Calculation of MAX Test p-Value with Geometric Characterization of 2x3 Table Tests

• Activity Number: 452
• Type: Topic Contributed
• Date/Time: Wednesday, August 4, 2010 : 8:30 AM to 10:20 AM
• Sponsor: Biometrics Section
• Author(s): Ryo Yamada*+
• Companies: Kyoto University
• Keywords: SNP ; association test ; MAX test ; geometry

Abstract

Single nucleotide polymorphisms (SNPs) are popular markers in genetic epidemiolgy. In many cases SNPs have two types and they make three diplotypes of SNPs in autosomal chromosomes. Therefore 2x3 contingency tables are the units of analysis in case-control association with SNPs. Multiple tests have been applied to evaluate of genetic effect of SNPs, such as Pearson's test with two degrees of freedom, three tests with one degree of freedom (Chi-square tests for dominant and recessive modes and Cockran-Armitage trend test for additive mode) as well as MAX3 test and MAX test which are combination of four tests mentioned earlier. Recently all of these tests were reported as trend test with different scores. In this presentation I further characterize these tests with a new diagram to characterize these tests and propose a method to calculate P-value of MAX test.