• Genomics & Informatics
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• v.7 no.4
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• pp.187-194
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• 2009

Cytochrome P450 2E1 (CYP2E1) is a member of the cytochrome P450 superfamily, and it is a key enzyme responsible for the metabolic activation of many smallmolecular-weight compounds such as alcohol, which is classified as a human carcinogen. In this study, we identified 19 single nucleotide polymorphisms (SNPs) in CYP2E1 in Korean population. In these SNPs, we examined possible genetic association of CYP2E1 polymorphisms with HBV clearance and the risk of hepatocellular carcinoma (HCC). Five common polymorphic sites were selected, CYP2E1 polymorphisms at rs381-3867, rs3813870, rs2070673, rs2515641 and rs2480257, considering their allele frequencies, haplotype-tagging status and LDs for genotyping in larger-scale subjects (n=1,092). Statistical analysis demonstrated that CYP2E1 polymorphisms and haplotypes show no significant association with HBV clearance, HCC occurrence and onset age of HCC (p>0.05). Previous studies, however, have shown contradictory findings on associations of CYP2E1 polymorphisms with CYP2E1 activities and HCC risk. Comparing the contrasting results of previous researches suggest that CYP2E1 polymorphism is associated with CYP2E1 activity induced by ethanol, but is not directly associated with HCC risk. CYP2E1 variation/haploype information identified in this study will provide valuable information for future studies on CYP2E1.

• Journal of Convergence for Information Technology
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• v.8 no.6
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• pp.201-207
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• 2018

A genome contains all genetic information of an organism. Within a specific species, unique traits appear for each individual, which can be identified by analyzing nucleotide sequences. Many Genome-Wide Associations Studies have been carried out to find genetic associations and cause of diseases from slightly different base among the individuals. It is important to identify occurrence of slight variations for polymorphisms of individuals. In this paper, we introduce an analysis and visualization tool for specific variation pattern identification of polymorphisms in nucleotide sequences and show the validity of the tool by applying it to analyzing nucleotide sequences of subcultured pOka strain of varicella-zoster virus. The tool is expected to help efficiently explore allele frequency variations and genetic factors within a species.

• Laboraroty Animal Research
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• v.34 no.4
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• pp.311-316
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• 2018

Laboratory inbred mice are used widely and commonly in biomedical research, but inbred mice do not have a big enough gene pool for the research. In this study, genetic and morphometric analyses were performed to obtain data on the characteristics of a newly developing inbred strain (KWM/Hym) captured from Chuncheon, Korea. All of five Korean wild male mice have the zinc-finger Y (ZfY) gene. Also, all of 19 Korean wild mice used in this analysis have the AKV-type murine leukemia virus gene, indicating that Korean wild mice might be Mus musculus musculus. To identify the genetic polymorphism in KWM/Hym, SNP analysis was performed. In a comparison with 28 SNP markers, there was a considerable difference between KWM/Hym and several inbred strains. The homogeneity between KWM/Hym and the inbred strains was as follows: C57BL/6J (39.3%), BALB/c AJic (42.9%), and DBA/2J (50%). KWM/Hym is most similar to the PWK/PhJ inbred strain (96.4%) derived from wild mice (Czech Republic). To identify the morphometric characteristics of KWM/Hym, the external morphology was measured. The tail ratio of male and female was $79.60{\pm}3.09$ and $73.55{\pm}6.14%$, respectively. KWM/Hym has short and agouticolored hairs and its belly is white with golden hair. Taking these results together, KWM/Hym, a newly developing inbred mouse originated from wild mouse, might be use as new genetic resources to overcome the limitations of the current laboratory mice.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.6
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• pp.3555-3559
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• 2013

Chronic hepatitis B virus (HBV) infection and dietary exposure to aflatoxin B1 (AFB1) are major risk factors for hepatocellular carcinoma (HCC). The aim of this study was to evaluate the role of HBV genetic variation and the R249S mutation of the p53 gene, a marker of AFB1-induced HCC, in Thai patients chronically infected with HBV. Sixty-five patients with and 89 patients without HCC were included. Viral mutations and R249S mutation were characterized by direct sequencing and restriction fragment length polymorphism (RFLP) in serum samples, respectively. The prevalences of T1753C/A/G and A1762T/G1764A mutations in the basal core promotor (BCP) region were significantly higher in the HCC group compared to the non-HCC group. R249S mutation was detected in 6.2% and 3.4% of the HCC and non-HCC groups, respectively, which was not significantly different. By multiple logistic regression analysis, the presence of A1762T/G1764A mutations was independently associated with the risk of HCC in Thai patients.

