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ON THE REPRESENTATION OF PROBABILITY VECTOR WITH SPECIAL DIFFUSION OPERATOR USING THE MUTATION AND GENE CONVERSION RATE

  • Choi, Won
    • Korean Journal of Mathematics
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    • v.27 no.1
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    • pp.1-8
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    • 2019
  • We will deal with an n locus model in which mutation and gene conversion are taken into consideration. Also random partitions of the number n determined by chromosomes with n loci should be investigated. The diffusion process describes the time evolution of distributions of the random partitions. In this paper, we find the probability of distribution of the diffusion process with special diffusion operator $L_1$ and we show that the average probability of genes at different loci on one chromosome can be described by the rate of gene frequency of mutation and gene conversion.

ON THE LIMITING DIFFUSION OF SPECIAL DIPLOID MODEL IN POPULATION GENETICS

  • CHOI, WON
    • Bulletin of the Korean Mathematical Society
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    • v.42 no.2
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    • pp.397-404
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    • 2005
  • In this note, we characterize the limiting diffusion of a diploid model by defining the discrete generator for the resealed Markov chain. We conclude that this limiting diffusion model is with uncountable state space and mutation selection and special 'mutation or gene conversion rate'.

Significance of HPV Infection and Genic Mutation of APC and K-ras in Patients with Rectal Cancer

  • Sun, Zhen-Qiang;Wang, Hai-Jiang;Zhao, Ze-Liang;Wang, Qi-San;Fan, Chuan-Wen;Kureshi, Kureshi;Fang, Fa
    • Asian Pacific Journal of Cancer Prevention
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    • v.14 no.1
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    • pp.121-126
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    • 2013
  • Background: Significance of HPV infection and genic mutation of APC and K-ras in rectal cancer has been investigated but not clarified. The objective of our study was to investigate these parameters in patients with rectal cancer to analyze correlations with biological behaviour, to determine relationships among the three, and also to demonstrate survival prognosis effects. Methods: From December 2007 to September 2008, 75 rectal cancer cases confirmed by histopathology in the Tumor Hospital of Xinjiang Medical University were enrolled. The control group consisted of normal rectal mucous membrane taken simultaneously, a least 10 cm distant from the carcinoma fringe. HPV DNA, the MCR of APC and exon-1 of K-ras were detected by PCR and PCR-SSCP. All results were analyzed in relation to clinical pathological material, using chi-square and correlation analysis via SPSS.13 and Fisher's Exact Probability via STATA. 9.0. All 75 patients were followed up for survival analysis using Kaplan-Meier and Log-rank tests. Results: 55 out of 75 cases demonstrated gene HPV L1 while it was notdetected in normal rectal mucosa tissue. HPV infection was correlated with age and lymphatic metastasis (P<0.05) but not other characteristics, such as ethnicity, tumor size, histological type, tumor type, Duke's stage and infiltration depth. Some 43 cases exhibited APC genic mutation (57.3%) and 34 K-ras genic mutation (45.3%). APC genic mutation was correlated with gender(P<0.05), but not age, histological type, infiltration depth, lymphatic metastasis and Duke's stage. In 55 cases of rectal cancer with HPV infection, there were 31 cases with genic mutation of APC (56.4%) and 24 with genic mutation of K-ras (43.6%). For the 20 cases of rectal cancer with non-HPV infection, the figures were 12 cases (60%) and 10 (50.0%), respectively, with no significant relation. Survival analysis showed no statistical significance for K-ras genic mutation, APC genic mutation or HPV infection (P>0.05). However, the survival time of the patients with HPV infection was a little shorter than in cases without HPV infection. Conclusions: Our results suggest that HPV infection might be an important factor to bring about malignant phenotype of rectal cancer and influence prognosis. Genic mutation of APC and K-ras might be common early molecular events of rectal cancer, but without prognostic effects on medium-term or early stage patients with rectal cancer.

