• Proceedings of the Zoological Society Korea Conference
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• 2001.10a
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• pp.249.2-249
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• 2001

• Proceedings of the Korean Society of Crop Science Conference
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• 1988.02a
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• pp.12-13
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• 1988

• Genomics & Informatics
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• v.6 no.4
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• pp.231-234
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• 2008

Precise and reliable identification of CNV is still important to fully understand the effect of CNV on genetic diversity and background of complex diseases. SNP marker has been used frequently to detect CNVs, but the analysis of SNP chip data for identifying CNV has not been well established. We compared various normalization methods for CNV analysis and suggest optimal normalization procedure for reliable CNV call. Four normal Koreans and NA10851 HapMap male samples were genotyped using Affymetrix Genome-Wide Human SNP array 5.0. We evaluated the effect of median and quantile normalization to find the optimal normalization for CNV detection based on SNP array data. We also explored the effect of Robust Multichip Average (RMA) background correction for each normalization process. In total, the following 4 combinations of normalization were tried: 1) Median normalization without RMA background correction, 2) Quantile normalization without RMA background correction, 3) Median normalization with RMA background correction, and 4) Quantile normalization with RMA background correction. CNV was called using SW-ARRAY algorithm. We applied 4 different combinations of normalization and compared the effect using intensity ratio profile, box plot, and MA plot. When we applied median and quantile normalizations without RMA background correction, both methods showed similar normalization effect and the final CNV calls were also similar in terms of number and size. In both median and quantile normalizations, RMA backgroundcorrection resulted in widening the range of intensity ratio distribution, which may suggest that RMA background correction may help to detect more CNVs compared to no correction.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.9
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• pp.4095-4099
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• 2014

The X-ray repair cross-complementing group 1 protein (XRCC1) plays important roles in the DNA base excision repair pathway which may influence the development of lung cancer. This study aimed to evaluate the potential association of the XRCC1 c.1178G>A genetic polymorphism with lung cancer risk. The created restriction site-polymerase chain reaction (CRS-PCR) and DNA sequencing methods were utilized to evaluate the XRCC1 c.1178G>A genetic polymorphism among 376 lung cancer patients and 379 controls. Associations between the genetic polymorphism and lung cancer risk were determined with an unconditional logistic regression model. Our data suggested that the distribution of allele and genotype in lung cancer patients was significantly different from that of controls. The XRCC1 c.1178G>A genetic polymorphism was associated with an increased risk of lung cancer (AA vs GG: OR=2.91, 95%CI 1.70-4.98, p<0.001; A vs G: OR=1.52, 95%CI 1.22-1.90, p<0.001). The allele A and genotype AA may contribute to risk of lung cancer. These preliminary results suggested that the XRCC1 c.1178G>A genetic polymorphism is statistically associated with lung cancer risk in the Chinese population.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.8
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• pp.1075-1081
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• 2014

CRBP1 (cellular retinol binding protein 1) and CRBP3 (cellular retinol binding protein 3), are important components of the retinoid signaling pathway and take part in vitamin A absorption, transport and metabolism. Based on the role of vitamin A in chicken laying performance, we investigated the polymorphism of CRBP1 and CRBP3 genes in 349 chickens using single strand conformation polymorphism and DNA sequencing methods. Only one polymorphism was identified in the third intron of CRBP1, two polymorphisms were detected in CRBP3; they were located in the second intron and the third intron respectively. The association studies between these three SNPs and laying performance traits were performed in Erlang mountainous chicken. Notably, the SNP g.14604G>T of CRBP1 was shown to be significantly associated with body weight at first egg (BWFE), age at first egg (AFE), weight at first egg (WFE) and total number of eggs with 300 age (EN). The CRBP3 polymorphism g.934C>G was associated with AFE, and the g.1324A>G was associated with AFE and BWFE, but none of these polymorphisms were associated with egg quality traits. Haplotype combinations constructed on these two SNPs of CRBP3 gene were associated with BWFE and AFE. In particular, diplotype H2H2 had positive effect on AFE, BWFE, EN, and average egg-laying interval. We herein describe for the first time basic research on the polymorphism of chicken CRBP1 and CRBP3 genes that is predictive of genetic potential for laying performance in chicken.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.16
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• pp.7249-7254
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• 2015

Background: Previous studies evaluated associations between the CYP1A2 rs762551 polymorphism and bladder cancer risk. However, the results were inconsistent. We therefore performed a meta-analysis of the published case-control studies to assess in detail the association between CYP1A2 rs762551 polymorphism and bladder cancer risk. Materials and Methods: PubMed, Embase and Web of Science were searched to identify relevant studies and the pooled odds ratio (OR) and 95 % confidence interval (95%CI) were calculated. Results: A total of seven articles including 3,013 cases and 2,771 controls were finally included. Overall, a significant association was found between the CYP1A2 rs762551 polymorphism and bladder cancer susceptibility for CC vs AA (OR=0.82, 95% CI=0.69~0.99), but no significant associations were found for the other three models (AC vs AA: OR=0.91, 95% CI=0.81~1.02; the dominant model: OR=0.90, 95% CI=0.80~1.00; the recessive model: OR=0.84, 95% CI =0.72~1.00). In the subgroup analysis by ethnicity, we detected significant associations between the CYP1A2 rs762551 polymorphism and bladder cancer susceptibility for GA vs GG (OR = 0.78, 95% CI =0.64~0.96) and for the recessive model (OR=0.80, 95% CI=0.66~0.96) in Caucasians, but not for Asians. Conclusions: The results from the meta-analysis suggested that the CYP1A2 rs762551 polymorphism is a protective factor for bladder cancer, especially in Caucasians.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.16
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• pp.7243-7248
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• 2015

Background: Monocyte chemoattractant protein-1 (MCP-1) is a major chemokine thought to be responsible for monocyte and T-lymphocyte recruitment in acute inflammatory conditions and recruitment of macrophages in tumors. It is also implicated in cardiovascular disease, rheumatoid arthritis and chronic obstructive pulmonary disease. The aim of the present study was to investigate the correlation between MCP-1 -2518 A/G polymorphism and breast cancer risk in patients from Amritsar city of Punjab state in North-West India. Materials and Methods: We screened DNA samples of 200 sporadic breast cancer patients and 200 age and gender matched unrelated healthy individuals for MCP-1 -2518 A/G polymorphism using the PCR-RFLP method. Results: A significantly increased frequency of the GG genotype was observed in patients as compared to controls. Individuals carrying the MCP1 -2518GG genotype had a two fold risk for breast cancer (OR=2.06, 95%CI, 1.06-3.98; p=0.03). Genetic models analysis revealed a significant association between MCP-1 -2518 A/G polymorphism and cancer risk in homozygous co-dominant (OR=2.06, 95%CI, 1.06-3.98; p=0.03) and recessive (OR=1.97, 95%CI, 1.05-3.70; p=0.03) models. Conclusions: We conclude that the GG genotype of the MCP-1-2518 A/G polymorphism is associated with increased risk to breast cancer in Punjab, North-West India.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.9
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• pp.4327-4330
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• 2012

The mouse double minute 2 (MDM2) gene plays a key role in the p53 pathway, and the SNP 309T/G single-nucleotide polymorphism in the promoter region of MDM2 has been shown to be associated with increased risk of cancer. However, no consistent results were found concerning the relationships between the polymorphism and prostate cancer risk. This meta-analysis, covering 4 independent case-control studies, was conducted to better understand the association between MDM2-SNP T309G and prostate cancer risk focusing on overall and subgroup aspects. The analysis revealed, no matter what kind of genetic model was used, no significant association between MDM2-SNP T309G and prostate cancer risk in overall analysis (GT/TT: OR = 0.84, 95%CI = 0.60-1.19; GG/TT: OR = 0.69, 95%CI = 0.43-1.11; dominant model: OR = 0.81, 95%CI= 0.58-1.13; recessive model: OR = 1.23, 95%CI = 0.95-1.59). In subgroup analysis, the polymorphism seemed more likely to be a protective factor in Europeans (GG/TT: OR = 0.52, 95%CI = 0.31-0.87; recessive model: OR = 0.58, 95%CI = 0.36-0.95) than in Asian populations, and a protective effect of the polymorphism was also seen in hospital-based studies in all models (GT/TT: OR = 0.74, 95%CI = 0.57-0.97; GG/TT: OR = 0.55, 95%CI = 0.38-0.79; dominant model: OR = 0.69, 95%CI = 0.54-0.89; recessive model: OR = 0.70, 95%CI = 0.51-0.97). However, more primary studies with a larger number of samples are required to confirm our findings.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.5
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• pp.2415-2421
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• 2016

E-cadherin (CDH1) genetic variations alter gene transcriptional activity of epithelial cells in vitro and may cause susceptibility to various cancers. Associations of CDH1 -160C>A polymorphism with various cancers have been widely reported. However, the results are controversial and inconsistent. To derive a more accurate estimation of the relationship, a meta-analysis was performed with regard to gastrointestinal (GI) cancer risk. Eligible studies were identified through a search of PubMed database until December 2015. Associations between the CDH1 -160C>A polymorphism and GI cancer risk was considered by odds ratios (ORs) together with their 95% confidence intervals (CIs). A total of 31 studies including 11,606 cases and 12,655 controls were involved in this meta-analysis. Overall, this meta-analysis showed no association between CDH1 -160C>A polymorphism and GI cancer risk (A vs. C: OR = 1.08, 95%CI = 0.98-1.18, P = 0.086;CA vs. CC: OR = 1.09, 95%CI = 0.97-1.22, P = 0.118; AA vs. CC: OR = 1.10, 95%CI = 0.89-1.35, P = 0.356; AA vs. CC + CA: OR = 1.06, 95%CI = 0.96-1.18, P = 0.207; CA+AA vs. CC: OR = 1.01, 95%CI = 0.84-1.22, P = 0.89). In subgroup analysis, similar results were found. In conclusion, this meta-analysis has demonstrated that there is a lack of association of the CDH1-160C>A polymorphism with GI cancer susceptibility.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.10
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• pp.4599-4608
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• 2016

Background: The x-ray repair cross-complementing group 3 (XRCC3) encodes a protein involved in the homologous recombination repair (HRR) pathway for double-strand DNA repair. Associations of the XRCC3 Thr241Met polymorphism with various cancers have been widely reported. However, published data on links between XRCC3 Thr241Met and gastrointestinal (GI) cancer risk are inconsistent. Objective and Methods: A meta-analysis was conducted to characterize the relationship between XRCC3 Thr241Met polymorphisms and GI cancer risk. Pooled odds ratios (ORs) and 95.0% confidence intervals were assessed using random- or fixed- effect models for 28.0 relevant articles with 30.0 studies containing 7,649.0 cases and 11,123.0 controls. Results: The results of the overall meta-analysis suggested a borderline association between the XRCC3 Thr241Met polymorphism and GI cancer susceptibility (T vs. C: OR=1.18, 9 % CI=1.0-1.4, POR=0.04; TT vs. CT+CC: OR=1.3, 95 % CI=1.0-1.6, POR=0.04). After removing studies not conforming to Hardy-Weinberg equilibrium (HWE), however, this association disappeared (T vs. C: OR=1.00, 95 % CI=0.9-1.1, POR=0.96; TT vs. CT+CC: OR=0.9, 95 % CI=0.8-1.1, POR=0.72). When stratified by ethnicity, source of controls or cancer type, although some associations between XRCC3 Thr241Met polymorphism and GI cancer susceptibility were detected, these associations no longer existed after removing studies not conforming to HWE. Conclusion: Our meta-analysis suggests that the XRCC3 Thr241Met polymorphism is not associated with risk of GI cancer based on current evidence.