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Evaluation of CNTNAP2 gene polymorphisms for exfoliation syndrome in Japanese.

Shimizu A, Takano Y, Shi D, Yokokura S, Yokoyama Y, Zheng X, Shiraishi A, Ohashi Y, Nakazawa T, Fuse N - Mol. Vis. (2012)

Bottom Line: One hundred and eight unrelated Japanese patients with the XFS, and 199 normal controls were studied.The allele frequencies of rs1404699 (p=8.57XE-3, odds ratio (OR)=1.59, 95% confidential intervals (CI); 1,12-2.24) and rs7803992 (p=5.43XE-4, OR=1.86, 95% CI; 1.31-2.65) were statistically significantly different between XFS and controls.The variants, rs1404699 and rs7803992, of CNTNAP2 should be associated with XFS in the Japanese population.

View Article: PubMed Central - PubMed

Affiliation: Department of Ophthalmology, Tohoku University Graduate School of Medicine, Aoba-ku, Sendai, Japan.

ABSTRACT

Purpose: To investigate the contactin-associated protein-like 2 (CNTNAP2) gene for single-nucleotide polymorphisms (SNPs) in Japanese patients with the exfoliation syndrome (XFS).

Methods: One hundred and eight unrelated Japanese patients with the XFS, and 199 normal controls were studied. Genomic DNA was extracted from the leukocytes of the peripheral blood, and 8 SNPs, rs826802, rs1404699, rs7803992, rs700308, rs4725736, rs2107856, rs2141388, and rs6970064, were amplified by polymerase chain reaction (PCR), directly sequenced, and genotyped.

Results: The allele frequencies of rs1404699 (p=8.57XE-3, odds ratio (OR)=1.59, 95% confidential intervals (CI); 1,12-2.24) and rs7803992 (p=5.43XE-4, OR=1.86, 95% CI; 1.31-2.65) were statistically significantly different between XFS and controls. In addition, there were significant differences in these genotype frequencies (p=0.0197 and 1.75XE-3). The allele and the genotype frequencies of rs2107856 and rs2141388, which were statistically significant SNPs in an earlier study, were not significantly different.

Conclusions: The variants, rs1404699 and rs7803992, of CNTNAP2 should be associated with XFS in the Japanese population.

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Related in: MedlinePlus

CNTNAP2 gene structure. The 8 SNPs studied were; 1. rs826802, 2. rs144699, 3. rs7803992, 4. rs700308, 5. rs4725736, 6. rs2107856, 7. rs2141388, and 8. rs6970064. SP, signal peptide; DISC, discoidin-like domain; LamG, laminin-G domain; EGF, epidermal growth factor like domain; FIB, fibrinogen-like domain;TM, transmembrane region; PDZBD, PDZ-domain binding site.
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f1: CNTNAP2 gene structure. The 8 SNPs studied were; 1. rs826802, 2. rs144699, 3. rs7803992, 4. rs700308, 5. rs4725736, 6. rs2107856, 7. rs2141388, and 8. rs6970064. SP, signal peptide; DISC, discoidin-like domain; LamG, laminin-G domain; EGF, epidermal growth factor like domain; FIB, fibrinogen-like domain;TM, transmembrane region; PDZBD, PDZ-domain binding site.

Mentions: Genomic DNA was extracted from the leukocytes of peripheral blood and purified with the Qiagen QIAamp Blood Kit (Qiagen, Valencia, CA). Genomic DNA was extracted from the leukocytes of the peripheral blood, and the 6 SNPs, rs1404699, rs700308, rs4725736, rs2107856, rs2141388, and rs6970064, were chosen from the earlier studies. Two newly identified SNPs, rs826802 and rs7803992, were designed around intron 9 of the gene. The CNTNAP2 gene structure with the location of the 8 SNPs is shown in Figure 1. They were amplified by polymerase chain reaction (PCR), directly sequenced, and genotyped. The amplifications were performed at 60 °C annealing temperature. The PCR fragments were purified with ExoSAP-IT (USB, Cleveland, OH), sequenced by the BigDyeTM Terminator v3.1 Cycle Sequencing Kit (Perkin-Elmer, Foster City, CA) by an automated DNA sequencer (ABI PRISMTM 3100 Genetic Analyzer, Perkin-Elmer). The allele frequencies, genotypes, and haplotypes of the CNTNAP2 SNPs were determined.