Comparison of Clinical Outcomes of BRCA1/2 Pathologic Mutation, Variants of Unknown Significance, or Wild Type Epithelial Ovarian Cancer Patients

  • Eoh, Kyung Jin;Park, Hyung Seok;Park, Ji Soo;Lee, Seung-Tae;Han, Jeongwoo;Lee, Jung-Yun;Kim, Sang Wun;Kim, Sunghoon;Kim, Young Tae;Nam, Eun Ji
    • Cancer Research and Treatment
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    • v.49 no.2
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    • pp.408-415
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    • 2017
  • Purpose The purpose of this study was to investigate the clinical features of epithelial ovarian cancer (EOC) patients according to BRCA1/2 mutation status (mutation, variant of uncertain significance [VUS], or wild type). Materials and Methods We analyzed 116 patients whose BRCA1/2 genetic test results were available for mutation type and clinical features, including progression-free survival (PFS), overall survival (OS), and response rate. These characteristics were compared according to BRCA1/2 mutation status. Results Thirty-seven (37/116, 31.9%) BRCA1/2 mutations were identified (BRCA1, 30; BRCA2, 7). Mutation of c.3627_3628insA (p.Leu1209_Glu1210?fs) in BRCA1 was observed in five patients (5/37, 13.5%). Twenty-five patients had BRCA1/2 VUSs (25/116, 21.6%). Personal histories of breast cancer were observed in 48.6% of patients with BRCA1/2 mutation (18/37), 16.0% of patients with BRCA1/2 VUS (4/25), and 7.4% of patients with BRCA wild type (4/54) (p < 0.001). Patients with BRCA1/2 mutation showed longer OS than those with BRCA1/2 wild type (p=0.005). No significant differences were detected in PFS, OS, or response rates between patients with BRCA1/2 VUS and BRCA1/2 mutation (p=0.772, p=0.459, and p=0.898, respectively). Conclusion Patients with BRCA1/2 mutation had longer OS than those with BRCA1/2wild type. Patients with BRCA1/2 mutation and BRCA1/2 VUS displayed similar prognoses.

Mutations of ${\beta}3$ Adrenergic Receptor in Korean Patients treated with Herbal Dieting Program for Obesity (한방비만치료임상례중 ${\beta}3$ Adrenergic Receptor 변이율에 대한 고찰 (비만유전자보유유무에 따른 치료효과 비교))

  • Kim, Dong-Yeol;Kim, Kil-Soo;Kim, Sun-Min
    • Journal of Korean Medicine for Obesity Research
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    • v.2 no.1
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    • pp.43-52
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    • 2002
  • Purpose & Methods: In order to study obese gene mutation rate in obese Korean patients and to investigate the effect at Chegamuiyiin-tang and electro-lipolysis-acupuncture on obesity treatment. the difference of the reaction to herbal dieting between patients with ${\beta}3$ adrenergic receptor mutation and the patients with wild type ${\beta}3$ adrenergic receptor is observed. Results: Chegamuiyiin-tang and electro-lipolysis-acupuncture treatment are effective on the treatment of obesity in weight reduction. body fat reduction and the circumferences of arm, abdomen, hip and thigh. In the comparison of ${\beta}3$ adrenergic receptor wild type and ${\beta}3$ adrenergic receptor mutation groups, body fat was more reduced with statistical significance, and as for BMI change and body weight change were higher in ${\beta}3$ adrenergic receptor mutation groups with no statistical significance. In the comparison of ${\beta}3$ adrenergic receptor wild type and ${\beta}3$ adrenergic receptor mutation groups among BMI under 25 patients change rate of body weight. BMI, body fact percentage, WHR and body circumference were higher in ${\beta}3$ adrenergic receptor mutation group than in ${\beta}3$ adrenergic receptor wild type group. Conclusion: These results imply that herbal dieting program combined with electro-lipolysis-acupuncture is more effective on reducing body weight and body fat in ${\beta}3$ adrenergic receptor mutation group than wild type group, and that the earlier the treatment is applied, the more effective it is.

