• Asian Pacific Journal of Cancer Prevention
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• v.16 no.2
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• pp.713-718
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• 2015

Background: A number of association studies have been carried out to investigate the relationship between genetic polymorphisms in DNA repair genes and response to radiotherapy-based multimodality treatment of patients with rectal cancer. However, their conclusions were inconsistent. The objective of the present study was to assess the role of DNA repair gene genetic polymorphisms in predicting genetic biomarkers of the response in rectal cancer patients treated with neoadjuvant chemoradiation. Materials and Methods: Studies were retrieved by searching the PubMed database, Cochrane Library, Embase, and ISI Web of Knowledge. We conducted a meta-analysis to evaluate the association between genetic polymorphisms and the response in rectal cancer treated with neoadjuvant chemoradiation by checking odds ratios (ORs) and 95% confidence intervals (CIs). Results: Data were extracted from 5 clinical studies for this meta-analysis. The results showed that XRCC1 RS25487, XRCC1 RS179978, XRCC3 RS861539, ERCC1 RS11615 and ERCC2 RS13181 were not associated with the response in the radiotherapy-based multimodality treatment of patients with rectal cancer (p>0.05). Conclusions: This study shows that DNA repair gene common genetic polymorphisms are not significantly correlated with the radiotherapy-based multimodality treatment in rectal cancer patients.

• Genomics & Informatics
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• v.21 no.4
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• pp.48.1-48.8
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• 2023

Liver cancer is the fourth leading cause of death worldwide. Well-known risk factors include hepatitis B virus and hepatitis C virus, along with exposure to aflatoxins, excessive alcohol consumption, obesity, and type 2 diabetes. Genomic variants play a crucial role in mediating the associations between these risk factors and liver cancer. However, the specific variants involved in this process remain under-explored. This study utilized a bioinformatics approach to identify genetic variants associated with liver cancer from various continents. Single-nucleotide polymorphisms associated with liver cancer were retrieved from the genome-wide association studies catalog. Prioritization was then performed using functional annotation with HaploReg v4.1 and the Ensembl database. The prevalence and allele frequencies of each variant were evaluated using Pearson correlation coefficients. Two variants, rs2294915 and rs2896019, encoded by the PNPLA3 gene, were found to be highly expressed in the liver tissue, as well as in the skin, cell-cultured fibroblasts, and adipose-subcutaneous tissue, all of which contribute to the risk of liver cancer. We further found that these two SNPs (rs2294915 and rs2896019) were positively correlated with the prevalence rate. Positive associations with the prevalence rate were more frequent in East Asian and African populations. We highlight the utility of this population-specific PNPLA3 genetic variant for genetic association studies and for the early prognosis and treatment of liver cancer. This study highlights the potential of integrating genomic databases with bioinformatic analysis to identify genetic variations involved in the pathogenesis of liver cancer. The genetic variants investigated in this study are likely to predispose to liver cancer and could affect its progression and aggressiveness. We recommend future research prioritizing the validation of these variations in clinical settings.

• Toxicological Research
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• v.35 no.4
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• pp.319-330
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• 2019

Adverse drug reactions (ADRs) constitute key factors in determining successful medication therapy in clinical situations. Integrative analysis of electronic medical record (EMR) data and use of proper analytical tools are requisite to conduct retrospective surveillance of clinical decisions on medications. Thus, we suggest that electronic medical recording and human genetic databases are considered together in future directions of pharmacovigilance. We analyzed EMR-based ADR studies indexed on PubMed during the period from 2005 to 2017 and retrospectively acquired 1161 (29.6%) articles describing drug-induced adverse reactions (e.g., liver, kidney, nervous system, immune system, and inflammatory responses). Of them, only 102 (8.79%) articles contained useful information to detect or predict ADRs in the context of clinical medication alerts. Since insufficiency of EMR datasets and their improper analyses may provide false warnings on clinical decision, efforts should be made to overcome possible problems on data-mining, analysis, statistics, and standardization. Thus, we address the characteristics and limitations on retrospective EMR database studies in hospital settings. Since gene expression and genetic variations among individuals impact ADRs, pharmacokinetics, and pharmacodynamics, appropriate paths for pharmacovigilance may be optimized using suitable databases available in public domain (e.g., genome-wide association studies (GWAS), non-coding RNAs, microRNAs, proteomics, and genetic variations), novel targets, and biomarkers. These efforts with new validated biomarker analyses would be of help to repurpose clinical and translational research infrastructure and ultimately future personalized therapy considering ADRs.

