• Asian Pacific Journal of Cancer Prevention
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• 제15권21호
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• pp.9327-9333
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• 2014

Breast cancer is the second most common cancer and second leading cause of cancer deaths in women. Phosphatidylinositol-3-kinase (PI3K)/AKT pathway mutations are associated with cancer and phosphatidylinositol-4, 5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) gene mutations have been observed in 25-45% of breast cancer samples. Insulin growth factor binding protein-5 (IGFBP-5) can show different effects on apoptosis, cell motility and survival in breast cancer. We here aimed to determine the association between PIK3CA gene mutations and IGFBP-5 expressions for the first time in breast cancer patients. Frozen tumor samples from 101 Turkish breast cancer patients were analyzed with high resolution melting (HRM) for PIK3CA mutations (exon 9 and exon 20) and 37 HRM positive tumor samples were analyzed by DNA sequencing, mutations being found in 31. PIK3CA exon 9 mutations (Q546R, E542Q, E545K, E542K and E545D) were found in 10 tumor samples, exon 20 mutations (H1047L, H1047R, T1025T and G1049R) in 21, where only 1 tumor sample had two exon 20 mutations (T1025T and H1047R). Moreover, we detected one sample with both exon 9 (E542Q) and exon 20 (H1047R) mutations. 35% of the tumor samples with high IGFBP-5 mRNA expression and 29.4% of the tumor samples with low IGFBP-5 mRNA expression had PIK3CA mutations (p=0.9924). This is the first study of PIK3CA mutation screening results in Turkish breast cancer population using HRM analysis. This approach appears to be a very effective and reliable screening method for the PIK3CA exon 9 and 20 mutation detection. Further analysis with a greater number of samples is needed to clarify association between PIK3CA gene mutations and IGFBP-5 mRNA expression, and also clinical outcome in breast cancer patients.

• 한국수산과학회지
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• 제47권3호
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• pp.247-254
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• 2014

To investigate the acquisition of quinolone resistance, we examined mutations in the quinolone resistance-determining region (QRDR) of type II topoisomerase genes in ciprofloxacin (CIP)-resistant clinical isolates and in vitro mutants of Streptococcus parauberis. The CIP-resistant clinical isolates had one base change responsible for a Ser-79${\rightarrow}$Thr in the QRDR of parC. However, the CIP-resistant in vitro mutants had an altered QRDR of parC (Ser-79${\rightarrow}$Ile) that differed from that of the isolates. None of the CIP-resistant S. parauberis clinical isolates or in vitro mutants exhibited amino acid changes in gyrA or gyrB. However, even though involvement in the increased resistance was not clear, an Arg-449${\rightarrow}$Ser mutation outside of the QRDR of parE was detected in CIP-resistant mutant 2P1. These results suggest that the topoisomerase IV gene, parC (and possibly parE, as well), is the primary ciprofloxacin target in S. parauberis. Additionally we established a high-resolution melting (HRM) assay capable of detecting the dominant mutation in four type II topoisomerase genes conferring ciprofloxacin resistance. These rapid and reliable assays may provide a convenient method of surveillance for genetic mutations conferring antibiotic resistance.

• 농업과학연구
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• 제45권3호
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• pp.385-400
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• 2018

Marker-assisted backcrossing (MABC) is useful for selecting offspring with a highly recovered genetic background for a recurrent parent at early generation unlike rice and other field crops. Molecular marker sets applicable to practical MABC are scarce in vegetable crops including tomatoes. In this study, we used the National Center for Biotechnology Information- short read archive (NCBI-SRA) database that provided the whole genome sequences of 234 tomato accessions and selected 27,680 tag-single nucleotide polymorphisms (tag-SNPs) that can identify haplotypes in the tomato genome. From this SNP dataset, a total of 143 tag-SNPs that have a high polymorphism information content (PIC) value (> 0.3) and are physically evenly distributed on each chromosome were selected as a MABC marker set. This marker set was tested for its polymorphism in each pairwise cross combination constructed with 124 of the 234 tomato accessions, and a relatively high number of SNP markers polymorphic for the cross combination was observed. The reliability of the MABC SNP set was assessed by converting 18 SNPs into Luna probe-based high-resolution melting (HRM) markers and genotyping nine tomato accessions. The results show that the SNP information and HRM marker genotype matched in 98.6% of the experiment data points, indicating that our sequence analysis pipeline for SNP mining worked successfully. The tag-SNP set for the MABC developed in this study can be useful for not only a practical backcrossing program but also for cultivar identification and F1 seed purity test in tomatoes.

