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    Application of Dempster-Schafer Method in Family-Based Association Studies
    (Ieee Computer Soc, 2013) Rajabli, Farid; Goktas, Unal; Inan, Gul
    In experiments designed for family-based association studies, methods such as transmission disequilibrium test require large number of trios to identify single-nucleotide polymorphisms associated with the disease. However, unavailability of a large number of trios is the Achilles' heel of many complex diseases, especially for late-onset diseases. In this paper, we propose a novel approach to this problem by means of the Dempster-Shafer method. The simulation studies show that the Dempster-Shafer method has a promising overall performance, in identifying single-nucleotide polymorphisms in the correct association class, as it has 90 percent accuracy even with 60 trios.
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    Dempster-Schafer Method in Family Based Association Studies
    (Turgut Ozal Univ, 2012) Rajabli, Farid; Goktas, Unal; Inan, Gul
    In experiments designed for family-based association studies, methods such as transmission disequilibrium test (TDT) require large number of trios to identify single nucleotide polymorphisms (SNPs) associated with the disease. However, unavailability of large number of trios is the Achilles' heel of many complex disease studies, especially for the late-onset diseases since parents might have passed away or unavailable. This problem motivated us to look for new approaches that require smaller number of trios to detect associations in family based studies. Aiming this, we propose using Dempster-Shafer method of evidence to detect the associations in family-based studies and show that this approach has a good performance in identifying associations with moderate to small sized samples.
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    Power Analysis of C-TDT for Small Sample Size Genome-Wide Association Studies by the Joint Use of Case-Parent Trios and Pairs
    (Hindawi Ltd, 2013) Rajabli, Farid; Inan, Gul; Ilk, Ozlem
    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.