• Journal of Science and Technology Studies
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• v.3 no.2 s.6
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• pp.83-104
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• 2003

The use of DNA in identification is growing. The criminal DNA databases are in operation in some countries including the UK, Austria, Germany, and US. The militaries and law enforcement agencies in these countries have used the DNA profile. In Korea, DNA identification has been used in determining paternity and in criminal cases since the middle 1990's, and in recent years law enforcement agencies are promoting a national DNA database for identification. The DNA database threatens our civil liberties because of its potential to be used as an instrument of surveillance. Expanding the database puts increasing numbers of people on a 'list of suspects'. Nevertheless, there is little social concern about using DNA database for identification. This paper reviews social issues related to the establishment of DNA database and investigates the features of DNA profile and DNA Database establishment project promoted law enforcement agencies.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.10
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• pp.5075-5079
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• 2012

Purpose: The results of recent published studies focusing on IL-8 polymorphism in colorectal cancer susceptibility have often been inconsistent. We therefore carried out a meta-analysis based on independent studies to assess the association. Methods: Nine case-control studies with 7,003 individuals (3,019 cases and 3,984 controls) were included in this meta-analysis through searching the databases of PubMed, Excerpta Medica Database (EMBASE), and Chinese Biomedical Literature Database (CBM; Chinese) (up to Aug 1st, 2012). The odds ratio (OR) and 95% confidence interval (95%CI) were used to assess the strength of the association. Meta-analysis was conducted in a fixed/random effect model. Results: No obvious associations were found for all genetic models when all studies were pooled into the meta-analysis (for A vs. T: OR = 1.084, 95% CI = 0.971-1.209, P = 0.019; for TA vs. TT: OR = 1.18, 95% CI = 0.943-1.475, P = 0.001; for AA vs. TT: OR = 1.155, 95% CI = 0.916-1.456, P = 0.014; for AA+TA vs. TT: OR = 1.170, 95% CI =0.953-1.437, P = 0.001; for AA vs. TT+TA: OR = 1.044, 95% CI = 0.886-1.230, P = 0.097). In the subgroup analyses by ethnicity (Caucasian) and source of controls (population based), also no significant associations were found for all genetic models. Conclusions: Result suggests that the IL-8-251T>A polymorphism is not associated with colorectal cancer risk. Because of the limitations of this meta-analysis, this finding demands further investigation.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.9
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• pp.1223-1228
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• 2012

The population sizes of three Korean indigenous cattle populations have been drastically reduced over the past decades. In this study, we examined the extent to which reduction in populations influenced genetic diversity, population structure and demographic history using complete mitochondrial DNA (mtDNA) control region sequences. The complete mtDNA control region was sequenced in 56 individuals from Korean Black (KB), Jeju Black (JEB) and Korean Brindle (BRI) cattle populations. We included 27 mtDNA sequences of Korean Brown (BRO) from the GenBank database. Haplotype diversity estimate for the total population was high (0.870) while nucleotide diversity was low (0.004). The KB showed considerably low nucleotide (${\pi}$ = 0.001) and haplotype (h = 0.368) diversities. Analysis of molecular variance revealed a low level of genetic differentiation but this was highly significant (p<0.001) among the cattle populations. Of the total genetic diversity, 7.6% was attributable to among cattle populations diversity and the rest (92.4%) to differences within populations. The mismatch distribution analysis and neutrality tests revealed that KB population was in genetic equilibrium or decline. Indeed, unless an appropriate breeding management practice is developed, inbreeding and genetic drift will further impoverish genetic diversity of these cattle populations. Rational breed development and conservation strategy is needed to safeguard these cattle population.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.6
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• pp.804-811
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• 2018