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Correlation Analysis of KCNQ1 S140G Mutation Expression and Ventricular Fibrillation: Computer Simulation Study (KCNQ1 S140G 돌연변이 발현과 심실세동과의 상관관계 분석을 위한 컴퓨터 시뮬레이션 연구)

  • Jeong, Daun;Lim, Ki Moo
    • Journal of Biomedical Engineering Research
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    • v.38 no.3
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    • pp.123-128
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    • 2017
  • Background and aims: The KCNQ1 S140G mutation involved in $I_{ks}$ channel is a typical gene mutation affecting atrial fibrillation. However, despite the possibility that the S140G gene mutation may affect not only atrial but also ventricular action potential shape and ventricular responses, there is a lack of research on the relationship between this mutation and ventricular fibrillation. Therefore, in this study, we analyzed the correlation and the influence of the KCNQ1 S140G mutant gene on ventricular fibrillation through computer simulation studies. Method: This study simulated a 3-dimensional ventricular model of the wild type(WT) and the S140G mutant conditions. It was performed by dividing into normal sinus rhythm simulation and reentrant wave propagation simulation. For the sinus rhythm, a ventricular model with Purkinje fiber was used. For the reentrant propagation simulation, a ventricular model was used to confirm the occurrence of spiral wave using S1-S2 protocol. Results: The result showed that 41% shortening of action potential duration(APD) was observed due to augmented $I_{ks}$ current in S140G mutation group. The shortened APD contributed to reduce wavelength 39% in sinus rhythm simulation. The shortened wavelength in cardiac tissue allowed re-entrant circuits to form and increased the probability of sustaining ventricular fibrillation, while ventricular electrical propagation with normal wavelength(20.8 cm in wild type) are unlikely to initiate re-entry. Conclusion: In conclusion, KCNQ1 S140G mutation can reduce the threshold of the re-entrant wave substrate in ventricular cells, increasing the spatial vulnerability of tissue and the sensitivity of the fibrillation. That is, S140G mutation can induce ventricular fibrillation easily. It means that S140G mutant can increase the risk of arrhythmias such as cardiac arrest due to heart failure.

Comparison of Test Case Effectiveness Based on Dynamic Diagrams Using Mutation Testing (뮤테이션 테스트를 이용한 동적 다이어그램에 근거한 테스트 케이스의 효율 비교)

  • Lee, Hyuck-Su;Choi, Eun-Man
    • The KIPS Transactions:PartD
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    • v.16D no.4
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    • pp.517-526
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    • 2009
  • It is possible to indicate the complex design and execution of object-oriented program with dynamic UML diagram. This paper shows the way how to make several test cases from sequence, state, and activity diagram among dynamic UML diagram. Three dynamic UML diagrams about withdrawal work of ATM simulation program are drawn. Then different test cases are created from these diagrams using previously described ways. To evaluate effectiveness of test cases, mutation testing is executed. Mutants are made from MuClipse plug-in tool based on Eclipse which supports many traditional and class mutation operators. Finally we've got the result of mutation testing and compare effectiveness of test cases, etc. Through this document, we've known some hints that how to choose the way of making test cases.

Current Evidence on the Relationship Between Two Polymorphisms in the NBS1 Gene and Breast Cancer Risk: a Meta-analysis

  • Zhang, Zhi-Hua;Yang, Lin-Sheng;Huang, Fen;Hao, Jia-Hu;Su, Pu-Yu;Sun, Ye-Huan
    • Asian Pacific Journal of Cancer Prevention
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    • v.13 no.11
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    • pp.5375-5379
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    • 2012
  • Introduction: Published studies on the association between Nijmegen breakage syndrome 1(NBS1) gene polymorphisms and breast cancer risk have been inconclusive, and a meta-analysis was therefore performed for clarification. Methods: Eligible articles were identified by a search of MEDLINE and EMBASE bibliographic databases for the period up to March 2012. The presence of between-study heterogeneity was investigated using the chi-square-based Cochran's Q statistic test. When there was statistical heterogeneity, the random effects model was chosen; otherwise, fixed effects estimates were reported as an alternative approach. Results: A total of 11 eligible articles (14 case-control studies) were identified, nine case-control studies were for the 657del5 mutation (7,534 breast cancer cases, 14,034 controls) and five case-control studies were for the I171V mutation (3,273 breast cancer cases, 4,004 controls). Our analysis results indicated that the 657del5 mutation was associated with breast cancer risk (carriers vs. non-carriers: pooled OR =2.63, 95% CI: 1.76-3.93), whereas the I171V mutation was not (carriers vs. non-carriers: pooled OR =1.52, 95% CI: 0.70-3.28). Conclusion: The present meta-analysis suggests that the 657del5 gene mutation in the NBS1 gene plays a role in breast cancer risk, while the I171V mutation does not exert a significant influence.

