• Korean Journal of Head & Neck Oncology
• /
• v.14 no.1
• /
• pp.20-26
• /
• 1998

Objectives: Deletion in the short arm of chromosome 3 is common in many human cancers, including sporadic and hereditary renal carcinomas, small cell lung carcinomas, non-small cell lung carcinomas, and carcinomas of the ovary, breast, and cervix. A high frequency of chromosomal aberrations in head and neck cancers involving chromosome 3p has also been reported. These findings suggest that multiple tumor suppressor genes may be present on the short arm of chromosome 3. Materials and Methods: To investigate the possibility of chromosome 3p deletions in the Korean head and neck cancer patients, we applied a polymerase chain reaction(PCR)-based Restriction Fragment Length Polymorphism analysis to the DNA samples of matched normal mucosa and head and neck squamous cell carcinomas from 19 patients. Results: In the 19 normal samples heterozygosity at the polymorphic loci varied: 6 at the D3F15S2 locus(on telomeric 3p21), 2 at the D3S32 locus(on centromeric 3p21), and 4 at the THRB locus(on centromeric 3p24). In 12 matched carcinoma specimens, LOH(loss of heterozygosity) was observed at D3F15S2 in 1 of 6(17%), D3S32 in 1 of 2(50%), and at THRB in 2 of 4 cases(50%). Conclusion: The frequency of chromosome 3p deletion in the Korean head and neck carcinomas appear as other country did.

• Plant Breeding and Biotechnology
• /
• v.6 no.4
• /
• pp.413-425
• /
• 2018

A previous work developed and identified a new omega-5 gliadin deficient wheat line named O-free by crossing Keumkang and Olgeuru, which is nutritionally quite meaningful in that omega-5 gliadin is one of the known wheat allergens. To verify the characteristics of the O-free, we performed RNA sequencing (RNAseq) analysis of the O-free and the two parent lines (Keumkang and Olgeuru). The results of the similarity analysis with the ESTs for gliadins and glutenins showed that the O-free ESTs had no similarity with the omega-5 gliadin sequences but had similarity to other gliadins and glutenins. Furthermore, mapping results between the raw RNAseq data from the O-free and the omega-5 gliadin sequence showed a clear deletion of the N-terminal sequences which are an important signature of omega-5 gliadin. We also designed specific PCR primers that could identify omega-5 gliadin in the genomic DNA. The results showed that no omega-5 gliadin fragments were detected in the O-free. According to these results, we confirmed that the deficiency of omega-5 gliadin in the O-free is not caused by post-transcriptional or post-translational regulations such as epigenetic phenomena but by a simple deletion in the chromosome. Furthermore, we showed that the low-molecular weight glutenin subunit (LMW-GS) gene in the O-free had a single nucleotide polymorphism (SNP) causing a premature stop codon, resulting in a truncated polypeptide. We expect that the O-free line may serve as an excellent source of wheat that could prevail in the hypo-allergen wheat market, which has recently gained interest world-wide.

• Journal of Genetic Medicine
• /
• v.15 no.2
• /
• pp.64-71
• /
• 2018

Purpose: Overgrowth syndromes are conditions that involve generalized or localized areas of excess growth. In this study, the clinical, molecular, and genetic characteristics of Korean patients with overgrowth syndrome were analyzed. Materials and Methods: We recruited 13 patients who presented with overgrowth syndrome. All patients fulfilled inclusion criteria of overgrowth syndrome. Analysis of the clinical and molecular investigations of patients with overgrowth syndrome was performed retrospectively. Results: Among the 13 patients with overgrowth syndrome, 9 patients (69.2%) were found to have molecular and genetic causes. Among the seven patients with Sotos syndrome (SS), two had a 5q35microdeletion that was confirmed by fluorescent in situ hybridization. In two patients with SS, intragenic mutations including a novel mutation, c.5993T>A (p.M1998L), were found by Sanger sequencing. One patient had one copy deletion of NDS1 gene which was confirmed by multiplex ligation-dependent probe amplification. Among five patients with Beckwith-Wiedemann syndrome, three had aberrant imprinting control regions; 2 hypermethylation of the differentially methylated region of H19, 1 hypomethylation of the differentially methylated region of Kv. In one patient displaying overlapping clinical features of SS, a de novo heterozygous deletion in the chromosomal region 7q22.1-22.3 was found by single nucleotide polymorphism-based microarray. Conclusion: Considering high detection rate of molecular and genetic abnormalities in this study, rigorous investigations of overgrowth syndrome may be an important tool for the early diagnosis and genetic counseling. A detailed molecular analysis of the rearranged regions may supply the clues for the identification of genes involved in growth regulation.

