• 한국산학기술학회논문지
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• 제11권6호
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• pp.2093-2098
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• 2010

지방간은 대사증후군의 한 형태로 인슐린저항성이 중요한 역할을 한다. 본 연구는 당뇨 및 대사 인자들과 연관성이 있는 것으로 알려진 말초혈액의 사립체 DNA (mtDNA) copy 수와 지방간 및 인슐린저항성 관련 인자와의 연관성을 알아보고자 하였다. 지방간 진단을 위해 음주력 설문과 복부 초음파 검사를 시행하였으며 실시간 중합효소 연쇄반응을 이용하여 말초혈액의 백혈구에서 mtDNA copy 수를 측정하였다. 총 445 명의 대상자 중 지방간이 있는군(fatty liver group)은 148 명이고 정상군은 297 명이었다. 지방간이 있는 군에서 정상군에 비해 mtDNA copy수가 유의하게 낮았다. 비알콜성 지방간과 알코올성 지방간 모두 지방간이 있는 군에서 말초혈액 mtDNA copy 수가 낮았다. 말초혈액의 mtDNA copy 수는 ALT, AST, $\gamma$-GTP, 체질량지수, 허리둘레, 이완기혈압, 유리지방산 수치와 역의 상관관계를 보였다. 말초혈액에서의 mtDNA copy 수는 지방간 여부 및 인슐린저항성 관련 대사 인자들과 높은 연관성이 있었다.

• Asian Pacific Journal of Cancer Prevention
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• 제14권4호
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• pp.2393-2399
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• 2013

Objective: Mitochondrial DNA (mtDNA) is considered a hotspot of mutations in various tumors. However, the relationship between microsatellite instability (MSI) and mtDNA copy number alterations in lung cancer has yet to be fully clarifieds. In the current study, we investigated the copy number and MSI of mitochondrial genome in lung carcinomas, as well as their significance for cancer development. Methods: The copy number and MSI of mtDNA in 37 matched lung carcinoma/adjacent histological normal lung tissue samples were examined by polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) assays for sequence variation, followed by sequence analysis and fluorogenic 5'-nuclease real-time PCR. Student's t test and linear regression analyses were employed to analyze the association between mtDNA copy number alterations and mitochondrial MSI (mtMSI). Results: The mean copy number of mtDNA in lung carcinoma tissue samples was significantly lower than that of the adjacent histologically normal lung tissue samples (p<0.001). mtMSI was detected in 32.4% (12/37) of lung carcinoma samples. The average copy number of mtDNA in lung carcinoma samples containing mtMSI was significantly lower than that in the other lung carcinoma samples (P<0.05). Conclusions: Results suggest that mtMSI may be an early and important event in the progression of lung carcinogenesis, particularly in association with variation in mtDNA copy number.

• Asian Pacific Journal of Cancer Prevention
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• 제17권10호
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• pp.4719-4722
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• 2016

Background: Glutathione S-transferase M1 (GSTM1) is involved in the detoxification of carcinogenic agents. DNA copy number variants of GSTM1 may be associated with cancer progression and may result in reduced survival time of various cancers. Determination of DNA copy number variants was here used to assess the association between GSTM1 copy number variant and pathological status and survival time of colorectal-cancer patients treated with 5-fluorouracil-based chemotherapy. Methods: One hundred thirteen Thai colorectal-cancer patients were investigated for GSTM1 copy number variant by real-time PCR. Relationships between gene copy number variants and clinico-pathological parameters were determined. Result: Associations were evident between GSTM1 copy number and stage of tumor (P = 0.026) and metastasis at diagnosis (P = 0.049), with odds ratio values of 0.2 and 0.3 respectively. Conclusions: GSTM1 copy number variant was here not related with reduced overall survival for the colorectal-cancer patients receiving 5-FU-based chemotherapy.

• Genomics & Informatics
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• 제12권4호
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• pp.136-144
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• 2014

Besides single-nucleotide variants in the human genome, large-scale genomic variants, such as copy number variations (CNVs), are being increasingly discovered as a genetic source of human diversity and the pathogenic factors of diseases. Recent experimental findings have shed light on the links between different genome architectures and CNV mutagenesis. In this review, we summarize various genomic features and discuss their contributions to CNV formation. Genomic repeats, including both low-copy and high-copy repeats, play important roles in CNV instability, which was initially known as DNA recombination events. Furthermore, it has been found that human genomic repeats can also induce DNA replication errors and consequently result in CNV mutations. Some recent studies showed that DNA replication timing, which reflects the high-order information of genomic organization, is involved in human CNV mutations. Our review highlights that genome architecture, from DNA sequence to high-order genomic organization, is an important molecular factor in CNV mutagenesis and human genomic instability.

