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The Effective Sample Size of Relative Pairs in Genetic Case-Control Association Analysis | | Wentian Li
; Yaning Yang
; Peter K. Gregersen
; | | Date: |
28 Nov 2006 | | Subject: | Quantitative Methods | | Abstract: | We address an issue in the transition from genetic linkage analysis to genetic association analysis: how to correctly account for correlations between samples obtained from a pedigree for a case-control analysis. Since correlation does not affect the mean of genotype or allele frequency estimation (it only affects the variance), we introduce the concept of "effective sample size" to account for this effect. The concept of effective sample size much simplifies the handling of complicated relationship between correlated samples. For example, for allele frequency estimation, sibpairs and parent-child pairs are equivalent to 1.5 samples, first cousins and uncle-nephew pairs are equivalent 1.6 samples, etc., without considering the affection status. For genotype frequency estimation, the effective sample size concept is perhaps less convenient because its value depends on a particular genotype and depends on the allele frequency. We present the formula for chi-square test statistic and 95% confidence interval of odd-ratio, the two most frequently used quantities in case-control analysis, for correlated samples using the effective sample size. | | Source: | arXiv, q-bio/0611093 | | Services: | Forum | Review | PDF | Favorites | |
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