Dataset Information

Genetic variants at 6p21, 10q23, 16q21 and 22q12 are associated with esophageal cancer risk in a Chinese Han population.

ABSTRACT: OBJECTIVE:A number of recently published genome-wide association studies (GWAS) identified several genetic loci at 6p21, 10q23, 16q12 and 22q12 that were associated with digestive tract tumors, including esophageal cancer (EC). We conducted a case-control study in a Chinese Han population including 360 EC cases and 310 controls to evaluate whether these variants are related to EC susceptibility. METHODS:All these SNPs were genotyped using Sequenom Mass-ARRAY technology. For each SNP, genotypic frequencies in controls were tested for departure from Hardy-Weinberg Equilibrium (HWE) using an exact test. A P-value of 0.05 was considered the threshold for statistical significance. We compared the allele frequencies of cases and controls using the chi-squared (?(2)) test. Associations between the gene and the risk of esophagus cancer were tested using various genetic models (co-dominant, dominant, recessive, and log-additive) and analysis by SNP stats. Odds ratios and 95% confidence intervals (CIs) were calculated by unconditional logistic regression with adjustments for age and gender. RESULTS:We found significant association with risk of EC for five reported SNPs, including rs2274223 in PLCE1 at 10q23 [odds ratio (OR) = 1.390; 95% confidence interval (CI) = 1.075-1.798], rs10484761 near UNC5CL at 6p21 (OR = 1.422, 95% CI = 1.014-1.994), rs4785204 in HEATR3 at 16q12 (OR = 1.427; 95% CI = 1.116-1.824), rs4822983 in CHEK2 at 22q12 (OR = 1.361, 95% CI = 1.052-1.762), and rs738722 in CHEK2 at 22q12 (OR = 1.343, 95% CI = 1.053-1.713). CONCLUSION:Our findings, combined with previous studies, indicated that rs10484761 at 6p21, rs2274223 at 10q23, rs4785204 at 16q12, rs4822983 and rs738722 at 22q12 may be used as genetic biomarkers for EC susceptibility in Chinese Han population.

SUBMITTER: Jia X

PROVIDER: S-EPMC4694479 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Genetic variants at 6p21, 10q23, 16q21 and 22q12 are associated with esophageal cancer risk in a Chinese Han population.

Jia Xiaobin X Liu Peng P Zhang Mingxia M Feng Tian T Tang Hongtao H Tang Zhigang Z Zhao Huaqian H Jin Tianbo T

International journal of clinical and experimental medicine 20151015 10

<h4>Objective</h4>A number of recently published genome-wide association studies (GWAS) identified several genetic loci at 6p21, 10q23, 16q12 and 22q12 that were associated with digestive tract tumors, including esophageal cancer (EC). We conducted a case-control study in a Chinese Han population including 360 EC cases and 310 controls to evaluate whether these variants are related to EC susceptibility.<h4>Methods</h4>All these SNPs were genotyped using Sequenom Mass-ARRAY technology. For each S ...[more]

PMID: 26770579

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Project description:Chromosome 6p21-p22.1, spanning the extended major histocompatibility complex (MHC) region, is a highly polymorphic, gene-dense region. It has been identified as a susceptibility locus of schizophrenia in Europeans, Japanese, and Chinese. In our previous two-stage genome-wide association study (GWAS), polymorphisms of zinc finger with KRAB and SCAN domains 4 (ZKSCAN4), nuclear factor-?B-activating protein-like (NKAPL), and piggyBac transposable element derived 1 (PGBD1), localized to chromosome 6p21-p22.1, were strongly associated with schizophrenia. To further investigate the association between polymorphisms at this locus and schizophrenia in the Chinese Han population, we selected eight other single-nucleotide polymorphisms (SNPs) distributed in or near these genes for a case-control association study in an independent sample of 902 cases and 1,091 healthy controls in an attempt to replicate the GWAS results. Four of these eight SNPs (rs12214383, rs1150724, rs3800324, and rs1997660) displayed a nominal difference in allele frequencies between the case and control groups. The association between two of these SNPs and schizophrenia were significant even after Bonferroni correction (rs12000: allele A>G, P = 2.50E-04, odds ratio [OR] = 1.27, 95% confidence interval [CI] = 1.12-1.45; rs1150722: allele C>T, P = 4.28E-05, OR = 0.55, 95% CI = 0.41-0.73). Haplotype ATTGACGC, comprising these eight SNPs (rs2235359, rs2185955, rs12214383, rs12000, rs1150724, rs1150722, rs3800324, and rs1997660), was significantly associated with schizophrenia (P = 6.60E-05). We also performed a combined study of this replication sample and the first-stage GWAS sample. The combined study revealed that rs12000 and rs1150722 were still strongly associated with schizophrenia (rs12000: allele G>A, P(combined) = 0.0019, OR = 0.81; rs1150722: allele G>A, P(combined) = 3.00E-04, OR = 0.61). These results support our findings that locus 6p21-p22.1 is significantly associated with schizophrenia in the Chinese Han population and encourage further studies of the functions of these genetic factors.

Dataset Information

Genetic variants at 6p21, 10q23, 16q21 and 22q12 are associated with esophageal cancer risk in a Chinese Han population.

Publications

Genetic variants at 6p21, 10q23, 16q21 and 22q12 are associated with esophageal cancer risk in a Chinese Han population.

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