Objective: Complete mtDNA D-loop sequences of four Thai indigenous chicken varieties, including Pra-dhu-hang-dam (PD), Leung-hang-khao (LK), Chee (CH), and Dang (DA) were explored for genetic diversity and relationships with their potential ancestor and possible associates to address chicken domestication in Thailand. Methods: A total of 220 complete mtDNA D-loop sequences of the four Thai indigenous chicken varieties were obtained by Sanger direct sequencing of polymerase chain reaction amplicons of 1,231 to 1,232 base pair in size. A neighbor-joining dendrogram was constructed with reference complete mtDNA D-loop sequences of Red Junglefowl (RJF) and those different chicken breeds available on National Center for Biotechnology Information database. Genetic diversity indices and neutrality test by Tajima's D test were performed. Genetic differences both within and among populations were estimated using analysis of molecular variance (AMOVA). Pairwise fixation index ($F_{ST}$) was conducted to evaluated genetic relationships between these varieties. Results: Twenty-three identified haplotypes were classified in six haplogroups (A-E and H) with the majority clustered in haplogroup A and B. Each variety was in multiple haplogroups with haplogroups A, B, D, and E being shared by all studied varieties. The averaged haplotype and nucleotide diversities were, respectively 0.8607 and 0.00579 with non-significant Tajima's D values being observed in all populations. Haplogroup distribution was closely related to that of RJF particularly Gallus gallus gallus (G. g. gallus) and G. g. spadiceus. As denoted by AMOVA, the mean diversity was mostly due to within-population variation (90.53%) while between-population variation (9.47%) accounted for much less. By pairwise $F_{ST}$, LK was most closely related to DA ($F_{ST}=0.00879$) while DA was farthest from CH ($F_{ST}=0.24882$). Conclusion: All 4 Thai indigenous chickens are in close relationship with their potential ancestor, the RJF. A contribution of shared, multiple maternal lineages was in the nature of these varieties, which have been domesticated under neutral selection.

• Genomics & Informatics
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• v.14 no.4
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• pp.255-264
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• 2016

The plethora of genome sequence information of bacteria in recent times has ushered in many novel strategies for antibacterial drug discovery and facilitated medical science to take up the challenge of the increasing resistance of pathogenic bacteria to current antibiotics. In this study, we adopted subtractive genomics approach to analyze the whole genome sequence of the Fusobacterium nucleatum, a human oral pathogen having association with colorectal cancer. Our study divulged 1,499 proteins of F. nucleatum, which have no homolog's in human genome. These proteins were subjected to screening further by using the Database of Essential Genes (DEG) that resulted in the identification of 32 vitally important proteins for the bacterium. Subsequent analysis of the identified pivotal proteins, using the Kyoto Encyclopedia of Genes and Genomes (KEGG) Automated Annotation Server (KAAS) resulted in sorting 3 key enzymes of F. nucleatum that may be good candidates as potential drug targets, since they are unique for the bacterium and absent in humans. In addition, we have demonstrated the three dimensional structure of these three proteins. Finally, determination of ligand binding sites of the 2 key proteins as well as screening for functional inhibitors that best fitted with the ligands sites were conducted to discover effective novel therapeutic compounds against F. nucleatum.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.9
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• pp.1236-1243
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• 2014

Genetics is important for breeding and selection of horses but there is a lack of well-established horse-related browsers or databases. In order to better understand horses, more variants and other integrated information are needed. Thus, we construct a horse genomic variants database including expression and other information. Horse Single Nucleotide Polymorphism and Expression Database (HSDB) (http://snugenome2.snu.ac.kr/HSDB) provides the number of unexplored genomic variants still remaining to be identified in the horse genome including rare variants by using population genome sequences of eighteen horses and RNA-seq of four horses. The identified single nucleotide polymorphisms (SNPs) were confirmed by comparing them with SNP chip data and variants of RNA-seq, which showed a concordance level of 99.02% and 96.6%, respectively. Moreover, the database provides the genomic variants with their corresponding transcriptional profiles from the same individuals to help understand the functional aspects of these variants. The database will contribute to genetic improvement and breeding strategies of Thoroughbreds.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.7
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• pp.3331-3333
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• 2014

Background: The results of previous researches that analyzed the association between genetic polymorphisms of transcription factor-7-like 2 (TCF7L2, rs7903146) and polycystic ovary syndrome (PCOS) were conflicting. Current systematic analysis was conducted to re-explore this association using updated materials. Materials and Methods: The PubMed database was used for data collection and the final search was conducted on January 3, 2014. For TCF7L2 rs7903146, a non-signficiant slight increase in risk of PCOS development was observed under three genetic models (dominant model: OR=1.06, 95%CI: 0.93-1.21, p>0.05; recessive model: OR=1.12, 95%CI: 0.87-1.43, p> 0.05; homozygous model: OR=1.14, 95%CI: 0.87-1.47, p>0.05). In the subgroup analyses in Asian group, allele susceptibility of PCOS was calculated (allele model: OR=1.00, 95%CI: 0.74-1.35, p>0.05; dominant model: OR=0.98, 95%CI: 0.71-1.35, p>0.05; recessive model: OR=1.79, 95%CI: 0.33-9.84, p>0.05; homozygous model: OR=1.78, 95%CI: 0.32-9.80, p>0.05), the differences were again not statistically significant. Conclusions: The findings of this systemic analysis suggest that the polymorphism of TCF7L2 rs7903146 may not be associated with the susceptibility to PCOS.