Evaluation of CNTNAP2 gene polymorphisms for exfoliation syndrome in Japanese.

Shimizu A, Takano Y, Shi D, Yokokura S, Yokoyama Y, Zheng X, Shiraishi A, Ohashi Y, Nakazawa T, Fuse N - Mol. Vis. (2012)

CNTNAP2 gene structure. The 8 SNPs studied were; 1. rs826802, 2. rs144699, 3. rs7803992, 4. rs700308, 5. rs4725736, 6. rs2107856, 7. rs2141388, and 8. rs6970064. SP, signal peptide; DISC, discoidin-like domain; LamG, laminin-G domain; EGF, epidermal growth factor like domain; FIB, fibrinogen-like domain;TM, transmembrane region; PDZBD, PDZ-domain binding site.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3369891&req=5

f1: CNTNAP2 gene structure. The 8 SNPs studied were; 1. rs826802, 2. rs144699, 3. rs7803992, 4. rs700308, 5. rs4725736, 6. rs2107856, 7. rs2141388, and 8. rs6970064. SP, signal peptide; DISC, discoidin-like domain; LamG, laminin-G domain; EGF, epidermal growth factor like domain; FIB, fibrinogen-like domain;TM, transmembrane region; PDZBD, PDZ-domain binding site.
Mentions: Genomic DNA was extracted from the leukocytes of peripheral blood and purified with the Qiagen QIAamp Blood Kit (Qiagen, Valencia, CA). Genomic DNA was extracted from the leukocytes of the peripheral blood, and the 6 SNPs, rs1404699, rs700308, rs4725736, rs2107856, rs2141388, and rs6970064, were chosen from the earlier studies. Two newly identified SNPs, rs826802 and rs7803992, were designed around intron 9 of the gene. The CNTNAP2 gene structure with the location of the 8 SNPs is shown in Figure 1. They were amplified by polymerase chain reaction (PCR), directly sequenced, and genotyped. The amplifications were performed at 60 °C annealing temperature. The PCR fragments were purified with ExoSAP-IT (USB, Cleveland, OH), sequenced by the BigDyeTM Terminator v3.1 Cycle Sequencing Kit (Perkin-Elmer, Foster City, CA) by an automated DNA sequencer (ABI PRISMTM 3100 Genetic Analyzer, Perkin-Elmer). The allele frequencies, genotypes, and haplotypes of the CNTNAP2 SNPs were determined.

Bottom Line: One hundred and eight unrelated Japanese patients with the XFS, and 199 normal controls were studied.The allele frequencies of rs1404699 (p=8.57XE-3, odds ratio (OR)=1.59, 95% confidential intervals (CI); 1,12-2.24) and rs7803992 (p=5.43XE-4, OR=1.86, 95% CI; 1.31-2.65) were statistically significantly different between XFS and controls.The variants, rs1404699 and rs7803992, of CNTNAP2 should be associated with XFS in the Japanese population.

View Article: PubMed Central - PubMed

Affiliation: Department of Ophthalmology, Tohoku University Graduate School of Medicine, Aoba-ku, Sendai, Japan.

ABSTRACT

Purpose: To investigate the contactin-associated protein-like 2 (CNTNAP2) gene for single-nucleotide polymorphisms (SNPs) in Japanese patients with the exfoliation syndrome (XFS).

Methods: One hundred and eight unrelated Japanese patients with the XFS, and 199 normal controls were studied. Genomic DNA was extracted from the leukocytes of the peripheral blood, and 8 SNPs, rs826802, rs1404699, rs7803992, rs700308, rs4725736, rs2107856, rs2141388, and rs6970064, were amplified by polymerase chain reaction (PCR), directly sequenced, and genotyped.

Results: The allele frequencies of rs1404699 (p=8.57XE-3, odds ratio (OR)=1.59, 95% confidential intervals (CI); 1,12-2.24) and rs7803992 (p=5.43XE-4, OR=1.86, 95% CI; 1.31-2.65) were statistically significantly different between XFS and controls. In addition, there were significant differences in these genotype frequencies (p=0.0197 and 1.75XE-3). The allele and the genotype frequencies of rs2107856 and rs2141388, which were statistically significant SNPs in an earlier study, were not significantly different.

Conclusions: The variants, rs1404699 and rs7803992, of CNTNAP2 should be associated with XFS in the Japanese population.

Show MeSH
Related in: MedlinePlus