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

Rajabli, Farid
Inan, Gul
İlk Dağ, Özlem
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.


Autoinflammation in addition to combined immunodeficiency: SLC29A3 gene defect
Cagdas, Deniz; Surucu, Naz; TAN, ÇAĞMAN; ÖZGÜL, RIZA KÖKSAL; Akkaya-Ulum, Yeliz Z.; Aydinoglu, Ayse Tulay; Aytac, Selin; GÜMRÜK, FATMA; Balci-Hayta, Burcu; Balci-Peynircioglu, Banu; ÖZEN, SEZA; Gürsel, Mayda; Tezcan, Ilhan (Elsevier BV, 2020-05-01)
Introduction: H Syndrome is an autosomal recessive (AR) disease caused by defects in SLCA29A3 gene. This gene encodes the equilibrative nucleoside transporter, the protein which is highly expressed in spleen, lymph node and bone marrow. Autoinflammation and autoimmunity accompanies H Syndrome (HS).
Assignment of biological functions to specific plasmids in a local isolate of Rhizobium cicer
Yıldız, Eda; Özcengiz, Gülay; İçgen, Bülent; Alaeddınoglu, Ng (Springer Science and Business Media LLC, 1999-01-01)
The genetic basis of symbiosis, mucoid structure and melanin biosynthesis in a local isolate of Rhizobium cicer was investigated. The strain was avery effective symbiont and produced substantial amounts of exopolysaccharides and melanin. It harbored three high-molar-mass plasmids of 55, 80 and 130 kb, respectively. Thirty-one melanin production-negative (Mep(-)) derivatives were obtained through plasmid curing. The plasmid patterns of cured derivatives indicated that the loss of 55 and/or 80 kb plasmids was...
Case-control and case-only designs with genotype and family history data: Estimating relative risk, residual familial aggregation, and cumulative risk
Chatterjee, N; Kalaylıoğlu Akyıldız, Zeynep Işıl; Shih, JH; Gail, MH (Wiley, 2006-03-01)
In case-control studies of inherited diseases, participating subjects (probands) are often interviewed to collect detailed data about disease history and age-at-onset information in their family members. Genotype data are typically collected from the probands, but not from their relatives. In this article, we introduce an approach that combines case-control analysis of data on the probands with kin-cohort analysis of disease history data on relatives. Assuming a marginally specified multivariate survival mo...
ImaGene: a convolutional neural network to quantify natural selection from genomic data
Torada, Luis; Lorenzon, Lucrezia; Beddis, Alice; Isildak, Ulas; Pattini, Linda; Mathieson, Sara; Fumagalli, Matteo (Springer Science and Business Media LLC, 2019-11-22)
Background: The genetic bases of many complex phenotypes are still largely unknown, mostly due to the polygenic nature of the traits and the small effect of each associated mutation. An alternative approach to classic association studies to determining such genetic bases is an evolutionary framework. As sites targeted by natural selection are likely to harbor important functionalities for the carrier, the identification of selection signatures in the genome has the potential to unveil the genetic mechanisms...
Novel BRCA2 pathogenic genotype and breast cancer phenotype discordance in monozygotic triplets
Duzkale, Neslihan; EYERCİ, NİLNUR; Oksuzoglu, Berna; Teker, Taner; Kandemir, Olcay (Elsevier BV, 2020-04-01)
BRCA1/2 genes with high-penetrance are tumor suppressor and tumor susceptibility genes that play important roles in the homologous recombination mechanism in DNA repair and increase breast cancer risk. Variants in BRCA1 or BRCA2 are the main causes of familial and early-onset breast cancer. This study investigated pathogenic variant belonging to the BRCA2 gene splice region in monozygotic triplets. A 44-year-old woman was diagnosed with breast cancer when she was 32 years old. Her monozygotic sister had a h...
Citation Formats
F. Rajabli, G. Inan, and Ö. İlk Dağ, “Power Analysis of C-TDT for Small Sample Size Genome-Wide Association Studies by the Joint Use of Case-Parent Trios and Pairs,” COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE, pp. 0–0, 2013, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/47833.