A genome-wide association study identifies new susceptibility loci for non-cardia gastric cancer at 3q13.31 and 5p13.1

Shi, Yongyong; Hu, Zhibin; Wu, Chen; Dai, Juncheng; Li, Huizhang; Dong, Jing; Wang, Meilin; Miao, Xiaoping; Zhou, Yifeng; Lu, Feng; Zhang, Hanze; Hu, Lingmin; Jiang, Yue; Li, Zhiqiang; Chu, Minjie; Ma, Hongxia; Chen, Jiaping; Jin, Guangfu; Tan, Wen; Wu, Tangchun; Zhang, Zhengdong; Lin, Dong; Shen, Hongbing

doi:10.1038/ng.978

Cited by 245 publications

(279 citation statements)

References 22 publications

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“…Recently, scientists found that PSCA gene is either abnormally expressed or shown different genetic variant in several cancers. GWAS have identified a strong association between PSCA gene rs2294008 C > T polymorphism and risk of GC, especially in Asians (Sakamoto et al, 2008;Shi et al, 2011 Qing-Hui Zhang*, Yong-Liang Yao, Tao Gu, Jin-Hua Gu, Ling Chen, Yun Liu and histological type of GC. More recently, several studies have assessed the relationship between the polymorphism of PSCA C > T and the susceptibility to GC.…”

Section: Introductionmentioning

confidence: 99%

Association of the PSCA rs2294008 C＞T Polymorphism with Gastric Cancer Risk: Evidence from a Meta-Analysis

Yao¹,

Gu²,

Gu³

et al. 2012

Asian Pacific Journal of Cancer Prevention

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Background: Multiple studies have reported associations between the PSCA rs2294008 C > T polymorphism and GC, but susceptibility has proven inconsistent. Therefore, we estimates the relationship between the rs2294008 C > T polymorphism and GC by meta-analysis. Methods: PubMed, Embase and Web of Science databases were searched and nine independent case-control studies were included in this meta-analysis. Crude ORs with 95% CIs were extracted according to the Mantal-Haenszel method and pooled to assess the strength of the association. Results: We observed that the PSCA rs2294008 C > T polymorphism was significantly correlated with GC risk when all studies were pooled into the meta-analysis. Further subgroup analysis showed the polymorphism to be linked with diffuse and noncardia GC in the allele contrast model, homozygote codominant model, dominant model, and recessive model. However, no connection was apparent for intestinal and cardia GC. In the stratified analysis by ethnicity, significant associations were observed in Asians for the recessive model. Interestingly, the relationship was particularly significant in the Chinese population. Conclusions: Our findings suggest that the PSCA rs2294008 C > T polymorphism is a risk factor for GC, especially in diffuse and noncardia GC and in Chinese.

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Section: Introductionmentioning

confidence: 99%

Association of the PSCA rs2294008 C＞T Polymorphism with Gastric Cancer Risk: Evidence from a Meta-Analysis

Yao¹,

Gu²,

Gu³

et al. 2012

Asian Pacific Journal of Cancer Prevention

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“…Gastric cancer risk SNPs were extracted from the original gastric cancer GWAS studies in GWAS Catalog 5, 6, 7, 8, 9, 10, 27. Only 1 SNP was remained when multiple variants were in linkage disequilibrium (LD, r 2 ≥ .8), and the minor‐allele frequency (MAF) should be greater or equal than .05.…”

Section: Methodsmentioning

confidence: 99%

“…Many genetic variations, most of which are single nucleotide polymorphisms (SNPs), have been detected over the past years by the genome‐wide association studies (GWAS) of gastric cancer 4. These common susceptibility loci included 1q22 ( MUC1 ), 3q13.32 ( ZBTB20 ), 5p13.1 ( PRKAA1 ), 5q14.3 ( lnc‐POLR3G‐4 ), 6p21.1 ( UNC5CL ), 8q24 ( PSCA ), and 10q23 ( PLCE1 ) 5, 6, 7, 8, 9, 10…”

