Systems-level analysis of genome wide association study results for a pilot juvenile idiopathic arthritis family study

Aydın Son, Yeşim
Demirkaya, Erkan
Unsal, Erbil
Genome wide association studies (GWAS) determine susceptibility profiles for complex diseases. In this study, GWAS was performed in 26 patients with oligo and rheumatoid factor negative polyarticular juvenile idiopathic artritis (JIA) and their healthy parents by Affymetrix 250K SNP arrays. Biological function and pathway enrichment analysis was done. This is the first GWAS reported for JIA families from the eastern Mediterranean population. Enrichment of Fc gamma R-mediated phagocytosis pathway and response to various stimuli were the leading discoveries, along with the presentation of the strong interaction of JIA-associated genes with HLA cluster in the co-expression network. The co-expression network also presented the direct interaction of a gene in Fc gamma R-mediated phagocytosis pathway, namely GAB2, with BLK, CDH13, IL4R and MICA. The systems biology approach helped us to investigate the interactions between the identified genes and biological pathways and molecular functions, expanding our understanding of JIA pathogenesis at molecular level.


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Kantar Özçırpan, Ekin; Weber, Gerhard Wilhelm; İyigün, Cem; Department of Biomedical Engineering (2015)
In many Genome Wide Association Studies (GWAS), the relation between SNPs and complex diseases has being tried to reveal. Moreover it is known that, in GWAS there exist a high amount of data which include relations between SNPs, phenotypes and diseases, etc. Many algorithms have been used to be able to reach the desired information from this huge data. Therefore, in this study, an algorithm one of whose important steps is based on linkage disequilibrium(LD), was constructed to eliminate the redundant inform...
Dempster-Schafer Method in Family Based Association Studies
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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...
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Kadioǧlu, Onat; Üstünkar, Gürkan; Aydın Son, Yeşim (2012-06-29)
Genome wide association studies (GWAS) aim to identify genomic variance associated with certain disease conditions. Major bottleneck of standard GWAS approaches are the prioritization and subset selection after the statistically significant SNPs are determined. Our group has recently developed an analysis pipeline, where p-value and combined p value statistics are integrated with the novel AHP based SNP prioritization algorithm for the detailed analysis of associated SNPs considering statistical significanc...
METU-SNP: An Integrated Software System for SNPComplex Disease Association Analysis
Recently, there has been increasing research to discover genomic biomarkers, haplotypes, and potentially other variables that together contribute to the development of diseases. Single Nucleotide Polymorphisms (SNPs) are the most common form of genomic variations and they can represent an individual's genetic variability in greatest detail. Genome-wide association studies (GWAS) of SNPs, high-dimensional case-control studies, are among the most promising approaches for identifying disease causing variants. ...
A multi-layered graphical model of the relation among SNPS, GENES, and pathways based on subgraph search
Ersoy, Gökhan; Aydın Son, Yeşim; Can, Tolga; Department of Bioinformatics (2015)
The analysis of Single Nucleotide Polymorphisms (SNPs) through Genome Wide Association Studies (GWAS) presents great potential for describing disease loci and gaining insight into the underlying etiology of diseases. Recently described combined p-value approach allows identification of associations at gene and pathway level. The integrated programs like METU-SNP produce simple lists of either SNP id/gene id/pathway title and their p-values and significance status or SNP id/disease id/pathway information. In...
Citation Formats
Y. Aydın Son et al., “Systems-level analysis of genome wide association study results for a pilot juvenile idiopathic arthritis family study,” TURKISH JOURNAL OF PEDIATRICS, pp. 324–333, 2015, Accessed: 00, 2020. [Online]. Available: