• Asian Pacific Journal of Cancer Prevention
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• 제14권11호
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• pp.6619-6623
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• 2013

Background:The aim of the research was to explore a cost effective, fast, easy to perform, and sensitive method for epidermal growth factor receptor (EGFR) mutation testing. Methods: High resolution melting analysis (HRM) was introduced to evaluate the efficacy of the analysis for dectecting EGFR mutations in exons 18 to 21 using formalin-fixed paraffin-embedded (FFPE) tissues and plasma free DNA from 120 patients. Results: The total EGFR mutation rate was 37.5% (45/120) detected by direct sequencing. There were 48 mutations in 120 FFPE tissues assessed by HRM. For plasma free DNA, the EGFR mutation rate was 25.8% (31/120). The sensitivity of HRM assays in FFPE samples was 100% by HRM. There was a low false-positive mutation rate but a high false-negative rate in plasma free DNA detected by HRM. Conclusions: Our results show that HRM analysis has the advantage of small tumor sample need. HRM applied with plasma free DNA showed a high false-negative rate but a low false-positive rate. Further research into appropriate methods and analysis needs to be performed before HRM for plasma free DNA could be accepted as an option in diagnostic or screening settings.

• Journal of Genetic Medicine
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• 제12권2호
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• pp.100-108
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• 2015

Purpose: Conventional methods for the prenatal detection of fetal RhD status involve invasive procedures such as fetal blood sampling and amniocentesis. The identification of cell-free fetal DNA (cffDNA) in maternal plasma creates the possibility of determining fetal RhD status by analyzing maternal plasma DNA. However, some technical problems still exist, especially the lack of a positive control marker for the presence of fetal DNA. Therefore, we assessed the feasibility and accuracy of fetal RHD genotyping incorporating the RASSF1A epigenetic fetal DNA marker from cffDNA in the maternal plasma of RhD-negative pregnant women in Korea. Materials and Methods: We analyzed maternal plasma from 41 pregnant women identified as RhD-negative by serological testing. Multiplex real-time PCR was performed by amplifying RHD exons 5 and 7 and the SRY gene, with RASSF1A being used as a gender-independent fetal epigenetic marker. The results were compared with those obtained by postnatal serological analysis of cord blood and gender identification. Results: Among the 41 fetuses, 37 were RhD-positive and 4 were RhD-negative according to the serological analysis of cord blood. There was 100% concordance between fetal RHD genotyping and serological cord blood results. Detection of the RASSF1A gene verified the presence of cffDNA, and the fetal SRY status was correctly detected in all 41 cases. Conclusion: Noninvasive fetal RHD genotyping with cffDNA incorporating RASSF1A is a feasible, reliable, and accurate method of determining fetal RhD status. It is an alternative to amniocentesis for the management of RhD-negative women and reduces the need for unnecessary RhIG prophylaxis.

• Genomics & Informatics
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• 제17권4호
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• pp.42.1-42.6
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• 2019

Robust identification of genetic alterations is important for the diagnosis and subsequent treatment of tumors. Screening for genetic alterations using tumor tissue samples may lead to biased interpretations because of the heterogeneous nature of the tumor mass. Liquid biopsy has been suggested as an attractive tool for the non-invasive follow-up of cancer treatment outcomes. In this study, we aimed to verify whether the mutations identified in primary tumor tissue samples could be consistently detected in plasma cell-free DNA (cfDNA) by digital polymerase chain reaction (dPCR). We first examined the genetic alteration profiles of three colorectal cancer (CRC) tissue samples by targeted next-generation sequencing (NGS) and identified 11 non-silent amino acid changes across six cancer-related genes (APC, KRAS, TP53, TERT, ARIDIA, and BRCA1). All three samples had KRAS mutations (G12V, G12C, and G13D), which were well-known driver events. Therefore, we examined the KRAS mutations by dPCR. When we examined the three KRAS mutations by dPCR using tumor tissue samples, all of them were consistently detected and the variant allele frequencies (VAFs) of the mutations were almost identical between targeted NGS and dPCR. When we examined the KRAS mutations using the plasma cfDNA of the three CRC patients by dPCR, all three mutations were consistently identified. However, the VAFs were lower (range, 0.166% to 2.638%) than those obtained using the CRC tissue samples. In conclusion, we confirmed that the KRAS mutations identified from CRC tumor tissue samples were consistently detected in the plasma cfDNA of the three CRC patients by dPCR.

• Journal of Nutrition and Health
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• 제34권4호
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• pp.401-408
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• 2001

The spontaneous frequency of genetic damage and the possible relationship of this damage to total radical-trapping antioxidant potential(TRAP) and antioxidant vitamins, including plasma levels of $\alpha$-carotene, $\beta$-carotene, cryptoxanthin, retinol, $\alpha$-tocopherol and ${\gamma}$-tocopherol in humans were investigated in 57 subjects using two indices of genetic damage, SCE & HFC frequency. The mean of SCE and HFC frequencies were weakly correlated with plasma TRAP(r=-0.305, p<0.1 for SCEs: r=-0.297, p<0.1 for HFCs, respectively), but those were strongly negatively correlated with plasma $\beta$-carotence(r=-0.385, p<0.01 for SCEs : r=-0.392, p<0.01 for HFCs) and cryptoxanthin(r=-0.312, p<0.05 for SCEs : r=0.335, p<0.05 for HFCs, respectively) levels in the subjects. However, those DNA damage markers including SCE and HFC did not correlate with either plasma $\alpha$-carotene, $\alpha$-tocopherol or retinol concentrations. The mean of SCE and HFC frequencies were positively correlated with plasma ${\gamma}$-tocopherol level(r=0.421, p<0.01 for SCEs : r=0.399, p<0.01 for HFCs, respectively). These findings indicate that increased cytogenetic DNA changes, as determined by SCE and HFC frequencies are possibly associated with generation of free radicals in lymphocytes and decreased plasma antioxidant vitamin($\beta$-carotene and cryptoxanthin) status in the subjects. (Korean J Nutrition 34(4) : 401~08, 2001)

• Journal of Genetic Medicine
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• 제8권1호
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• pp.1-16
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• 2011

현재 사용되고 있는 침습적 산전진단법(양수천자, 융모막샘플링)은 1-2%의 태아 손실이 초래되어, 비침습적 산전진단법이 산전진단의 궁극적인 목표로 대두되어 왔다. 1997년 Dr. Lo에 의해서 임신부 혈장 내에 세포 유리 태아 DNA (cffDNA)의 존재가 발견된 후 비침습적 산전진단의 새로운 가능성이 열렸으며, 과거 10년간 이에 대한 연구의 많은 진전을 보여주고 있다. 최근에 cffDNA를 이용한 Hemophilia A와 듀센형 근이영양증 등 반성 유전병(X-linked disorders) 진단에 필수적인 산전태아의 성 판정과 RhD-음성 임신부에서 태아의 RhD유전자 핵형 분석 등이 이미 외국에서 임상적으로 적용되고 있으나, 한국에서는 아직 실용화되지 않고 있다. CffDNA의 임상 사용에는 여전히 많은 제약점이 있으며, 이는 임신부 혈장 내 cffDNA 양에 비해 많은 양의 모태 DNA가 존재하고, 종래에 사용되었던 특이적인 Y염색체 유전자(Y-specific gene)는 남아 태아 임신 시에만 적용된다는 것에 기인한 다. 따라서 모든 태아에 적용할 수 있는 태아 성과 무관한 마커(sex-independent universal fetal marker as internal positive controls)가 요구되며, 이를 이용하여 정확한 태아 DNA를 검출할 수 있다. 본 연구진은 국내 처음으로 임신부 혈장 내에 cffDNA를 이용하여 SRY 유전자, RhD-exon 7, 태아 성과 무관한 DNA마커(universal fetal DNA marker)로써 RASSF1A 유전자를 실시간 중합효소연쇄반응(RT- PCR)을 사용하여 뛰어난 결과를 얻었다. 이는 한국에서 처음으로 성공적으로 시도된 것이다. 연구결과에서 산전 태아 성 판별과 산후 태아의 성이 100% 일치하였으며, 임신 주기별 SRY 수치는 임신이 진행할수록 증가함을 확인할 수 있었다. 따라서 이러한 방법은 혈우병 A, 듀센형 근이영양증, 선천성 부신증식증과 연골 무형성증의 진단과 치료 상담에 이용할 수 있으며 50%에서 침습적인 방법을 줄일 수가 있다. 또한, RhD-음성 임신부 대상으로 태아의 성 판정과 RhD 태아 유전자형을 분석한 결과 RhD-음성 태아를 정확히 검출함으로써 앞으로 기존 양수천자 등 침습적 검사를 대체할 수 있을 것이다. 특히 이는 치료가 필요 없는 RhD-음성 태아에서 RhD-면역글로불린의 예방적 치료를 사전에 막을 수 있어, 임신부 건강을 보호하고 의료 비용을 줄일 수 있는 큰 장점을 가진다. 한국에서 최초로 시도된 임신부 혈장 내 cffDNA를 이용한 본 연구의 성공은 비침습적 산전진단 임상 적용의 새 길을 제시하였다. 따라서 이를 각 유전질환의 산전진단에 유용하게 활용하는 것은 태아와 임신부의 건강 증진과 의료비용 절약 등 개인과 국가에 많은 기여를 할 것으로 사료된다.

