1. An Optimal Dose-effect Mode Trend Test for SNP Genotype Tables
OMTT
Yamada R(1)(2), Hirosawa K(2) Okada Y(1)
(1)Laboratory of Functional Genomics, Human Genome Center, IMS, U of Tokyo, Tokyo, Japan
(2)Unit of Human Disease Genomics, Center for Genomic Medicine, Kyoto University, Kyoto, Japan
October 15-17, 2008 Toronto, Canada (Human Genome Variation Meeting 2008)
The space of observable 2x3 tables is the overlap of two triangles.
SUMMARY
The genome-wide association studies have improved our understanding of the genetic basis of many complex traits. Two-by-three contingency tables are tested in these studies. The trend test for the additive mode is most often used, which is the test of 1 degree of freedom (df=1) and other tests, such as the genotype test (Χ2(df=2)) and the Χ2 (df=1) tests for the dominant and recessive modes are also used to increase the power for markers in the non-additive modes. However, any one of them or combination of them is not perfect. We describe the relations among the Χ2(df=2) test and Χ2(df=1) tests for the dominant and recessive modes and the trend test for the additive mode and propose a new statistic based on their relations that tests the hypothesis that the disease-susceptible allele has a dose effect somewhere between the recessive and dominant modes, which corresponds to the optimal dose-effect for the observed data.
The tables that fit the mode where risk-homozygotes are more susceptible than heterozygoutes are indicated by θ
The difference between the observed and the expected tables is a vector in the space.
Χ2(df=2)
Max(Χ2(dominant),Χ2(recessive))
Χ2(dominant)
Χ2(trend)
Χ2(recessive)
Exact statistics are also defined and available along with the asymptotic definition shown here.
Χ2(df=2)
OMTT:
Is more powerful for the markers with biologically like mode than df=2 test.
Is better coverage than simple combination of three mode-specific tests(trend, dominant nad recessive).
Gives only one p-value to individual markers, that lessen the multiple testing problem.
Gives the appropriate order for screened markers, even without spending time for exact calculation.
IS SIMPLE.
Max(Χ2(dominant), Χ2(trend), Χ2(recessive))
Proposed statistics OMTT
References An Optimal Dose-effect Mode Trend Test for SNP Genotype Tables Ryo Yamada, Yukinori Okada Gen. Epidemiol.　in press Application is available at
we appreciate any comments or questions on this poster to Ryo Yamada