A unified framework for detecting genetic association with multiple SNPs in a candidate gene or region: Contrasting genotype scores and ld patterns between cases and controls

Human Heredity

Volumn 69, Issue 1, 2009, Pages 1-13

  Pan, Wei ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

Genome wide association study; Linkage disequilibrium; Linkage disequilibrium contrast test; Logistic regression Multilocus analysis; Score test; SNP; Sum of squared score tests

Indexed keywords

ARTICLE; GENETIC ASSOCIATION; GENOME; GENOTYPE; HAPLOTYPE; HUMAN; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; GENETIC ASSOCIATION STUDIES; GENETIC PREDISPOSITION TO DISEASE; GENOME, HUMAN; GENOTYPE; HUMANS; LINKAGE DISEQUILIBRIUM; LOGISTIC MODELS; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 70349608366     PISSN: 00015652     EISSN: 14230062     Source Type: Journal    
DOI: 10.1159/000243149     Document Type: Article

References (32)

1. Abecasis GR, Cookson WO: GOLD-graphical overview of linkage disequilibrium. Bioin-formatics 2000; 16:182-183.
2. Altshuler D, Daly M, Lander ES: Genetic mapping in human disease. Science 2008; 322: 881-888.
3. Baksh MF, Balding DJ, Vyse TJ, Whittaker JC: A likelihood ratio approach to family-based association studies with covariates. Ann Hum Genet 2006; 70: 131-139.
4. Cardon LR, Abecasis GR: Using haplotype blocks to map human complex trait loci. Trends Genet 2003; 19:135-140.
5. Chapman JM, Whittaker J: Analysis of multiple SNPs in a candidate gene or region. Genet Epidemiol, Published Online: 21 Apr 2008.
6. Chatterjee N, Kalaliouglu Z, Moslehi R, Peters U, Wacholder S: Powerful multilocus tests of genetic association in the presence of gene-gene and gene-environment interactions. Am J Hum Genet 2006; 79:1002-1016.
7. Chen Y-H, Lin H-W: Simple association analysis combining data from trios/sibships and unrelated controls. Genet Epidemiol 2008; 32: 520-527.
8. Cheng R, Ma JZ, Elston RC, et al: Fine mapping functional sites or regions from case-control data using haplotypes of multiple linked SNPs. Ann Hum Genet 2005; 69:102-112.
9. Clayton D, Chapman J, Cooper J: Use of un-phased multilocus genotype data in indirect association studies. Genet Epidemiol 2004; 27: 415-428.
10. Durrant C, Zongdervan KT, Cardon LR, et al: Linkage disequilibrium mapping via cladis-tic analysis of single-nucleotide polymorphism haplotypes. Am J Hum Genet 2004; 75:35-43.
11. Fan R, Knapp M: Genome association studies of complex diseases by case-control designs. Am J Hum Genet 2003; 72: 850-868.
12. Fan R, Xiong M: Linkage and association studies of QTL for nuclear families by mixed models. Biostatistics 2003; 4:75-95.
13. Goeman J J, van de Geer S, van Houwel ingen HC: Testing against a high dimensional alternative. J R Stat Soc B 2006; 68:477-493.
14. Guo Y, Li J, Bonham A, Wang Y, Deng H: Gain in power for exhaustive analyses of haplo-types using variable-sized sliding window strategy: a comparison of association mapping strategies. To appear Eur J Hum Genet. Published online, 2009.
15. Hayes MG, del Bosque-Plata L, Tsuchiya T, Ha-nis CL, Cox NJ: Patterns of linkage disequilibrium in the type 2 diabetes gene calpain-10. Diabetes 2005; 54:3573-3576.
16. Hsu L, Starr JR, Zheng Y, Schwartz SM: On combining triads and unrelated subjects data in candidate gene studies: An application to data on testicular cancer. Hum Hered 2009; 67: 88-103.
17. Johnson NL, Kotz S: Distributions in Statistics, Continuous Univariate Distributions, vol 2. Boston: Houghton-Mifflin, 1970.
18. Lin DY: An efficient Monte Carlo approach to assessing statistical significance in genomic studies. Bioinformatics 2005; 21: 781-787.
19. Nielsen DM, Ehm MG, Zaykin DV, Weir BS: Effect of two-and three-locus linkage disequilibrium on the power to detect marker/ phenotype associations. Genetics 2004; 168: 1029-1040.
20. Pan W: Asymptotic tests of association with multiple SNPs in linkage disequilibrium. To appear in Genet Epidemiol. Published Online on Jan 23, 2009. DOI: 10.1002/gepi.20402. Available at www.biostat.umn.edu/rrs.php as Research Report 2008-018, Division of Biostatistics, University of Minnesota.
21. Plenge RM, et al: TRAF1-C5 as a risk locus for rheumatoid arthritis{a genomewide study. N Engl J Med 20 07; 357: 1199-209.
22. Roeder K, Bacanu SA, Sonpar V, Zhang X, Devlin B: Analysis of single-locus tests to detect gene/disease associations. Genet Epidemiol 2005; 28:207-219.
23. Seaman SR, Muller-Myhsok B: Rapid simulation of p values for product methods and multiple testing adjustment in association studies. Am J Hum Genet 2005; 76: 399-408.
24. Schaid DJ: Linkage disequilibrium testing when linkage phase is unknown. Genetics 2004; 166:505-512.
25. Wang T, Elston RC: Improved power by use of a weighted score test for linkage disequilibrium mapping. Am J Hum Genet 2007; 80:353-360.
26. Wang T, Zhu X, Elston RC: Improving power in contrasting linkage-disequilibrium patterns between cases and controls. Am J Hum Genet 2007; 80:911-920.
27. Wang X, Zhang S, Sha Q: A new association test to test multiple-marker association. Genet Epidemiol 2009 (in press).
28. Xiong M, Zhao J, Boerwinkle E: Generalized T2 test for genome association studies. Am J Hu m Genet 2002; 70: 1257-1268.
29. Zaykin DV, Meng Z, Ehm MG: Contrasting linkage-disequilibrium patterns between cases and controls as a novel association-mapping met hod. Am J Hum Genet 2006; 78: 737-746.
30. Zhang J-T: Approximate and asymptotic distributions of Chi-squared-type mixtures with applications. J Am Stat Ass 2005; 100:273-285.
31. Zhao L P, Li S, Khalid N: A method for the assessment of disease associations with single-nucleotide polymorphism haplotypes and environmental variables in case-control studies. Am J Hum Genet 2003; 72: 1231-1250.
32. Zhao J, Jin L, Xiong M: Test for interaction between two unlinked loci. Am J Hum Genet 2006;79:831-845.