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Selecting a contingency table in a population-based association study: allele frequency or positivity?
1Department of Human Genetics, School of International Health, Graduate School of Medical Sciences, University of Tokyo, Japan. juno@.m.u-tokyo.ac.jp
Journal of Human Genetics
|August 3, 1999
Summary
Choosing the right 2x2 contingency table is crucial for detecting gene-disease associations. Both allele frequency and positivity tables should be tested with the chi-squared test, especially for low penetrance genes.
Area of Science:
- Genetics
- Biostatistics
Background:
- Population-based association studies commonly use chi-squared tests to assess gene-disease links.
- These studies rely on 2x2 contingency tables derived from allele frequencies or disease/control group positivities.
Purpose of the Study:
- To investigate how different 2x2 contingency table types influence the power of the chi-squared test.
- To determine the optimal table selection for detecting genetic associations under various penetrance models.
Main Methods:
- Calculated P-values for chi-squared tests using both allele frequency and positivity tables.
- Evaluated test power under multiplicative and additive genetic penetrance models.
Main Results:
- Significant differences in chi-squared test power were observed between table types, particularly with low and similar genotype penetrance.
- The allele frequency table showed superior power in the multiplicative model.
- The positivity table was more suitable for the additive model.
Conclusions:
- Contingency table selection critically impacts the ability to detect true gene-disease associations, especially when correcting for multiple testing.
- Performing chi-squared tests on both table types is recommended for identifying susceptible genes with low penetrance, even if one table yields non-significant results.