• The Plant Pathology Journal
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• v.33 no.5
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• pp.508-513
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• 2017

The complete genome sequence of a Slovak SL-1 isolate of Tomato mosaic virus (ToMV) was determined from the next generation sequencing (NGS) data, further confirming a limited sequence divergence in this tobamovirus species. Tomato genotypes Monalbo, Mobaci and Moperou, respectively carrying the susceptible tm-2 allele or the Tm-1 and Tm-2 resistant alleles, were tested for their susceptibility to ToMV SL-1. Although the three tomato genotypes accumulated ToMV SL-1 to similar amounts as judged by semiquantitative DAS-ELISA, they showed variations in the rate of infection and symptomatology. Possible differences in the intra-isolate variability and polymorphism between viral populations propagating in these tomato genotypes were evaluated by analysis of the capsid protein (CP) encoding region. Irrespective of genotype infected, the intra-isolate haplotype structure showed the presence of the same highly dominant CP sequence and the low level of population diversity (0.08-0.19%). Our results suggest that ToMV CP encoding sequence is relatively stable in the viral population during its replication in vivo and provides further demonstration that RNA viruses may show high sequence stability, probably as a result of purifying selection.

• Genomics & Informatics
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• v.8 no.1
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• pp.1-8
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• 2010

Serpin peptidase inhibitor, Clade B (ovalbumin), Member 5 (SERPINB5), also known as maspin, is a potent tumor suppressor gene. It has correlations with many tumor cells, from pancreas cancer to breast cancer, so it is possible that it may also affect liver cancer. There has also been a report that SERPINB12, a gene placed right next to SERPINB5, is expressed in liver. For this study, 32 polymorphisms were identified in SERPINB5 by direct DNA sequencing, and 11 of them were selected to be tested with a larger scale subjects. The association of the 11 SERPINB5 polymorphisms with Hepatitis B virus (HBV) clearance, hepatocellular carcinoma (HCC) occurrence and the onset age of HCC were analyzed. There were no significant associations found between 11 SERPINB5 polymorphisms and HBV clearance. In the case of HCC occurrence, one of the haplotypes (ht) showed association with HCC occurrence (OR=2.26, p=0.005, $P^{Cor}=0.05$), albeit with a low statistical power (40.8%) and haplotype frequency (0.052). Further study with a bigger sample size will be needed to clearly verify the association between ht5 and HCC occurrence.

• Journal of Microbiology and Biotechnology
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• v.10 no.5
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• pp.620-627
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• 2000

To determine the prevalence of genetic polymorphisms in Epstein-Barr virus (EBV) strains in the Korean population, the restriction site polymorphisms for BamHI and XhoI enzymes were analyzed with 16 EBV isolates from cancer patients and 7 EBV isolates from healthy carriers, using polymerase chain reaction techniques. None of the 23 isolates were found to carry an extra BamHI site in the BamHI F-fragment (f-variant). Of the 12 type-1 isolates from the cancer patients, 10 lost both the LMP1 XhoI site and the BamHI site between the BamHi W1* and I1* fragments (a W1*I1* fusion variant or type C). The latter W1*I1* fusion variant was due to a mutation of thymidine to adenine, as evidenced by a sequence analysis. The remaining two type-1 isolates showed either no variation at both sites or the loss of only the XhoI site. In contrast, two type-2 isolates and two intertypic recombinants with a type-1 allele at the EBNA2 locus and type-2 alleles at all or some of the EBNA3 loci retained both enzyme sites. In similar analyses of the 7 isolates from the healthy carriers, five of six type-1 isolates lost these two sites, however, one type-2 isolate did not. These results clearly indicate a strong association of both the LMP1 XhoI site loss and the W1*I1* fusion variant with the type-1 rather than the type-2 EBV strains circulating in the immunocompetent Korean carriers.