Structural Bioinformatics Analysis of Disease-related Mutations

  • Park, Seong-Jin;Oh, Sang-Ho;Park, Dae-Ui;Bhak, Jong
    • Genomics & Informatics
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    • v.6 no.3
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    • pp.142-146
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    • 2008
  • In order to understand the protein functions that are related to disease, it is important to detect the correlation between amino acid mutations and disease. Many mutation studies about disease-related proteins have been carried out through molecular biology techniques, such as vector design, protein engineering, and protein crystallization. However, experimental protein mutation studies are time-consuming, be it in vivo or in vitro. We therefore performed a bioinformatic analysis of known disease-related mutations and their protein structure changes in order to analyze the correlation between mutation and disease. For this study, we selected 111 diseases that were related to 175 proteins from the PDB database and 710 mutations that were found in the protein structures. The mutations were acquired from the Human Gene Mutation Database (HGMD). We selected point mutations, excluding only insertions or deletions, for detecting structural changes. To detect a structural change by mutation, we analyzed not only the structural properties (distance of pocket and mutation, pocket size, surface size, and stability), but also the physico-chemical properties (weight, instability, isoelectric point (IEP), and GRAVY score) for the 710 mutations. We detected that the distance between the pocket and disease-related mutation lay within $20\;{\AA}$ (98.5%, 700 proteins). We found that there was no significant correlation between structural stability and disease-causing mutations or between hydrophobicity changes and critical mutations. For large-scale mutational analysis of disease-causing mutations, our bioinformatics approach, using 710 structural mutations, called "Structural Mutatomics," can help researchers to detect disease-specific mutations and to understand the biological functions of disease-related proteins.

Surgical Perspective of T1799A BRAF Mutation Diagnostic Value in Papillary Thyroid Carcinoma

  • Brahma, Bayu;Yulian, Erwin Danil;Ramli, Muchlis;Setianingsih, Iswari;Gautama, Walta;Brahma, Putri;Sastroasmoro, Sudigdo;Harimurti, Kuntjoro
    • Asian Pacific Journal of Cancer Prevention
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    • v.14 no.1
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    • pp.31-37
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    • 2013
  • Background: Throughout Indonesia, thyroid cancer is one of the ten commonest malignancies, with papillary thyroid carcinoma (PTC) in our hospital accounting for about 60% of all thyroid nodules. Although fine needle aspiration biopsy (FNAB) is the most reliable diagnostic tool, some nodules are diagnosed as indeterminate and second surgery is common for PTC. The aim of this study was to establish the diagnostic value and feasibility of testing the BRAF T1799A mutation on FNA specimens for improving PTC diagnosis. Materials and Methods: This prospective study enrolled 95 patients with thyroid nodules and future surgery planned. Results of mutational status were compared with surgical pathology diagnosis. Results: Of the 70 cases included in the final analysis, 62.8% were PTC and the prevalence of BRAF mutation was 38.6%. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) for BRAF mutation analysis were 36%, 100%, 100% and 48%, respectively. With other data findings, nodules with "onset less than 5 year" and "hard consistency" were proven as diagnostic determinants for BRAF mutation with a probability of 62.5%. This mutation was also a significant risk factor for extra-capsular extension. Conclusions: Molecular analysis of the BRAF T1799A mutation in FNAB specimens has high specificity and positive predictive value for PTC. It could be used in the selective patients with clinical characteristics to facilitate PTC diagnosis and for guidance regarding extent of thyroidectomy.