• Asian Pacific Journal of Cancer Prevention
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• 제17권3호
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• pp.1539-1546
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• 2016

Specific patterns of the hereditary breast and ovarian cancer (HBOC) syndrome are related to mutations in the BRCA1 gene. One hundred unrelated breast cancer patients were interviewed to obtain clinical symptoms and signs, pedigree and familial history of HBOC syndrome related cancer. Subsequently, data were calculated using the Breast and Ovarian Analysis of Disease Incidence and Carrier Estimation Algorithm (BOADICEA) risk prediction model. Patients with high score of BOADICEA were offered genetic testing. Eleven patients with high score of BOADICEA, 2 patients with low score of BOADICEA, 2 patient's family members and 15 controls underwent BRCA1 genetic testing. Mutation screening using PCR-HRM was carried out in 22 exons (41 amplicons) of BRCA1 gene. Sanger sequencing was subjected in all samples with aberrant graph. This study identified 10 variants in the BRCA1 gene, consisting of 6 missense mutations (c.1480C>A, c.2612C>T, c.2566T>C, c.3113A>G, c.3548 A>G, c.4837 A>G), 3 synonymous mutations (c.2082 C>T, c.2311 T>C and c.4308T>C) and one intronic mutation (c.134+35 G>T). All variants tend to be polymorphisms and unclassified variants. However, no known pathogenic mutations were found.

• 생명과학회지
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• 제29권5호
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• pp.524-529
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• 2019

엉겅퀴는 대표적인 다년생의 약용식물이다. 최근 국제적 추세에 따라 자국의 유전자원의 발굴, 보존 등이 강화 됨에 따라 인접국가와 국내 자생 엉겅퀴 계통을 판별 할 수 있는 기준 설정에 관한 연구의 필요성이 대두되고 있지만, 분자생물학적 판별 기술의 개발은 아직 미흡한 실정이다. 본 연구에서는 국내 토종과 해외 유래 엉겅퀴종의 기원을 판별하기 위해 엽록체에 존재하는 trnL-trnF와 MatK 유전자단편에서 SNP를 이용한 판별 프라이머를 확보하였으며 이를 보완하여 보다 신속하게 판별하기 위하여 HRM 분석 기술을 이용한 판별 마커와 그 조건을 확립하였다. 그러므로, 본 연구에서 개발된 SNP 마커는 다양한 지역 또는 국가에서 서식하는 엉겅퀴 종들의 신속한 확인을 위해 매우 유용하게 이용될 것으로 생각된다.

• 한국육종학회지
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• 제42권4호
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• pp.397-406
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• 2010

멜론과 참외의 국내 소비 시장이 확대됨에 따라 다양한 $F_1$ 품종이 개발되고 있다. 멜론과 참외의 $F_1$ 품종의 순도를 검정하기 위해 포장재배 등의 순도검정법이 이용되고 있으나 시간과 노력이 매우 많이 소요되기 때문에 분자마커를 이용한 순도검정법의 개발이 필요하다. 본 연구에서는 멜론의 EST 염기정보로부터 30개의 SNP 프라이머 조합을 고안하여 멜론과 참외의 순도 검정을 위한 HRM분석방법을 개발하였다. 멜론 두 품종과 참외 한 품종의 양친 사이에 HRM 해리곡선의 다형성을 보이는 10개의 마커를 선발하였으며 순도검정 마커를 선발하기 위해 blind test를 실시하였다. Blind test와 HRM 유전형 분석 결과가 일치하였으며 MEL SNP 2번과 12 마커를 이용하여 '레드 퀸'과 '얼쓰 VIP'의 $F_1$ 501개 개체에 대해 순도검정을 실시하였다. HRM분석한 결과 모두 이형집합체로 나타나 100%의 순도를 보였다. 또한 HRM 방법을 이용하여 개발한 SNP 마커를 CAPS 마커로 전환하였다. CAPS 마커는 HRM 분석 마커와 비교하여 볼 때 멜론과 참외의 순도검정용 마커로 더 유용하게 활용될 수 있을 것으로 기대된다.

• 대한임상검사과학회지
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• 제49권1호
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• pp.28-39
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• 2017