• Journal of the Korean Chemical Society
• /
• v.48 no.1
• /
• pp.33-38
• /
• 2004

Mutation of p53 tumor suppressor gene in HNSCC (head and neck squamous cell carcinoma) has been proposed high rate. We extracted genomic DNA from 50 head and neck cancer. The DNA was amplified by PCR at exon 5-8 in p53 tumor suppressor gene. We have compared single strand conformation polymorphism (SSCP) and denaturing high performance liquid chromatography (DHPLC) method for analysis of p53 somatic mutation. As a result, 16 deleted mutations (32%) were detected by SSCP analysis and 17 deleted mutations (34%) were detected by DHPLC analysis at exon 8. All of 17 mutations were proved by sequencing. We conclude that DHPLC is a fast and simple screening method rather than SSCP analysis.

• Asian-Australasian Journal of Animal Sciences
• /
• v.24 no.7
• /
• pp.1019-1025
• /
• 2011

Toll-like receptors (TLRs) play an important role in the recognition of invading pathogens and the modulation of innate immune responses in mammals. The TLR4 and TLR7 are well known to recognize the bacterial lipopolysaccharide (LPS) and single stranded (ssRNA) ligands, respectively and play important role in host defense against Gram-negative bacteria and ssRNA viruses. In the present study, coding exon fragments of these two TLRs were identified, cloned, sequenced and analyzed in terms of insertion-deletion polymorphism, within bovine TLRs 4 and 7, thereby facilitating future TLR signaling and association studies relevant to bovine innate immunity. Comparative sequence analysis of TLR 4 exons revealed that this gene is more variable, particularly the coding frame (E3P1), while other parts showed percent identity of 95.7% to 100% at nucleotide and amino acid level, respectivley with other Bos indicus and Bos taurus breeds from different parts of the world. In comparison to TLR4, sequence analysis of TLR7 showed more conservation among different B. indicus and B. taurus breeds, except single point mutation at 324 nucleotide position (AAA to AAM) altering a single amino acid at 108 position (K to X). Percent identity of TLR7 sequences (all 3 exons) was between 99.2% to 100% at nucleotide and amino acid level, when compared with available sequence database of B. indicus and B. taurus. Simple Modular Architecture Research Tool (SMART) analysis showed variations in the exon fragments located in the Leucine Rich Repeat (LRR) region, which is responsible for binding with the microbial associated molecular patterns and further, downstream signaling to initiate anti-microbial response. Considering importance of TLR polymorphism in terms of innate immunity, further research is warranted.

• The Journal of Korean Medicine
• /
• v.24 no.4
• /
• pp.102-112
• /
• 2003

The homozygous deletion allele of the angiotensin converting enzyme gene (ACF/DD), homozygous threonine allele of the angiotensinogen gene (AGN/TT), and the 4 allele of the apolipoprotein E gene (apoE/4) are reported to be associated with ischemic heart disease. Ischemic cerebrovascular disease (ICVD) is another atherosclerotic disease, and the effects of these polymorphisms on ICVD have been confusing. In this study, I investigated whether ACF/DD, AGN/TT, and apoE/4 genotypes are associated with ICVD and whether genetic risk is enhanced by the effect of one upon another. I ascertained these genotypes in patients with ICVD (n=121) diagnosed by brain computed tomography. Control subjects for the ICVD were randomly selected from subjects matched for age, gender, and history of hypertension with patients. Frequency of ACF/DD genotype was somewhat higher in the patients with ICVD than in the controls (18％ vs. 15％). Incidence of ICVD was higher in subjects with the apoE/4/4 genotype than in the other genotypes (50％ vs. 27-29％). Incidence of ICVD was much higher in subjects with the AGN/TT genotype than in AGN/MM genotype (36％ vs. 17％). Furthermore, the AGN/TT genotype greatly increased the relative risk for ICVD in the subjects with ACF/DD genotype (80.0％ vs. 20.0％, P=0.089). Finally, incidence of ICVD was much higher in the subjects with both apoE/2/4 and AGN/TT genotype than in the other genotypes (83.3％ vs. 16.7％, P=O.095). These results suggest that AGN/TT enhances the risk for ICVD associated with ACF/DD and apoE/2/4.