• Genomics & Informatics
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• 제15권1호
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• pp.2-10
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• 2017

Early detection and proper management of kidney rejection are crucial for the long-term health of a transplant recipient. Recipients are normally monitored by serum creatinine measurement and sometimes with graft biopsies. Donor-derived cell-free deoxyribonucleic acid (cfDNA) in the recipient's plasma and/or urine may be a better indicator of acute rejection. We evaluated digital PCR (dPCR) as a system for monitoring graft status using single nucleotide polymorphism (SNP)-based detection of donor DNA in plasma or urine. We compared the detection abilities of the QX200, RainDrop, and QuantStudio 3D dPCR systems. The QX200 was the most accurate and sensitive. Plasma and/or urine samples were isolated from 34 kidney recipients at multiple time points after transplantation, and analyzed by dPCR using the QX200. We found that donor DNA was almost undetectable in plasma DNA samples, whereas a high percentage of donor DNA was measured in urine DNA samples, indicating that urine is a good source of cfDNA for patient monitoring. We found that at least 24% of the highly polymorphic SNPs used to identify individuals could also identify donor cfDNA in transplant patient samples. Our results further showed that autosomal, sex-specific, and mitochondrial SNPs were suitable markers for identifying donor cfDNA. Finally, we found that donor-derived cfDNA measurement by dPCR was not sufficient to predict a patient's clinical condition. Our results indicate that donor-derived cfDNA is not an accurate predictor of kidney status in kidney transplant patients.

• Journal of Genetic Medicine
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• 제7권1호
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• pp.53-58
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• 2010

목 적: 모체 혈장으로부터 가장 효과적으로 세포 유리 DNA(cell free DNA, cf-DNA)를 추출하는 방법을 찾기 위해 우리는 viral DNA 추출 방법과 일반 혈액DNA 추출 방법을 이용하여 비침습적 임신 초기 태아 성별 확인 결과를 비교하였다. 대상 및 방법: 임신 초기 44명의 임산부로부터 모여진 모체 혈장을 통한 전향적 연구가 구성되었다. Cf-DNA는 viral DNA 추출 방법과 일반 혈액 DNA 추출 방법을 이용하여 각각 추출되었다. 정량 형광-중합효소 연쇄 반응(QF-PCR)을 이용하여SRY 와AMXY 유전자를 검출하였다. QF-PCR의 진단 정확도는 최종 분만 기록을 토대로 결정하였다. 결 과: 전체 44명의 여성이 실험에 참여하였지만, 최종 분만 기록은 단지 36명의 여성에서 획득하였다. 이들 중 16명은 남아를 20명은 여아를 임신하였다. 두 추출 방법에서 태아 성별의 진단적 정확도는 일반 혈액 DNA 추출 방법에 경우 63.9% (23/26)였으며 viral DNA 추출 방법에 경우 97.2% (35/36) 였다. 결 론: QF-PCR을 이용한 비침습적 임신초기 태아 성별 확인에 있어 viral kit를 사용하는 것이 높은 진단적 정확도를 이끌 수 있을 것으로 사료된다.

