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Öğe Application of Dempster-Schafer Method in Family-Based Association Studies(Ieee Computer Soc, 2013) Rajabli, Farid; Goktas, Unal; Inan, GulIn 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.Öğe Application of kappa statistics in sequential tests for family-based design(Tubitak Scientific & Technological Research Council Turkey, 2016) Rajabli, FaridFamily-based designs are commonly used in genetic association studies to locate markers associated with diseases. It is a challenging task to collect a large enough sample size, perform a statistical test, and obtain the desired statistical power. The sequential probability ratio test (SPRT) was introduced to overcome the limited sample size problem. However, the drawback of SPRT is that, for the sake of accuracy, the test leaves many markers in a gray zone meaning no decision. In this article, we propose a novel approach: a sequential probability ratio test 'plus' (SPRT+) to reduce the number of these gray zone markers. Using simulated data, the results of SPRT+ are compared with the results of SPRT. SPRT+ shows a promising overall performance in identifying highly and moderately associated markers in the correct association region without a loss of accuracy.Öğe Dempster-Schafer Method in Family Based Association Studies(Turgut Ozal Univ, 2012) Rajabli, Farid; Goktas, Unal; Inan, GulIn 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.Öğe Genome projects 5W1H: What, where, when, why, how and in which population?(Refik Saydam National Public Health Agency (RSNPHA) turkhijyen@rshm.gov.tr, 2014) Fidanoğlu, Pelin; Belder, Nevin; Doğanay Erdoğan, Beyza; Ilk, Ozlem; Rajabli, Farid; Özdağ, Hil?alGenome projects aim to decode an organism's complete set of deoxyribonucleic acid (DNA), which can be described as the living code of organism. The idea of the Human Genome Project (HGP) was conceived in the early 1980s. The project was started at 1990 and finished at 2003. The sequencing of the whole human genome derived from the DNA of several anonymous volunteers, costed 3.8 billion dollars. In order to annotate the genome data, the "topography of the genome" and the anatomy of the genes should have been revealed. For this purpose, genome projects of several model organisms was carried out in parallel with HGP with the aim to identify basic structural components, organizational structure and evolutionarily development of the genome. With the advent of microarray technology in the early 2000s, high-throughput screening of Single Nucleotide Polymorphisms (SNPs) and Copy Number Variations (CNVs) became feasible. After the completion of HGP in 13 years, James D. Watson's genome was sequenced with 1 million dollar budget in just 2 months using next generation sequencing technology. Today a human genome can be sequenced in just one day with the cost of 6.600 USD. In this reviev the HGP which created big expectations especially in medicine will be explained from its start to the present. Then we will summarize the studies paving the road to personalized medicine emphasizing the fact that to reveal the meaning of genomic information, it should become computable. © 2014 Elsevier B.V., All rights reserved.Öğe 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, OzlemIn 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.