• Genomics & Informatics
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• v.7 no.4
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• pp.195-202
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• 2009

BIRC5 (Survivin) belongs to the inhibitor of apoptosis gene family. The BIRC5 protein inhibits caspases and consequently blocks apoptosis. Thus, BIRC5 contributes to the progression of cancer allowing for continued cell proliferation and survival. In this study, we identified eight sequence variants of BIRC5 through direct DNA sequencing. Among the eight single nucleotide polymorphisms (SNPs), six common variants with frequencies higher than 0.05 were selected for larger-scale genotyping (n=1,066). Results of the study did not show any association between the promoter region polymorphisms and the clearance of hepatitis B virus (HBV) infection and hepatocellular carcinoma (HCC) occurrence. This is in line with a previous study in which polymorphisms in the promoter region does not influence the function of BIRC5. Initially, we were able to detect a signal with the ＋9194A>G, which disappeared after multiple corrections but led to a change in amino acid. Similarly, we were also able to detect an association signal between two haplotypes (haplotype-2 and haplotype-5) on the onset age of HCC and/or HCC occurrence, but the signals also disappeared after multiple corrections. As a result, we concluded that there was no association between BIRC5 polymorphisms and the clearance HBV infection and/or HCC occurrence. However, our results might useful to future studies.

• Korean Journal of Clinical Laboratory Science
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• v.47 no.2
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• pp.83-89
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• 2015

Although Mycobacterium tuberculosis complex strains remain responsible for the majority of diseases caused by mycobacterial infections worldwide, the increase in HIV (human immuno deficiency virus) infections has allowed for the emergence of other non-tuberculous mycobacteria as clinically significant pathogens. M. tuberculosis was detected by two-tube nested polymerase chain reaction (PCR) and non-tuberculous mycobacteria was detected by PCR-restriction fragment length polymorphism (RFLP) with Msp I. Result of niacin test is equal to result of two-tube nested PCR after culture for M. tuberculosis. In this study, acid fast bacilli stain (AFB. stain) >2+ case, Detection of Mycobacteria is similar to result before culture and after culture. AFB. stain <1+ case, result of mycobacteria is distinguished. Conclusionly, these results suggest that identification of mycobacteria must go side by side both culture and PCR for more fast and accuracy.

• Genomics & Informatics
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• v.12 no.1
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• pp.35-41
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• 2014

Single-nucleotide polymorphisms (SNPs) have been emerging out of the efforts to research human diseases and ethnic disparities. A semantic network is needed for in-depth understanding of the impacts of SNPs, because phenotypes are modulated by complex networks, including biochemical and physiological pathways. We identified ethnicity-specific SNPs by eliminating overlapped SNPs from HapMap samples, and the ethnicity-specific SNPs were mapped to the UCSC RefGene lists. Ethnicity-specific genes were identified as follows: 22 genes in the USA (CEU) individuals, 25 genes in the Japanese (JPT) individuals, and 332 genes in the African (YRI) individuals. To analyze the biologically functional implications for ethnicity-specific SNPs, we focused on constructing a semantic network model. Entities for the network represented by "Gene," "Pathway," "Disease," "Chemical," "Drug," "ClinicalTrials," "SNP," and relationships between entity-entity were obtained through curation. Our semantic modeling for ethnicity-specific SNPs showed interesting results in the three categories, including three diseases ("AIDS-associated nephropathy," "Hypertension," and "Pelvic infection"), one drug ("Methylphenidate"), and five pathways ("Hemostasis," "Systemic lupus erythematosus," "Prostate cancer," "Hepatitis C virus," and "Rheumatoid arthritis"). We found ethnicity-specific genes using the semantic modeling, and the majority of our findings was consistent with the previous studies - that an understanding of genetic variability explained ethnicity-specific disparities.