Section: Introductionmentioning

confidence: 99%

Germline genetic variants were interactively associated with somatic alterations in gastric cancer

et al. 2018

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Genome‐wide association studies have identified several germline variants in gastric cancer. Meanwhile, sequencing studies have characterized extensive somatic alterations that arise during gastric carcinogenesis. However, the relationship between the germline variants and somatic alterations is still unclear in gastric cancer. A total of 11 susceptibility loci and 276 driver genes of gastric cancer were determined based on previous studies and publicly available database. An enrichment analysis was made to detect whether driver genes were enriched in susceptibility regions. Besides, we performed a pathway enrichment analysis to find common‐enrich pathways of cancer driver genes and susceptibility genes. Finally, on the basis of the gastric cancer samples and data from TCGA STAD project, we evaluated the associations between susceptibility loci and somatic alterations. Enrichment analysis showed that gastric cancer susceptibility genes were more likely to be enriched in driver genes than in all the genes (P = .05). The susceptibility genes and driver genes were commonly enriched in 8 biological pathways. Gastric cancer susceptibility locus of rs2285947 was associated with truncation mutation within Signaling by PDGF pathway (OR = 0.26, 95%CI: 0.12‐0.55, P = 3.93 × 10−4). The rs1679709 was connected with COSMIC Signature15 (P = .026). Moreover, rs1679709 was also associated with copy number values of RFC4 which is related to Signature15. These results provide evidence for the relationship between germline variants and somatic alterations, which facilitate understanding the interactive mechanism of germline variations with somatic alterations in gastric cancer development.

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“…Gastric cancer includes non-cardia gastric and cardia gastric carcinoma. Two subtypes have differences in the etiology, pathology, carcinogenesis, and prognosis (Shi et al, 2011). So we restricted our cases to patients with non-cardia gastric cancer to supply relatively more homogeneous samples and improve the power of association study.…”

Section: Discussionmentioning

confidence: 99%

Association Analysis of Common Genetic Variations in MUC5AC Gene with the Risk of Non-cardia Gastric Cancer in a Chinese Population

Zhou¹,

Zhang²,

Gao³

et al. 2014

Asian Pacific Journal of Cancer Prevention

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Several lines of evidence suggest that genetic variation in MUC5AC gene might contribute to the risk of gastric cancer. We conducted a case-control study to evaluate the relationship between common genetic variations in MUC5AC gene and non-cardia gastric cancer using an LD-based tagSNP approach in Baotou, north-western China. We genotyped 12 tagSNPs by TaqMan method among 288 cases with non-cardia gastric cancer and 281 normal controls. Unconditional logistic regression was used to calculate odds ratios (ORs) and 95% confidence intervals (CIs) for non-cardia gastric cancer risk in association with alleles, genotypes and haplotypes. We observed that the frequencies of rs3793964 C allele and rs11040869 A allele were significantly lower in cases than in controls. Meanwhile, minor allele homozygotes of rs3793964 and rs11040869 were significantly associated with a decreased risk of non-cardia gastric cancer when compared with their major allele homozygotes. Furthermore, a statistically significantly protective effect of rs885454 genotypes on non-cardia gastric cancer was also observed (for CT vs. CC: OR=0.581, 95%CI=0.408-0.829; for CT/TT vs. CC: OR=0.623, 95%CI=0.451-0.884). Our results indicated that some common genetic variations in the MUC5AC gene might have effects on the risk of non-cardia gastric cancer in our studied population.

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A genome-wide association study identifies new susceptibility loci for non-cardia gastric cancer at 3q13.31 and 5p13.1

Cited by 245 publications

References 22 publications

Association of the PSCA rs2294008 C＞T Polymorphism with Gastric Cancer Risk: Evidence from a Meta-Analysis

Association of the PSCA rs2294008 C＞T Polymorphism with Gastric Cancer Risk: Evidence from a Meta-Analysis

Germline genetic variants were interactively associated with somatic alterations in gastric cancer

Association Analysis of Common Genetic Variations in MUC5AC Gene with the Risk of Non-cardia Gastric Cancer in a Chinese Population

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