• 대한의생명과학회지
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• 제15권3호
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• pp.229-232
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• 2009

DNA isolation for PCR-based short tandem repeat (STR) analysis is essential to recover high yields of amplifiable DNA from low copy number (LCN) DNA samples. There are different methods developed for DNA extraction from the small bloodstain and gloves, commonly found at crime scenes. In order to obtain STR profiles from LCN DNA samples, DNA extraction protocols, namely the automated $iPrep^{TM}$ $ChargeSwitch^{(R)}$ method, the automated $QIAcube^{TM}$ method, the automated $Maxwell^{(R)}$ 16 DNA $IQ^{TM}$ Resin method, and the manual $QIAamp^{(R)}$ DNA Micro Kit method, were evaluated. Extracted DNA was quantified by the $Quantifiler^{TM}$ Human DNA Quantification Kit and DNA profiled by $AmpFISTR^{(R)}$ $Identifiler^{(R)}$ Kit. Results were compared based on the amount of DNA obtained and the completeness of the STR profiles produced. The automated $iPrep^{TM}$ $ChargeSwitch^{(R)}$ and $QIAcube^{TM}$ methoas produced reproducible DNA of sufficient quantity and quality trom the dried blood spot. This two automated methods showed a quantity and quality comparable to those of the forensic manual standard protocols normally used in our laboratory. In our hands, the automated DNA extraction method is another obvious choice when the forensic case sample available is bloodstain. The findings of this study indicate that the manual simple modified $QIAamp^{(R)}$ DNA Micro Kit method is best method to recover high yields of amplifiable DNA from the numerous potential sources of LCN DNA samples.

• 한국응용곤충학회지
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• 제36권1호
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• pp.96-104
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• 1997

DNA 다형성을 이용한 누에 유전자 해석기술을 개발하기 위하여 광식성 누에 계통 J111과 비광식성계통 $C_3$의 DNA를 분리하여 유전자 은행을 제작하였다. 누에 유전자 은행은 genomic DNA를 EcoRI로 절단한후 pUC18에 ligation 시켜 DH5$\alpha$ E. coli에 형질전환 시켰다. 형질전환 후 얻어진 colony는 15개 누에 품종의 genomic DNA에 hybridization하였을 때 누에의 품종에 관계없이 highly repetitive, moderately repetitive 및 single 혹은 low copy number 로 구분되었다. RFLP마커에 적합한 single 및 low-copy number band만을 형성하는 colony probe을 신속하게 선발하고자 colony또는 genomic DNA로 hybridization하였다. Single 및 low-copy number의 특성을 가진 219개의 clone을 선발하여 Hind III등 8종의 제한효소별로 처리한 genomic DNA를 이용하여 다형성을 검정하여 J111과 $C_3$ 계통간 다형성을 보인 46개의 clone을 선발하였다. 선발된 clone의 일부를 J111과 $C_3$를 교배하여 얻은 $F_2$의 blot에 hybridization 결과 RFLP clone들이 양친검정에 이용가능하여 누에 RFLP 연관 지도 작성의 기반을 조성하게 되었다.

• Clinical and Experimental Reproductive Medicine
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• 제33권4호
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• pp.245-251
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• 2006

목 적: 제2형 당뇨의 위험도가 높은 PCOS 환자와 미토콘드리아와의 연관성을 보기 위하여 mitochondria DNA copy 수를 알아보고자 하였다. 연구방법: 연구대상자는 ESHRE의 진단 기준을 만족하는 다낭성난소증후군 여성 28명과 연령이 비슷하며 규칙적인 생리를 하는 여성 28명의 대조군을 대상으로 하였다. 연구대상자들의 genomic DNA는 혈액에서 추출하였으며, 미토콘드리아의 ribosomal RNA 부위를 중합효소 연쇄반응을 통해 증폭한 후 클로닝 하여 표준곡선을 작성한 후, 이를 토대로 다낭성난소증후군 환자의 미토콘드리아 initial quantity를 계산하였다. 결 과: Real-time PCR 결과 다낭성난소증후군 환자의 mtDNA copy 수는 $2,167,887.50{\pm}1,252,459.28$, 정상 대조군은 $1,726,410{\pm}407,858.519$으로 다낭성난소증후군 환자에서 약간 감소하였으나 유의한 차이는 없었다 (p=0.08). 결 론: 본 연구에서는 다낭성난소증후군 환자의 혈액에서 mtDNA copy 수를 조사한 결과, 정상 대조군과 다낭성난소증후군 환자 사이에서 mtDNA copy 수의 유의한 차이가 없었다. 다낭성난소증후군의 병인에는 상당히 복합적인 요소가 있는 것으로 보여지며 그 중 인종적, 지역적 그리고 유전적인 변이가 있는 것으로 보이기 때문에 앞으로 여러 인종에서 더 많은 다낭성난소증후군 환자를 대상으로 연구하여야 될 것으로 사료되는 바이다.

