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Genetic Case-Control Study for Eight Polymorphisms Associated with Rheumatoid Arthritis.

Saad MN, Mabrouk MS, Eldeib AM, Shaker OG - PLoS ONE (2015)

Bottom Line: TGFβ1 and MTHFR A1298C were associated with RA using the dominant and the co-dominant models.There were no significant differences for FokI and the presence of RA disease by the used models examination.For LD results, There was a high D' value between BsmI and FokI (D' = 0.91), but the r(2) value between them was poor.

View Article: PubMed Central - PubMed

Affiliation: Biomedical Engineering Department, Minia University, Minia, Egypt.

ABSTRACT
Rheumatoid arthritis (RA) is an autoimmune disease which has a significant socio-economic impact. The aim of the current study was to investigate eight candidate RA susceptibility loci to identify the associated variants in Egyptian population. Eight single nucleotide polymorphisms (SNPs) (MTHFR-C677T and A1298C, TGFβ1 T869C, TNFB A252G, and VDR-ApaI, BsmI, FokI, and TaqI) were tested by genotyping patients with RA (n = 105) and unrelated controls (n = 80). Associations were tested using multiplicative, dominant, recessive, and co-dominant models. Also, the linkage disequilibrium (LD) between the VDR SNPs was measured to detect any indirect association. By comparing RA patients with controls (TNFB, BsmI, and TaqI), SNPs were associated with RA using all models. MTHFR C677T was associated with RA using all models except the recessive model. TGFβ1 and MTHFR A1298C were associated with RA using the dominant and the co-dominant models. The recessive model represented the association for ApaI variant. There were no significant differences for FokI and the presence of RA disease by the used models examination. For LD results, There was a high D' value between BsmI and FokI (D' = 0.91), but the r(2) value between them was poor. All the studied SNPs may contribute to the susceptibility of RA disease in Egyptian population except for FokI SNP.

No MeSH data available.


Related in: MedlinePlus

Flow Chart of the Proposed Study.The eight SNPs were genotyped to detect the association with RA susceptibility either directly or indirectly. The SNP that fails to associate with the phenotype directly will undergo an LD study to detect any indirect association as a surrogate for direct disease association.
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pone.0131960.g001: Flow Chart of the Proposed Study.The eight SNPs were genotyped to detect the association with RA susceptibility either directly or indirectly. The SNP that fails to associate with the phenotype directly will undergo an LD study to detect any indirect association as a surrogate for direct disease association.

Mentions: The flow chart shown in Fig 1 illustrated the proposed association scheme. The LD should be measured between bi-allelic SNPs that lie on the same chromosome. So, LD could be measured between MTHFR (C677T and A1298C) SNPs to detect any indirect variant. Also, the VDR (ApaI, BsmI, FokI, and TaqI) SNPs were appropriate for LD study as they were all located on chromosome 12.


Genetic Case-Control Study for Eight Polymorphisms Associated with Rheumatoid Arthritis.

Saad MN, Mabrouk MS, Eldeib AM, Shaker OG - PLoS ONE (2015)

Flow Chart of the Proposed Study.The eight SNPs were genotyped to detect the association with RA susceptibility either directly or indirectly. The SNP that fails to associate with the phenotype directly will undergo an LD study to detect any indirect association as a surrogate for direct disease association.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4492599&req=5

pone.0131960.g001: Flow Chart of the Proposed Study.The eight SNPs were genotyped to detect the association with RA susceptibility either directly or indirectly. The SNP that fails to associate with the phenotype directly will undergo an LD study to detect any indirect association as a surrogate for direct disease association.
Mentions: The flow chart shown in Fig 1 illustrated the proposed association scheme. The LD should be measured between bi-allelic SNPs that lie on the same chromosome. So, LD could be measured between MTHFR (C677T and A1298C) SNPs to detect any indirect variant. Also, the VDR (ApaI, BsmI, FokI, and TaqI) SNPs were appropriate for LD study as they were all located on chromosome 12.

Bottom Line: TGFβ1 and MTHFR A1298C were associated with RA using the dominant and the co-dominant models.There were no significant differences for FokI and the presence of RA disease by the used models examination.For LD results, There was a high D' value between BsmI and FokI (D' = 0.91), but the r(2) value between them was poor.

View Article: PubMed Central - PubMed

Affiliation: Biomedical Engineering Department, Minia University, Minia, Egypt.

ABSTRACT
Rheumatoid arthritis (RA) is an autoimmune disease which has a significant socio-economic impact. The aim of the current study was to investigate eight candidate RA susceptibility loci to identify the associated variants in Egyptian population. Eight single nucleotide polymorphisms (SNPs) (MTHFR-C677T and A1298C, TGFβ1 T869C, TNFB A252G, and VDR-ApaI, BsmI, FokI, and TaqI) were tested by genotyping patients with RA (n = 105) and unrelated controls (n = 80). Associations were tested using multiplicative, dominant, recessive, and co-dominant models. Also, the linkage disequilibrium (LD) between the VDR SNPs was measured to detect any indirect association. By comparing RA patients with controls (TNFB, BsmI, and TaqI), SNPs were associated with RA using all models. MTHFR C677T was associated with RA using all models except the recessive model. TGFβ1 and MTHFR A1298C were associated with RA using the dominant and the co-dominant models. The recessive model represented the association for ApaI variant. There were no significant differences for FokI and the presence of RA disease by the used models examination. For LD results, There was a high D' value between BsmI and FokI (D' = 0.91), but the r(2) value between them was poor. All the studied SNPs may contribute to the susceptibility of RA disease in Egyptian population except for FokI SNP.

No MeSH data available.


Related in: MedlinePlus