Transmission disequilibrium test power and sample size in the presence of locus heterogeneity

Statistical Applications in Genetics and Molecular Biology

Volumn 8, Issue 1, 2009, Pages

  Chen, Chuanwen ^a   Yang, Guang ^a   Buyske, Steven ^a   Matise, Tara ^a   Finch, Stephen J ^b   Gordon, Derek ^a  

^a RUTGERS UNIVERSITY   (United States)

^b STONY BROOK UNIVERSITY   (United States)

Author keywords

Family based association; Mixture; Noncentrality parameter

Indexed keywords

ANALYTIC METHOD; ANALYTICAL PARAMETERS; ARTICLE; CALCULATION; EFFECT SIZE; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENETIC ASSOCIATION; GENETIC HETEROGENEITY; GENOTYPE; HOMOZYGOSITY; HUMAN; PREVALENCE; RISK FACTOR; SAMPLE SIZE; SIMULATION; CHROMOSOME MAP; COMPUTER PROGRAM; COMPUTER SIMULATION; GENETICS; METHODOLOGY;

CHROMOSOME MAPPING; COMPUTER SIMULATION; GENETIC LOCI; SAMPLE SIZE; SOFTWARE;

EID: 72049090952     PISSN: None     EISSN: 15446115     Source Type: Journal    
DOI: 10.2202/1544-6115.1501     Document Type: Article

References (19)

1. Smith CAB: Homogeneity test for linkage data. Proc Sec Int Congr Hum Genet 1961; 1: 212-213.
2. Ott J: Analysis of Human Genetic Linkage. Baltimore: Johns Hopkins, 1999.
3. Spielman RS, McGinnis RE, Ewens WJ: Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am J Hum Genet 1993; 52: 506-516.
4. Davies K: Cystic fibrosis. Complementary endeavours. Nature 1990; 348: 110-111.
5. Slager SL, Huang J, Vieland VJ: Effect of allelic heterogeneity on the power of the transmission disequilibrium test. Genet Epidemiol 2000; 18: 143-156.
6. Fisher SA, Lewis CM: Power of genetic association studies in the presence of linkage disequilibrium and allelic heterogeneity. Hum Hered 2008; 66: 210-222.
7. Wang D, Huang J: Detecting linkage disequilibrium in the presence of locus heterogeneity. Ann Hum Genet 2006; 70: 397-409.
8. Deng H, Chen W: The power of the transmission disequilibrium test (TDT) with both case-parent and control-parent trios. Genet Res 2001; 78: 289-302.
9. Buyske S, Yang G, Matise TC, Gordon D: When a Case Is Not a Case: Effects of Phenotype Misclassification on Power and Sample Size Requirements for the Transmission Disequilibrium Test with Affected Child Trios. Hum Hered 2009; 67: 287-292.
10. Schaid DJ, Sommer SS: Genotype relative risks: methods for design and analysis of candidate-gene association studies. Am J Hum Genet 1993; 53: 1114-1126.
11. Weeks DE, Ott J, Lathrop GM: SLINK: a general simulation program for linkage analysis. Am J Hum Genet 1990; 47: A204 (Supplement).
12. Terwilliger JD, Ott J: Handbook of Human Genetic Linkage. Baltimore: Johns Hopkins, 1994.
13. Hogg RV, Craig AT: Introduction to Mathematical Statistics, Fourth edn. New York: Macmillan, 1978.
14. Silverberg MS, Daly MJ, Moskovitz DN et al: Diagnostic misclassification reduces the ability to detect linkage in inflammatory bowel disease genetic studies. Gut 2001; 49: 773-776.
15. Gordon D, Finch SJ: Factors affecting statistical power in the detection of genetic association. J Clin Invest 2005; 115: 1408-1418.
16. Horvath S, Xu X, Laird NM: The family based association test method: strategies for studying general genotype--phenotype associations. Eur J Hum Genet 2001; 9: 301-306.
17. Martin ER, Monks SA, Warren LL, Kaplan NL: A test for linkage and association in general pedigrees: the pedigree disequilibrium test. Am J Hum Genet 2000; 67: 146-154.
18. Yang X, Huang J, Logue MW, Vieland VJ: The posterior probability of linkage allowing for linkage disequilibrium and a new estimate of disequilibrium between a trait and a marker. Hum Hered 2005; 59: 210-219.
19. Smith CAB: Testing for heterogeneity of recombination fraction values in human genetics. Ann Hum Genet 1963; 27: 175-182.