome. Nat Rev Genet 3:299-309.
2. Armitage P. 1955. Tests for linear trends in proportions and frequencies. Biometrics 11:375-386.
3. Balding DJ, Nichols RA. 1995. A method for quantifying differentiation between populations at multi-allelic loci and its implications for investigating identity and paternity. Genetica 96:3-12.
4. Breslow N, Day N. 1980. Statistical Methods in Cancer Research, Volume I: The Analysis of Case-Control Studies. Lyon: IARC Scientific Publications. IARC.
5. Chapman JM, Cooper JD, Todd JA, Clayton DG. 2003. Detecting disease associations due to linkage disequilibrium using haplotype tags: a class of tests and the determinants of statistical power. Hum Hered 56:18-31.
6. Chapman NH, Wijsman EM. 1998. Genome screens using linkage disequilibrium tests: optimal marker characteristics and feasibility. Am J Hum Genet 63:1872-1885.
7. Chen HS, Zhu X, Zhao H, Zhang S. 2003. Qualitative semi-parametric test for genetic associations in case-control designs under structured populations. Ann Hum Genet 67:250-264.
8. Clayton D, Chapman J, Cooper J. 2004. Use of unphased multilocus genotype data in indirect association studies. Genet Epidemiol 27:415-428.
9. 2 tests. Biometrics 10:417-451.
10. Fan R, Knapp M. 2003. Genome association studies of complex diseases by case-control designs. Am J Hum Genet 72:850-868.
11. Hayes MG, Roe CA, Ng M, Bosque-Plata L, Tsuchiya T, Wu X, Ambrose NG, Yairi E, Cook EH, Cox NJ. 2004. Case-control differences in linkage disequilibrium as a tool for gene mapping in complex diseases. Am J Hum Genet Suppl 54:A146.
12. Hildebrand JD, Soriano P. 1999. Shroom, a PDZ domain-containing actin-binding protein, is required for neural tube morphogenesis in mice. Cell 99:485-497.
13. Ionita-Laza I, McQueen MB, Laird NM, Lange C. 2007. Genome-wide weighted hypothesis testing in family-based association studies, with an application to a 100k scan. Am J Hum Genet 81:607-614.
14. Katoh H, Negishi M. 2003. RhoG activates Rac1 by direct interaction with the Dock180-binding protein Elmo. Nature 424:461-464.
15. Marchini J, Donnelly P, Cardon LR. 2005. Genome-wide strategies for detecting multiple loci that influence complex diseases. Nat Genet 37:413-417.
16. Nelder J, Wedderburn R. 1972. Generalized linear models. J R Stat Soc Ser A 135:370-384.
17. Nielsen DM, Ehm MG, Zaykin DV, Weir BS. 2004. Effect of two and three-locus linkage disequilibrium on the power to detect marker/phenotype associations. Genetics 168:1029-1040.
18. Olson JM, Wijsman EM. 1994. Design and sample size considerations in the detection of linkage disequilibrium with a marker locus. Am J Hum Genet 55:574-580.
19. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. 2006. Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38:904-909.
20. Qin H, Feng T, Zhang S, Sha Q. 2010. A data-driven weighting scheme for family-based genome-wide association studies. Eur J Hum Genet 18:596-603.
21. Rannala B, Reeve JP. 2001. High-resolution multipoint linkage-disequilibrium mapping in the context of a human genome sequence. Am J Hum Genet 69:159-178.
22. Schaid DJ, Rowland CM, Tines DE, Jacobson RM, Poland GA. 2002. Score test for association between traits and haplotypes when linkage phase is ambiguous. Am J Hum Genet 70:425-434.
23. Schymick JC, Scholz SW, Fung HC, Britton A, Arepalli S, Gibbs JR, Lombardo F, Matarin M, Kasperaviciute D, Hernandez DG, Crews C, Bruijn L, Rothstein J, Mora G, Restagno G, Chiò A, Singleton A, Hardy J, Traynor BJ. 2007. Genome-wide genotyping in amyotrophic lateral sclerosis and neurologically normal controls: first stage analysis and public release of data. Lancet Neurol 6:322-328.
24. Sha Q, Dong J, Jiang R, Zhang S. 2005. Test of association between quantitative traits and haplotypes in a reduced dimensional space. Ann Hum Genet 69:715-732.
25. Sha Q, Chen HS, Zhang S. 2007. A new association test using haplotype similarity. Genet Epidemiol 31:577-593.
26. Spielman RS, McGinnis RE, Ewens WJ. 1993. Transmission test for linkage disequilibrium: the insulin gene region and insulin dependent diabetes mellitus (IDDM). Am J Hum Genet 52:506-516.
27. Tang R, Feng T, Sha Q, Zhang S. 2010. A variable-sized sliding-window approach for genetic association studies via principal component analysis. Ann Hum Genet 73:631-637.
28. Tzeng JY, Devlin B, Wasserman L, Roeder K. 2003. On the identification of disease mutations by the analysis of haplotype similarity and goodness of fit. Am J Hum Genet 72:891-902.
29. Wallace C, Chapman JM, Clayton DJ. 2006. Score test for selective genotyping. Am J Hum Genet 78:498-504.
30. Wang T, Zhu X, Elston RC. 2007. Improving power in contrasting linkage-disequilibrium patterns between cases and controls. Am J Hum Genet 80:911-920.
31. Wang X, Zhang S, Sha Q. 2009. A new association test to test multiple-marker association. Genet Epidemiol 33:164-171.
32. 2 test for genome association studies. Am J Hum Genet 70:1257-1268.
33. Zaykin DV, Meng Z, Ehm MG. 2006. Contrasting linkage-disequilibrium patterns between cases and controls as a novel association mapping method. Am J Hum Genet 78:737-746.
34. Zhang S, Zhu X, Zhao H. 2003. On a semi-parametric test to detect associations between quantitative traits and candidate genes using unrelated individuals. Genet Epidemiol 24:44-56.
35. Zheng G, Freidlin B, Gastwirth JL. 2006. Robust genomic control for association studies. Am J Hum Genet 78:350-356.
36. Zhu X, Zhang S, Zhao H, Cooper RS. 2002. Association mapping, using a mixture model for complex traits. Genet Epidemiol 23:181-196.