• Journal of Animal Science and Technology
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• 제65권4호
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• pp.767-778
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• 2023

The aim of the research is to identify that porcine oocytes can function as recipients for interspecies cloning and have the ability to develop to blastocysts. Furthermore each mitochondrial DNA (mtDNA) in interspecises cloned embryos was analyzed. For the study, mouse-porcine and porcine-porcine cloned embryos were produced with mouse fetal fibroblasts (MFF) and porcine fetal fibroblasts (PFF), respectively, introduced as donor cells into enucleated porcine oocytes. The developmental rate and cell numbers of blastocysts between intraspecies porcine-porcine and interspecies mouse-porcine cloned embryos were compared and real-time polymerase chain reaction (PCR) was performed for the estimate of mouse and porcine mtDNA copy number in mouse-porcine cloned embryos at different stages.There was no significant difference in the developmental rate or total blastocyst number between mouse-porcine cloned embryos and porcine-porcine cloned embryos (11.1 ± 0.9%, 25 ± 3.5 vs. 10.1 ± 1.2%, 24 ± 6.3). In mouse-porcine reconstructed embryos, the copy numbers of mouse somatic cell-derived mtDNA decreased between the 1-cell and blastocyst stages, whereas the copy number of porcine oocyte-derived mtDNA significantly increased during this period, as assessed by real-time PCR analysis. In our real-time PCR analysis, we improved the standard curve construction-based method to analyze the level of mtDNA between mouse donor cells and porcine oocytes using the copy number of mouse beta-actin DNA as a standard. Our findings suggest that mouse-porcine cloned embryos have the ability to develop to blastocysts in vitro and exhibit mitochondrial heteroplasmy from the 1-cell to blastocyst stages and the mouse-derived mitochondria can be gradually replaced with those of the porcine oocyte in the early developmental stages of mouse-porcine cloned embryos.

• 응용통계연구
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• 제22권1호
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• pp.115-127
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• 2009

The purpose of statistical analyses of array-CGH experiment data is to divide the whole genome into regions of equal copy number, to quantify the copy number in each region and finally to evaluate its significance of being different from two. Several statistical procedures have been proposed which include the circular binary segmentation, and a Gaussian based local regression for detecting break points (GLAD) by estimating a piecewise constant function. We propose in this note a penalized spline regression and its simultaneous confidence band(SCB) approach to evaluate the statistical significance of regions of genetic gain/loss. The region of which the simultaneous confidence band stays above 0 or below 0 can be considered as a region of genetic gain or loss. We compare the performance of the SCB procedure with GLAD and hidden Markov model approaches through a simulation study in which the data were generated from AR(1) and AR(2) models to reflect spatial dependence of the array-CGH data in addition to the independence model. We found that the SCB method is more sensitive in detecting the low level copy number alterations.

• Asian Pacific Journal of Cancer Prevention
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• 제16권1호
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• pp.87-90
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• 2015

Alterations in mitochondrial DNA (mtDNA) have been studied in various cancers. However, the clinical value of mtDNA copy number (mtCN) alterations in gastric cancer (GC) is poorly understood. In the present study, we investigated whether alterations in mtCNs might be associated with clinicopathological parameters in GC cases. mtCN was measured in 109 patients with GC by quantitative real-time PCR. Then, correlations with clinicopathological characteristics were analyzed. mtCN was elevated in 64.2% of GC tissues compared with paired, adjacent, non-cancerous tissue. However, the observed alterations in mtCN were not associated with any clinicopathological characteristics, including age, gender, TN stage, Lauren classification, lymph node metastasis, and depth of invasion. Moreover, Kaplan-Meier survival curves revealed that mtCN was not significantly associated with the survival of GC patients. In this study, we demonstrated that mtCN was not a significant marker for predicting clinical characteristics or prognosis in GC.