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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

Pairwise LD Plot for the VDR SNPs.The ID of each SNP was taken as reference. The rs731236, rs7975232, rs1544410, and rs2228570 correspond to TaqI, ApaI, BsmI, and FokI respectively. (a) D′ values. (b) r2 values. The plot was generated using the Haploview 4.2 program.
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pone.0131960.g004: Pairwise LD Plot for the VDR SNPs.The ID of each SNP was taken as reference. The rs731236, rs7975232, rs1544410, and rs2228570 correspond to TaqI, ApaI, BsmI, and FokI respectively. (a) D′ values. (b) r2 values. The plot was generated using the Haploview 4.2 program.

Mentions: FokI was the only variant that was not associated with RA susceptibility directly. LD between the VDR SNPs was measured to detect whether FokI variant was associated with RA indirectly. LD results for all VDR SNPs were shown in Fig 4. The VDR SNPs were shown in the order in which they appear on the genome. Each D′ value and r2 value in the plot were multiplied by 100. Generally, the nearer SNPs tend to have high D′ values while the SNPs that are farther apart tend to have lower D′ values. The four VDR SNPs were in close proximity. Despite these proximities, the LD results were poor. Only two D′ values were greater than 0.8 which were between (FokI, ApaI) and BsmI. All the r2 values were poor. While the D′ value between FokI and BsmI equaled 0.91, but the r2 value between them equaled 0.15. This was due to one SNP being much rarer than the other. So, the SNPs could not substitute each other. At last, both D′ and r2 values must be specified to take the correct decision.


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

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

Pairwise LD Plot for the VDR SNPs.The ID of each SNP was taken as reference. The rs731236, rs7975232, rs1544410, and rs2228570 correspond to TaqI, ApaI, BsmI, and FokI respectively. (a) D′ values. (b) r2 values. The plot was generated using the Haploview 4.2 program.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0131960.g004: Pairwise LD Plot for the VDR SNPs.The ID of each SNP was taken as reference. The rs731236, rs7975232, rs1544410, and rs2228570 correspond to TaqI, ApaI, BsmI, and FokI respectively. (a) D′ values. (b) r2 values. The plot was generated using the Haploview 4.2 program.
Mentions: FokI was the only variant that was not associated with RA susceptibility directly. LD between the VDR SNPs was measured to detect whether FokI variant was associated with RA indirectly. LD results for all VDR SNPs were shown in Fig 4. The VDR SNPs were shown in the order in which they appear on the genome. Each D′ value and r2 value in the plot were multiplied by 100. Generally, the nearer SNPs tend to have high D′ values while the SNPs that are farther apart tend to have lower D′ values. The four VDR SNPs were in close proximity. Despite these proximities, the LD results were poor. Only two D′ values were greater than 0.8 which were between (FokI, ApaI) and BsmI. All the r2 values were poor. While the D′ value between FokI and BsmI equaled 0.91, but the r2 value between them equaled 0.15. This was due to one SNP being much rarer than the other. So, the SNPs could not substitute each other. At last, both D′ and r2 values must be specified to take the correct decision.

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