• Animal cells and systems
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• v.5 no.2
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• pp.153-156
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• 2001

A key aspect of genomic research in the “post-genome era”is to associate sequence variations with heritable phenotypes. The most common variations in the human genome are single nucleotide polymorphisms (SNPs) that occur approximately once in every 500 to 1,000 bases. Although analyzing the phenotypic outcome of these SNPs is crucial to facilitate large-scale association studies of genetic diseases, detection of SNPs from an extended number of human DNA samples is often difficult, labor-intensive and time-consuming. Recent development in SNP detection methods using DNA microarrays and mass spectrophotometry has allowed automated high throughput analyses, but such equipments are not accessible to many scientists. In this study, we demonstrate that a simple PCR-based method using primers with a mismatched base at the 3'-end provides a fast and easy tool to identify known SNPs from human genomic DNA in a regular molecular biology laboratory. Results from this PCR amplification of specific alleles (PASA) analysis efficiently and accurately typed the Q576R polymorphism of human IL4 receptor from the genomic DNAs of 29 Koreans, including 9 samples whose genotype could not be discerned by the conventiona1 PCR-SSCP (single strand conformation polymorphism) method. Given the increasing attention to disease-associated polymorphisms in genomic research, this alternative technique will be very useful to identify SNPs in large-scale population studies.

• Proceedings of the Korean Society for Food Science of Animal Resources Conference
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• 2005.10a
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• pp.123-126
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• 2005

본 연구는 고등동물의 불포화지방산 생합성의 핵심 효소로 알려져 있는 Stearoyl-CoA desaturase(SCD) 유전자의 특정한 단일염기다형(single nucleotide polymorphism; SNP)이 한우의 도체 및 육질형질에 미치는 영향을 분석하기 위해 SCD 유전자의 Intron 7번 영역의 특정부위를 포함하는 primer를 제작하고, 염기서열 분석을 통하여 유전자 구조를 해석한 결과 총 211bp 크기를 갖는 염기서열의 122번째에서 아데닌(A)${\leftrightarrow}$구아닌(G) 염기치환으로 발생한 단일염기다형(SNP) 부위를 발견하였다. 이들 단일염기다형 염기서열 부위를 PCR-SSCP(single-strand conformation polymorphism) 기법을 이용하여 분석한 결과 3종류의 SNP 유전자형(A/A, A/G 및 G/G)을 검출하였다. 이 가운데 A/G 유전자형이 한우의 근내지방도와 등지방두께와 고도의 유의적 연관성이 있다는 새로운 사실을 발견하였다. 따라서, 본 연구를 통해 개발된 한우 SCD 유전자의 특정한 단일 염기다형 표지인자는 한우의 연령 및 성별에 관계없이 육질이 우수한 고급육을 생산하는 우량 한우의 조기식별에 매우 유용한 DNA 표지인자로 활용할 수 있을 것으로 기대된다.

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

• BMB Reports
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• v.36 no.4
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• pp.399-402
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• 2003

Early detection of bladder cancer is particularly important since it dramatically affects the survival rates. However, neither urinary cytology nor tumor markers that are currently used are sensitive enough for the early detection of bladder cancer or recurrent disease. The ras genes are frequently mutated in cancer. In this study, we investigated the diagnostic potential of ras mutation analysis in urinary sediments of patients with bladder cancer using a single-strand conformation polymorphism analysis and polymerase chain reaction. Mutation in codon 12 of the H-ras gene was observed in 39% of the patients. Our results indicate that this approach may significantly improve diagnostic sensitivity in detecting bladder tumors.

• Journal of Microbiology
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• v.34 no.3
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• pp.236-240
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• 1996

Rifampin is the most powerful drug for treating leprosy and tuberculosis today. It inhibits initiation and elongation of RNA transcription by binding to $\beta$-subunit of RNA polymerase, leading to kill mycobacteria. We isolated one variant strain of Mycobacterium leprae from 24 Korean leprosy patients who are less susceptible to rifampin or have suffered from relapse by polymerase chain reaction and single strand conformation polymorphism (PCR-SSCP) of the rpoB gene. Direct sequencing of the rpoB region of M. leprae variant revealed missense mutations which altered the amino acids sequenceof RpoB to Ser-464, Arg-465, Arg-467 and Ala-468. This is the first finding on rpoB gene mutation of M. leprae from Korean patients ; moreover the mutant type was found to be different from the previously reported cases in other countries.

• 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.

