Computational and Mathematical Methods in Medicine
Volume 2013 (2013), Article ID 235825, 7 pages
http://dx.doi.org/10.1155/2013/235825
Research Article

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

Farid Rajabli,1 Gul Inan,2 and Ozlem Ilk2

1Department of Electrical and Electronic Engineering, Faculty of Engineering, Turgut Ozal University, 06010 Ankara, Turkey
2Department of Statistics, Faculty of Arts and Sciences, Middle East Technical University, 06800 Ankara, Turkey

Received 2 January 2013; Revised 8 April 2013; Accepted 13 April 2013

Academic Editor: Shinto Eguchi

Copyright © 2013 Farid Rajabli et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

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.