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CNV Analysis Associates AKNAD1 with Type-2 Diabetes in Jordan Subpopulations.

Dajani R, Li J, Wei Z, Glessner JT, Chang X, Cardinale CJ, Pellegrino R, Wang T, Hakooz N, Khader Y, Sheshani A, Zandaki D, Hakonarson H - Sci Rep (2015)

Bottom Line: We found a CNV region in protein tyrosine phosphatase receptor type D (PTPRD) with significant association with T2D.Endoplasmic reticulum (ER)-related pathways were significantly enriched among genes which are predicted to be functionally associated with human or mouse homologues of AKNAD1.We identified and experimentally validated a significant CNVR in gene AKNAD1 associated with T2D.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology and Biotechnology, Hashemite University, Zarqa, Jordan.

ABSTRACT
Previous studies have identified a number of single nucleotide polymorphisms (SNPs) associated with type-2 diabetes (T2D), but copy number variation (CNV) association has rarely been addressed, especially in populations from Jordan. To investigate CNV associations for T2D in populations in Jordan, we conducted a CNV analysis based on intensity data from genome-wide SNP array, including 34 T2D cases and 110 healthy controls of Chechen ethnicity, as well as 34 T2D cases and 106 healthy controls of Circassian ethnicity. We found a CNV region in protein tyrosine phosphatase receptor type D (PTPRD) with significant association with T2D. PTPRD has been reported to be associated with T2D in genome-wide association studies (GWAS). We additionally identified 16 CNV regions associated with T2D which overlapped with gene exons. Of particular interest, a CNV region in the gene AKNA Domain Containing 1 (AKNAD1) surpassed the experiment-wide significance threshold. Endoplasmic reticulum (ER)-related pathways were significantly enriched among genes which are predicted to be functionally associated with human or mouse homologues of AKNAD1. This is the first CNV analysis of a complex disease in populations of Jordan. We identified and experimentally validated a significant CNVR in gene AKNAD1 associated with T2D.

No MeSH data available.


Related in: MedlinePlus

Principal component analysis of the combined cohort.High overlap between diabetic cases and controls are observed within each ethnic group.
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f1: Principal component analysis of the combined cohort.High overlap between diabetic cases and controls are observed within each ethnic group.

Mentions: To study the potential CNV association with T2D in Jordan, we recruited 284 participants. Specifically, for the Chechen population, we have 34 cases and 110 controls, of which 60 are males and 84 are females. For Circassians, we have 34 cases and 106 controls, of which 61 are males and 79 are females. After quality control (QC) of genotyping data, 208 samples were retained in the analysis. By principal component analysis (PCA), we successfully separate the Chechen and the Circassian ethnic groups and we observed the high overlap between cases and controls within each ethnic group on the PCA plot (Fig. 1). The sample information after QC is summarized in Supplementary Table 1. To boost power in statistical analysis, as well as because of their common ancient origin and distinct population structure from other ethnic groups by continent, we combined the data from these two ethnic groups for further analysis.


CNV Analysis Associates AKNAD1 with Type-2 Diabetes in Jordan Subpopulations.

Dajani R, Li J, Wei Z, Glessner JT, Chang X, Cardinale CJ, Pellegrino R, Wang T, Hakooz N, Khader Y, Sheshani A, Zandaki D, Hakonarson H - Sci Rep (2015)

Principal component analysis of the combined cohort.High overlap between diabetic cases and controls are observed within each ethnic group.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4543987&req=5

f1: Principal component analysis of the combined cohort.High overlap between diabetic cases and controls are observed within each ethnic group.
Mentions: To study the potential CNV association with T2D in Jordan, we recruited 284 participants. Specifically, for the Chechen population, we have 34 cases and 110 controls, of which 60 are males and 84 are females. For Circassians, we have 34 cases and 106 controls, of which 61 are males and 79 are females. After quality control (QC) of genotyping data, 208 samples were retained in the analysis. By principal component analysis (PCA), we successfully separate the Chechen and the Circassian ethnic groups and we observed the high overlap between cases and controls within each ethnic group on the PCA plot (Fig. 1). The sample information after QC is summarized in Supplementary Table 1. To boost power in statistical analysis, as well as because of their common ancient origin and distinct population structure from other ethnic groups by continent, we combined the data from these two ethnic groups for further analysis.

Bottom Line: We found a CNV region in protein tyrosine phosphatase receptor type D (PTPRD) with significant association with T2D.Endoplasmic reticulum (ER)-related pathways were significantly enriched among genes which are predicted to be functionally associated with human or mouse homologues of AKNAD1.We identified and experimentally validated a significant CNVR in gene AKNAD1 associated with T2D.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology and Biotechnology, Hashemite University, Zarqa, Jordan.

ABSTRACT
Previous studies have identified a number of single nucleotide polymorphisms (SNPs) associated with type-2 diabetes (T2D), but copy number variation (CNV) association has rarely been addressed, especially in populations from Jordan. To investigate CNV associations for T2D in populations in Jordan, we conducted a CNV analysis based on intensity data from genome-wide SNP array, including 34 T2D cases and 110 healthy controls of Chechen ethnicity, as well as 34 T2D cases and 106 healthy controls of Circassian ethnicity. We found a CNV region in protein tyrosine phosphatase receptor type D (PTPRD) with significant association with T2D. PTPRD has been reported to be associated with T2D in genome-wide association studies (GWAS). We additionally identified 16 CNV regions associated with T2D which overlapped with gene exons. Of particular interest, a CNV region in the gene AKNA Domain Containing 1 (AKNAD1) surpassed the experiment-wide significance threshold. Endoplasmic reticulum (ER)-related pathways were significantly enriched among genes which are predicted to be functionally associated with human or mouse homologues of AKNAD1. This is the first CNV analysis of a complex disease in populations of Jordan. We identified and experimentally validated a significant CNVR in gene AKNAD1 associated with T2D.

No MeSH data available.


Related in: MedlinePlus