• Korean Journal of Biological Psychiatry
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• v.10 no.1
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• pp.80-84
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• 2003

Objective : Bipolar disorder is known to have strong genetic background and cellular immune activation. Based on the hypothesis that abnormalities of normal inhibitory control of T cell immunity can contribute to the pathophysiology of bipolar disorder, we investigated the relationship between the first exon at position +49(A/G) polymorphism of cytotoxic T lymphocyte antigen 4(CTLA4) gene and bipolar disorder. Method : Among the Korean patients diagnosed as bipolar disorder according to DSM-IV, 90 patients without serious medical illness, neurologic illness, hormonal disorder, or concomitant mental illness were selected. The normal control group consisted of 149 age-and sex-matched subjects without current or past history of autoimmune diseases or mental disorder. DNA was extracted from whole blood and the exon 1 region of CTLA-4 gene was amplified by polymerase chain reaction. Gene typing was performed using single strand conformation polymorphism. Results : There were no significant differences in genotype frequencies of G/G, G/A, and A/A between the patients with bipolar disorder and the control group(48.9% vs 46.3%, 44.4% vs 39.6%, and 6.7% vs 14.1%, respectively). There were no significant differences in allelic frequencies of G and A between the patients with bipolar disorder and the control group(71.1% vs 66.1%, and 28.9% vs 33.9%, respectively). Conclusion : This study did not show the association of exon 1 polymorphism of CTLA-4 gene with bipolar disorder.

• Journal of Gastric Cancer
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• v.6 no.4
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• pp.214-220
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• 2006

Purpose: p53 is one of the most commonly mutated genes in human tumors. The aim of this study was to analyze p53 mutation in gastric cancer and its correlations with the clinicopathologic variables to clarify the usefulness of p53 mutation as a prognostic factor. Materials and Methods: Specimens from 331 patients with gastric cancer who underwent a gastrectomy between March 1999 and April 2001 at the Kyungpook National University Hospital were used. p53 gene mutations were assessed by using a polymerase chain-reaction single-strand conformation polymorphism (PCR-SSCP) analysis. The correlations between p53 gene mutation and clinocopathologic parameters were analyzed. Results: p53 mutations were found in 66 (19.9%) tumors. Among those 66 cases, mutations were seen in 23 tumors at axon 5, in 8 at exon 6, in 21 at exon 7, and in 17 at exon 8. Two mutations were shown in 3 tumors. Thiriy-six (23.1%) of 156 intestinal-type tumors and 19 (13.1%) of 145 diffuse-type tumors showed p53 gene mutation (P=0.007). The frequency of p53 gene mutation didn't show any significant differences according to age, sex, stage, location, or gross type. Exon 5 mutations showed more frequently in intestinal-type tumors than in diffuse-type tumors (9.7% vs. 2.8%, P=0.024), and p53 mutation were more frequent in lymph nodes metastasis group than lymph nodes non-metastasis group with statistical significance (25.0% vs 15.6%, P=0.034). The five-year survival rate showed no statistically significant difference with p53 mutation (P=0.704). Conclusion: p53 mutations assessed by PCR-SSCP had little value as a prognostic factor after gastrectomy in patients with gastric cancer.

• Journal of Korean Society of Forest Science
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• v.95 no.6
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• pp.631-635
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• 2006

Single-strand conformation polymorphism (SSCP) analysis of MD and JWB phytopalsma isolates which amplified PCR products using the R16F2n/R2 phytoplamsa universal primer pair were compared for variations of their nucleotide sequence. The MD and JWB phytoplasmas were clearly distinct each of the band patterns from about 1.2 kb PCR products. To clearly distinct of close SSCP band patterns, the MD and JWB phytoplasma PCR products were mixed and performed to detect their polymorphism. The SSCP band patterns show all of bands of MD and JWB on single lane and easily distinct their each band patterns. The PCR-SSCP analysis was possible to detect of 1.2 kb nucleotide sequence and near close band patterns were easily distinct by mixing two samples.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.9
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• pp.1244-1249
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• 2014

Goose fatty liver is one of the most delicious and popular foods in the world, but there is no reliable genetic marker for the early selection and breeding of geese with good liver-producing potential. In our study, one hundred and twenty-four 78-day-old Landes geese bred in Shunda Landes goose breeding farm, Jiutai, Jilin, China were selected randomly. The fatty livers were sampled each week after overfeeding during a three week period. Polymerase chain reaction-single strand conformation polymorphism and DNA sequencing were used to identify single nucleotide polymorphisms (SNPs) of fatty acid synthase (FAS), which is an important enzyme involved in the synthesis of fat under both physiological and pathological conditions. Least-squares correlation was established between these SNPs and fatty liver weight, abdominal fat weight, and intestinal fat weight of the overfed Landes geese, respectively. The results showed that fatty liver weight of geese with EF and FF genotypes (amplified by primer P1) was significantly higher than that of the EE genotype (p<0.05), and liver weight of CD and DD genotypes (amplified by primer P2) was significantly higher than that of the CC genotype (p<0.05). Different genotype combinations showed different liver weights, and from highest to lowest were ABDD, DDEF, DDFF, DDEE, ABEF, ABFF, AADD, and CDEF. Further analysis of DNA sequencing showed that there were two SNPs within the 5' promoter region the FAS gene. The geese of EF and FF genotypes carried a change of T to C, and the geese of CD and DD genotypes carried a change of A to G. The changes of the bases could potentially influence the binding of some transcription factors to this region as to regulate FAS gene. To our knowledge, this is the first report of SNPs found within the 5' promoter region of the Landes goose FAS gene, and our data will provide an insight for early selection of geese for liver production.