잔류성 유기 오염 물질은 후성학적 메커니즘과 비만의 발달에 영향을 줄 수가 있다. 폴리브롬화 디페닐 에테르는 주요한 잔류성 유기 오염 물질 중 하나이며, 난연제로 널리 쓰인다. 출생전 잔류성 유기 오염 물질과 같은 내분비교란물질에 노출시 LINE-1 (long interspersed nuclear elements)의 global DNA 메틸화와 비만 위험도의 증가에 영향을 미칠 수 있다. 따라서, 이번 연구는 임신한 스프라그-돌리 백서를 이용하여 태반과 모유를 통하여 전달된 BDE-47, BDE-209가 LINE-1에서의 후성학적인 변화와 obesogen으로서 발달과정에 따른 유전적 비만 감수성의 증가에 영향을 줄 수 있는지에 대해서 보고자 하였다. 어미와 새끼에서 LINE-1의 광범위 DNA 메틸화와 비만과 관련된 유전자 발현은 methylation-sensitive high resolution melting analysis (MS-HRM), direct bisulfite sequencing와 quantitative real time polymerase chain reaction (qPCR)을 사용하여 각각 분석하였다. MS-HRM 결과는 출생 후 4일의 노출군 새끼에서 (4마리 중 2마리) LINE-1의 광범위 DNA 저메틸화 양상을 보여주었지만, bisulfite sequencing은 노출군과 비노출군에서 차이가 없었다. ${\beta}$-산화 경로와 adipokines과 관련된 어미의 유전자 발현은 두 그룹간 차이를 보였다. 반면에, 새끼의 유전자 발현은 비슷한 양상을 나타내었다. ${\beta}$-산화 경로와 비만과 관련된 유전자 발현 중 $PPAR-{\alpha}$를 제외하고는 출생 시에 유의하게 증가하였다. 결론적으로, 이번 연구는 BDE-47, BDE-209의 동시 노출이 태반과 모유를 통해서 새끼에서의 후성학적인 변화와 비만과 관련된 유전자 발현 변화에 영향을 미칠 수 있는 것을 보여주었다.

• Journal of Plant Biotechnology
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• 제42권1호
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• pp.6-12
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• 2015

Medicinal plants resources are becoming important assets since their usages have been expanded to the development of functional foods for human health, more attractive cosmetics, and pharmaceutical industries. However, their phylogenetic origins and names are different from each country and quite often they are mixed each other resulting in the confusion for consumers. In particular, when they are very similar based on their morphological characteristics and distributed as dried roots, it is extremely difficult to differentiate their origins even by specialists. Recently, "DNA barcodes" have been extensively applied to identify their origin of medicinal plant species. In this review, we tried to overview the current research achievements for the development of suitable "DNA barcodes" regarding to the differentiation of medicinal plant species. Furthermore, more advanced techniques including amplification refractory mutation system (ARMS)-PCR, multiplex single base extension (MSBE), high-resolution melting (HRM) curve analyses are also discussed for their practical applications in the authentification of particular medicinal plant species.

• 원예과학기술지
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• 제33권5호
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• pp.730-736
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• 2015

Tomato spotted wilt virus (TSWV) causes one of the most destructive viral diseases that threatens global tomato production. Sw-5b was reported as the resistance gene effective against TSWV. The objective of this research was to develop a single-nucleotide polymorphism (SNP) marker to distinguish tomato cultivars resistant to TSWV from susceptible cultivars for marker-assisted breeding. First, we determined genotypes for TSWV resistance in 32 commercial tomato cultivars using the previously reported Sw-5b gene-based marker. Then, DNA sequences of Sw-5b alleles in tomato cultivars showing resistant or susceptible genotypes were analyzed; a single SNP was found to distinguish tomato cultivars resistant to TSWV from susceptible cultivars. Based on the confirmed SNP, a SNP primer pair was designed. Using this new SNP sequence and high-resolution melting analysis, the same 32 tomato cultivars were screened. The results were perfectly correlated with those from screening with the Sw-5b gene-based marker. These results indicate that the SNP maker developed in this study will be useful for better tracking of resistance to TSWV in tomato breeding.

• Asian Pacific Journal of Cancer Prevention
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• 제17권2호
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• pp.603-608
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• 2016

Background: The investigation of mutation patterns in oncogenes potentially can make available a reliable mechanism for management and treatment decisions for patients with colorectal cancer (CRC). This study concerns the rate of KRAS and BRAF genes mutations in Iranian metastatic colorectal cancer (mCRC) patients, as well as associations of genotypes with clinicopathological features. Materials and Methods: A total of 1,000 mCRC specimens collected from 2008 to 2012 that referred to the Mehr Hospital and Partolab center, Tehran, Iran enrolled in this cross sectional study. Using HRM, Dxs Therascreen and Pyrosequencing methods, we analyzed the mutational status of KRAS and BRAF genes in these. Results: KRAS mutations were present in 33.6% cases (n=336). Of KRAS mutation positive cases, 85.1% were in codon 12 and 14.9% were in codon 13. The most frequent mutation at KRAS codon 12 was Gly12Asp; BRAF mutations were not found in any mCRC patients (n=242). In addition, we observed a strong correlation of KRAS mutations with some clinicopathological characteristics. Conclusions: KRAS mutations are frequent in mCRCs while presence of BRAF mutations in these patients is rare. Moreover, associations of KRAS genotypes with non-mucinous adenocarcinoma and depth of invasion (pT3) were remarkable.