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Open Access Research

RTEL1 tagging SNPs and haplotypes were associated with glioma development

Gang Li1, Tianbo Jin2, Hongjuan Liang1, Zhiguo Zhang1, Shiming He1, Yanyang Tu3, Haixia Yang1, Tingting Geng4, Guangbin Cui5, Chao Chen2* and Guodong Gao1*

Author Affiliations

1 Department of Neurosurgery, Tangdu hospital, the Fourth Military Medical University, Xi’an, 710038, China

2 National Engineering Research Center for Miniaturized Detection Systems, School of Life Sciences, Northwest University, Xi’an, 710069, China

3 Department of Clinical Experimental Surgery, Tangdu hospital, the Fourth Military Medical University, Xi’an, 710038, China

4 Shaanxi Lifegen Co. Ltd, Xi’an, 710069, China

5 Department of Radiology, Tangdu hospital, the Fourth Military Medical University, Xi’an, 710038, China

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Diagnostic Pathology 2013, 8:83  doi:10.1186/1746-1596-8-83

Published: 17 May 2013

Abstract

As glioma ranks as the first most prevalent solid tumors in primary central nervous system, certain single-nucleotide polymorphisms (SNPs) may be related to increased glioma risk, and have implications in carcinogenesis. The present case–control study was carried out to elucidate how common variants contribute to glioma susceptibility. Ten candidate tagging SNPs (tSNPs) were selected from seven genes whose polymorphisms have been proven by classical literatures and reliable databases to be tended to relate with gliomas, and with the minor allele frequency (MAF) > 5% in the HapMap Asian population. The selected tSNPs were genotyped in 629 glioma patients and 645 controls from a Han Chinese population using the multiplexed SNP MassEXTEND assay calibrated. Two significant tSNPs in RTEL1 gene were observed to be associated with glioma risk (rs6010620, P = 0.0016, OR: 1.32, 95% CI: 1.11-1.56; rs2297440, P = 0.001, OR: 1.33, 95% CI: 1.12-1.58) by χ2 test. It was identified the genotype “GG” of rs6010620 acted as the protective genotype for glioma (OR, 0.46; 95% CI, 0.31-0.7; P = 0.0002), while the genotype “CC” of rs2297440 as the protective genotype in glioma (OR, 0.47; 95% CI, 0.31-0.71; P = 0.0003). Furthermore, haplotype “GCT” in RTEL1 gene was found to be associated with risk of glioma (OR, 0.7; 95% CI, 0.57-0.86; Fisher’s P = 0.0005; Pearson’s P = 0.0005), and haplotype “ATT” was detected to be associated with risk of glioma (OR, 1.32; 95% CI, 1.12-1.57; Fisher’s P = 0.0013; Pearson’s P = 0.0013). Two single variants, the genotypes of “GG” of rs6010620 and “CC” of rs2297440 (rs6010620 and rs2297440) in the RTEL1 gene, together with two haplotypes of GCT and ATT, were identified to be associated with glioma development. And it might be used to evaluate the glioma development risks to screen the above RTEL1 tagging SNPs and haplotypes.

The virtual slides for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1993021136961998 webcite

Keywords:
Tagging single nucleotide polymorphism (tSNP); Glioma; RTEL1; Haplotype; Case - control studies