• Journal of Nutrition and Health
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• 제39권8호
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• pp.773-785
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• 2006

Vitamin E in the body system plays an important role in preventing chronic diseases by decreasing the oxidative stress by free-radicals. However, there are not enough researches on analyzing the primary factors affecting vitamin E levels in the blood in Korean adults. Therefore, the purpose of this research was to examine blood tocopherol levels and the primary factors affecting the status. A complete lifestyle survey was performed on 314 Korean adult men and surveyed their smoking, drinking and exercising habits. The average plasma level of ${\alpha}-\;and\;{\gamma}-tocopherol$ showed similar mutual relations with plasma total cholesterol (TC), triglyceride (TG), or low density lipoprotein cholesterol (LDL-C) levels (p<0.001). Plasma ${\alpha}-tocopherol$ level of the subjects did not show any difference as smoking, drinking and exercising habits changed. However, ${\gamma}-tocopherol$ per TG showed much lower figure in smokers than non smokers (p < 0.05). Amongst diet factors, plasma ${\alpha}-tocopherol$ level showed negative correlations with Vitamin E intake, while ${\gamma}-tocopherol$ level showed positive correlations with Vitamin E intake. Erythrocyte superoxide dismutase (SOD) activity and plasma tocopherol showed negative correlations, and catalase activity and plasma ${\alpha}-tocopherol$ showed positive correlationship. The level of cell DNA damage of Iymphocyte and plasma ${\alpha}-\;or\;{\gamma}-tocopherol$ showed negative correlations. As a result of this research, the factors that affect Korean adult men's plasma ${\alpha}-tocopherol$ level are plasma TG, LDL-C and cell DNA damage in Iymphocyte, while the factors that affect ${\gamma}-tocopherol$ level are plasma TG, LDL-C and vitamin E intake based on multiple regression analysis. These findings implies that the level of different types of tocopherol depends on slightly different factors. A further research is needed on the factors involved in the differentiation of the types of tocopherol.

• Journal of Nutrition and Health
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• 제36권3호
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• pp.255-261
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• 2003

Food irradiation has been steadily increasing in many countries in line with increasing international trade and concerns about naturally occurring harmful contaminants in food. Although irradiation provides an excellent safeguard for the consumer by destroying almost 100% of harmful bacteria, it is necessary to ensure the safety of irradiated foods. This study was performed to investigate the effect of an irradiated diet on lipid peroxidation in the plasma, liver, small intestinal mucosa, and lymphocyte DNA damage in mice. Eight-week old ICR mice were assigned to two groups to receive either non-irradiated or irradiated (10 kGy) diets containing 20.38% fish powder and 6.06% sesame seeds for 4 weeks. The resulting changes in the degrees of lipid peroxidation were evaluated based on the level of plasma and liver thiobarbituric acid reactive substance (TBARS), transmission electron micrograph of jejunal mucosa, and free radical-induced oxidative DNA damage in lymphocytes, as measured by alkaline comet assay (single cell gel electrophoresis). The peroxide values of the gamma irradiated diet were measured every week, and the sample for comet assay was taken at the end of the four week experimental period. There was no significant difference in food efficiency ratio between the two groups. The peroxide values of the diet were immediately increased to 35.5% after gamma irradiation and kept on increasing during storage. After 4 weeks, no differences in tissue or plasma TBARS value were observed between the two groups, but epithelial cells of jejumum showed osmiophillic laminated membranous structures, considered as myelin figures,. The oxidative DNA damage expressed as tail moment (TM) increased 30% in the blood lymphocytes of the mice fed the irradiated diet. In conclusion, the comet assay sensitively detected differences in lymphocyte DNA damage after feeding with the irradiated diet for 4 weeks. However, in order to ensure the safety of irradiated foods, it would be more useful to conduct a long-term feeding regimen using an irradiated diet and examine the level of lipid peroxidation and the state of oxidative stress in a greater range of organs.

• Journal of Genetic Medicine
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• 제12권2호
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• pp.66-71
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• 2015

Down syndrome screening with cell-free DNA (cfDNA) in the maternal plasma has recently received much attention in the prenatal diagnostic field. Indeed, a large amount of evidence has already accumulated to show that screening tests with cfDNA are more sensitive and specific than conventional maternal serum and/or ultrasound screening. Globally, more than 1,000,000 of these noninvasive prenatal tests (NIPTs) have been performed to date. There are several different methods for NIPTs that are currently commercially available, including shotgun massively parallel sequencing, targeted massively parallel sequencing, and single nucleotide polymorphism (SNP)-based methods. All of these methods have their own advantages and disadvantages. In this review, I will focus specifically on the SNP-based NIPT.