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CDH1 polymorphisms and haplotypes in sporadic diffuse and intestinal gastric cancer: a case-control study based on direct sequencing analysis.

Chu CM, Chen CJ, Chan DC, Wu HS, Liu YC, Shen CY, Chang TM, Yu JC, Harn HJ, Yu CP, Yang MH - World J Surg Oncol (2014)

Bottom Line: The genotypic polymorphisms in the -160 promoter region, exons and intron-exon boundaries of CDH1 were detected by direct sequencing analysis.The CDH1 - 160C → A promoter polymorphism and four polymorphisms (48 + 6 T → C, 2076C → T, 2253C → T and 1937-13 T → C) were included in the haplotype analyses, which were estimated using the expectation-maximization algorithm.Compared to controls, the frequency of the -160A allele was significantly higher in diffuse gastric cancer cases (P = 0.005), but it was not significantly different in intestinal gastric cancer cases (P = 0.119).

View Article: PubMed Central - HTML - PubMed

Affiliation: Division of General Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, No, 325, Sec, 2, Cheng-Kung Road, Neihu, Taipei 11490, Taiwan. dlyaochi@gmail.com.

ABSTRACT

Background: Findings related to the influence of the -160C → A promoter polymorphism and haplotypes of the E-cadherin (CDH1) gene have not been consistent in previous studies regarding the risk for sporadic gastric cancer. Investigators in most previous studies detected those genotypes using restriction fragment length polymorphism analysis. Therefore, we conducted a case-control study to investigate the association of the CDH1 - 160C → A promoter polymorphism and haplotypes for cancer risk related to sporadic diffuse and intestinal gastric cancer by direct sequencing analysis.

Methods: We included 107 diffuse gastric cancer cases, 60 intestinal gastric cancer cases and 134 controls. The genotypic polymorphisms in the -160 promoter region, exons and intron-exon boundaries of CDH1 were detected by direct sequencing analysis. Genotype frequencies were compared. The CDH1 - 160C → A promoter polymorphism and four polymorphisms (48 + 6 T → C, 2076C → T, 2253C → T and 1937-13 T → C) were included in the haplotype analyses, which were estimated using the expectation-maximization algorithm.

Results: Compared to controls, the frequency of the -160A allele was significantly higher in diffuse gastric cancer cases (P = 0.005), but it was not significantly different in intestinal gastric cancer cases (P = 0.119). Two sets of three-marker haplotypes (-160C → A, 48 + 6 T → C, 2076C → T and -160C → A, 1937-13 T → C, 2253C → T) were associated with the risk of diffuse gastric cancer (P = 0.011 and P = 0.042, respectively).

Conclusion: Based on direct sequencing analysis, our findings suggest that the CDH1 - 160C → A promoter polymorphism and haplotypes play significant roles in cancer risk for sporadic diffuse gastric cancer, but not for intestinal gastric cancer, in a Taiwanese population.

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Related in: MedlinePlus

Genotypes of CDH1 polymorphisms detected by direct sequencing. (a) Promoter polymorphism −160C → A. (b) Intron 1 polymorphism 48 + 6 T → C. (c) Exon 13 polymorphism 2076C → T. (d) Exon 14 polymorphism 2253C → T. (e) Intron 12 polymorphism 1937–13 T → C.
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Figure 2: Genotypes of CDH1 polymorphisms detected by direct sequencing. (a) Promoter polymorphism −160C → A. (b) Intron 1 polymorphism 48 + 6 T → C. (c) Exon 13 polymorphism 2076C → T. (d) Exon 14 polymorphism 2253C → T. (e) Intron 12 polymorphism 1937–13 T → C.

Mentions: The genotypes of the CDH1 − 160C → A (dbSNP:rs16260), 48 + 6 T → C (dbSNP:rs3743674), 2076C → T (dbSNP:rs1801552), 2253C → T (dbSNP:rs33964119) and 1937–13 T → C (dbSNP:rs2276330) polymorphisms detected by direct sequencing in the cases and controls are shown in Figure 2.