• Asian Pacific Journal of Cancer Prevention
• /
• v.15 no.12
• /
• pp.4851-4856
• /
• 2014

Background: Glutathione S-transferase M1 (GSTM1) have been reported to be associated with hepatocellular carcinoma. However, the effect of the GSTMl null genotype was divergent in the literature and we therefore performed the present meta-analysis to explore the relationship in detail. Materials and Metbods: Reported studies were searched from 1990 to March 1, 2014 in PubMed and Wanfang Med Online. The total odds oatio (OR) and 95% CI were calculated and analyzed by Review Manager 5.1 and STATE 12. Results: Total OR was calculated from 26 articles with 3,769 cases and 5,517 controls and the association proved significant (OR [95%CI]=1.50 [1.25, 1.80], P<0.05) in the Chinese population. However, there was no significant association between hepatocellular carcinoma risk among subjects carrying the GSTM1 null genotype (OR [95%CI]=1.20 [0.88-1.64], P=0.24) in subgroups of publication in English and in Indian populations (OR [95%CI]=1.80 [0.80-4.20], P=0.15). Conclusions: The GSTM1 deletion polymorphism might not have a significant effect on the susceptibility of hepatocellular carcinoma overall.

• Asian Pacific Journal of Cancer Prevention
• /
• v.15 no.7
• /
• pp.3201-3205
• /
• 2014

The aim of this study was to investigate the frequencies of GSTT1 and GSTM1 deletion polymorphisms in newly-diagnosed patients with uterine cervical lesions from central Serbia. Polymorphisms of GST genes were genotyped in 97 patients with cervical lesions and 50 healthy women using a multiplex polymerase chain reaction (PCR). The GSTM1 null genotype was significantly more prominent among the patients than in controls (74.2% vs 56.0%), the risk associated with lesions being almost 2.3-fold increased (OR=2.26, 95%CI=1.10-4.65, p=0.03) and 3.17-fold higher in patients above >45 years old (95%CI=1.02-9.79, p=0.04). The analysis of the two genotypes demonstrated that GSTM1 null genotype significantly increased risk only for low grade squamous intraepithelial lesion-LSIL (OR=2.81, 95%CI=1.03-7.68, p=0.04). GSTT1 null genotype or different genotype combinations were not found to be risk factors, irrespective to lesion stages, age or smoking. We found that the risk of cervical lesions might be significantly related to the GSTM1 null genotype, especially in women aged above 45 years. Furthermore, the GSTM1 polymorphism might have greater role in development of early stage lesions.

• Asian Pacific Journal of Cancer Prevention
• /
• v.13 no.5
• /
• pp.1999-2002
• /
• 2012

Background: DNA polymerase is a single-copy gene that is considered to be part of the DNA repair machinery in mammalian cells. The encoded enzyme is a key to the base excision repair (BER) pathway. It is evident that pol beta has mutations in various cancer samples, but little is known about ovarian cancer. Aim: Identification of any variant form of $pol{\beta}$ cDNA in ovarian carcinoma and determination of association between the polymorphism and ovarian cancer risk in Indian patients. We used 152 samples to isolate and perform RT-PCR and sequencing. Results: A variant of polymerase beta (deletion of exon 4-6 and 11-13, comprising of amino acid 63-123, and 208-304) is detected in heterozygous condition. The product size of this variant is 532 bp while wild type pol beta is 1 kb. Our study of association between the variant and the endometrioid type shows that it is a statistically significant factor for ovarian cancer [OR=31.9 (4.12-246.25) with p<0.001]. The association between variant and stage IV patients further indicated risk (${\chi}^2$ value of 29.7, and OR value 6.77 with 95% CI values 3.3-13.86). The correlation study also confirms the association data (Pearson correlation values for variant/stage IV and variant/endometrioid of 0.44 and 0.39). Conclusion: Individuals from this part of India with this type of variant may be at risk of stage IV, endometrioid type ovarian carcinoma.

• Korean Journal of Medicinal Crop Science
• /
• v.3 no.1
• /
• pp.50-55
• /
• 1995

This study was conducted to determine the optimum conditions for induction and different somatic of somatic embryos as well as germination of encapsulated and stored somatic embryos. Somatic embryos was better formed in 1/2X MS medium than full - strength MS medium. 0.1 to 1.0mg/lBA and kinetin promoted shoot differentiation of somatic embryos. Higher concentration tend to inhibit differentiation. IAA affect positively both root and shoot growth. In vitro germination of somatic embryos encapsulated with 2% alginate matrix containing 1/2 MS nutrient medium and $AgNO_3$ 5mg/l was 86%. Storage of somatic embryos was effecive at $5^{\circ}C$ but the germination rate decreased with longer storage period. RAPD analyses with plants regenerated from the somatic embryos showed DNA polymorphism, indicating abolition of primer binding site by point mutation, deletion, or insertion of certain sequences.