Power Analysis of C-TDT for Small Sample Size Genome-Wide Association Studies by the Joint Use of Case-Parent Trios and Pairs

Abstract EN

In family-based genetic association studies, it is possible to encounter missing genotype information for one of the parents.

This leads to a study consisting of both case-parent trios and case-parent pairs.

One of the approaches to this problem is permutation-based combined transmission disequilibrium test statistic.

However, it is still unknown how powerful this test statistic is with small sample sizes.

In this paper, a simulation study is carried out to estimate the power and false positive rate of this test across different sample sizes for a family-based genome-wide association study.

It is observed that a statistical power of over 80% and a reasonable false positive rate estimate can be achieved even with a combination of 50 trios and 30 pairs when 2% of the SNPs are assumed to be associated.

Moreover, even smaller samples provide high power when smaller percentages of SNPs are associated with the disease.