CDH1 polymorphisms and haplotypes in sporadic diffuse and intestinal gastric cancer: a case-control study based on direct sequencing analysis.

Chu CM, Chen CJ, Chan DC, Wu HS, Liu YC, Shen CY, Chang TM, Yu JC, Harn HJ, Yu CP, Yang MH - World J Surg Oncol (2014)

Genotypes of CDH1 polymorphisms detected by direct sequencing. (a) Promoter polymorphism −160C → A. (b) Intron 1 polymorphism 48 + 6 T → C. (c) Exon 13 polymorphism 2076C → T. (d) Exon 14 polymorphism 2253C → T. (e) Intron 12 polymorphism 1937–13 T → C.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4230630&req=5

Figure 2: Genotypes of CDH1 polymorphisms detected by direct sequencing. (a) Promoter polymorphism −160C → A. (b) Intron 1 polymorphism 48 + 6 T → C. (c) Exon 13 polymorphism 2076C → T. (d) Exon 14 polymorphism 2253C → T. (e) Intron 12 polymorphism 1937–13 T → C.
Mentions: The genotypes of the CDH1 − 160C → A (dbSNP:rs16260), 48 + 6 T → C (dbSNP:rs3743674), 2076C → T (dbSNP:rs1801552), 2253C → T (dbSNP:rs33964119) and 1937–13 T → C (dbSNP:rs2276330) polymorphisms detected by direct sequencing in the cases and controls are shown in Figure 2.

Bottom Line: The genotypic polymorphisms in the -160 promoter region, exons and intron-exon boundaries of CDH1 were detected by direct sequencing analysis.The CDH1 - 160C → A promoter polymorphism and four polymorphisms (48 + 6 T → C, 2076C → T, 2253C → T and 1937-13 T → C) were included in the haplotype analyses, which were estimated using the expectation-maximization algorithm.Compared to controls, the frequency of the -160A allele was significantly higher in diffuse gastric cancer cases (P = 0.005), but it was not significantly different in intestinal gastric cancer cases (P = 0.119).

View Article: PubMed Central - HTML - PubMed

Affiliation: Division of General Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, No, 325, Sec, 2, Cheng-Kung Road, Neihu, Taipei 11490, Taiwan. dlyaochi@gmail.com.

ABSTRACT

Background: Findings related to the influence of the -160C → A promoter polymorphism and haplotypes of the E-cadherin (CDH1) gene have not been consistent in previous studies regarding the risk for sporadic gastric cancer. Investigators in most previous studies detected those genotypes using restriction fragment length polymorphism analysis. Therefore, we conducted a case-control study to investigate the association of the CDH1 - 160C → A promoter polymorphism and haplotypes for cancer risk related to sporadic diffuse and intestinal gastric cancer by direct sequencing analysis.

Methods: We included 107 diffuse gastric cancer cases, 60 intestinal gastric cancer cases and 134 controls. The genotypic polymorphisms in the -160 promoter region, exons and intron-exon boundaries of CDH1 were detected by direct sequencing analysis. Genotype frequencies were compared. The CDH1 - 160C → A promoter polymorphism and four polymorphisms (48 + 6 T → C, 2076C → T, 2253C → T and 1937-13 T → C) were included in the haplotype analyses, which were estimated using the expectation-maximization algorithm.

Results: Compared to controls, the frequency of the -160A allele was significantly higher in diffuse gastric cancer cases (P = 0.005), but it was not significantly different in intestinal gastric cancer cases (P = 0.119). Two sets of three-marker haplotypes (-160C → A, 48 + 6 T → C, 2076C → T and -160C → A, 1937-13 T → C, 2253C → T) were associated with the risk of diffuse gastric cancer (P = 0.011 and P = 0.042, respectively).

Conclusion: Based on direct sequencing analysis, our findings suggest that the CDH1 - 160C → A promoter polymorphism and haplotypes play significant roles in cancer risk for sporadic diffuse gastric cancer, but not for intestinal gastric cancer, in a Taiwanese population.

Show MeSH
Related in: MedlinePlus