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Lee S.Y.,Bio Core Co. | Shim S.H.,Korea University | Youn J.-P.,Bio Core Co. | Kim S.J.,Bio Core Co. | And 7 more authors.
Biochip Journal | Year: 2015

The probability of hereditary diseases occurring in the fetus and the childbearing age of the recently-married population have both rapidly increased over the last 10 years. That occupies a large part of such genetic diseases was greater than or equal to the number of chromosomes and genes, the probability of these chromosomal abnormalities occurring increases as the mother’s age increases. Regarding these genetic diseases that are caused by chromosomal abnormalities, it has been possible to reduce the pain of the mother and child if the abnormalities are detected early because schemes can be prepared to address them; therefore, early diagnosis is important. Recently, as part of an analysis that involved the use of very small samples, a digital PCR that allowed for the simultaneous processing of a number of samples was actively developed due to the corresponding advantage. Digital-PCR technology means that a real-time diagnosis with a high sensitivity can be obtained, and it enables the development of a variety of diagnostic techniques-without requiring the use of NGS deep sequencing- through advantages such as digitized measurement results. After extracting the circulating nucleic acid from maternal blood for the screening of fetal DNA, after first confirming that the blood contained fetal DNA, the nucleic acid was selectively applied to the digital PCR for the detection of chromosomal abnormalities, thereby developing a new detection application. The results of 43 samples were analyzed, and the experimental results of the newly developed analytical method show that 9 samples are “high risk,” whereas 34 samples are “low risk.” We consider the accuracy of each test as very reliable. The non-invasive prenatal-screening methods that use digital PCR were developed in this research study due to their lower monetary costs that are derived from an experimental testing time that is less than that of the conventional NGS; provided that the mother is easily accessible, this method can confirm the health status of a fetus. Also, the biomarker knowledge and the analysis methods that were developed in this research study can be applied in chromosomal-abnormality tests. It is expected that the development of a non-invasive examination method to replace the existing invasive testing method will be useful in the improvement of maternal and fetal safety. © 2015, The Korean BioChip Society and Springer-Verlag Berlin Heidelberg.


Kim T.,Yonsei University | Park J.C.,BioCore Co. | Park J.C.,Hanyang University | Roh M.R.,Yonsei University | And 3 more authors.
Dermatology | Year: 2010

Epidermodysplasia verruciformis (EV) is a rare genetic disease characterized by abnormal susceptibility to infection with EV-related human papillomavirus (HPV), now known as the β-papillomavirus (β-PV). Clinically specific β-PV-type-associated EV, especially HPV-5 and -8, shows a high rate of progression to squamous cell carcinoma (SCC). In this report, we describe a 39-year-old Korean man with HPV-22b-associated EV who developed a rapidly progressing SCC. The patient presented with a huge destructive mass on the nose. Histopathological evaluation of the mass was compatible with well-differentiated SCC. HPV typing results from both EV and SCC specimens demonstrated HPV-22b which has not been considered to be associated with SCC in EV patients so far. The patient underwent surgical excision and postoperative radiotherapy for locoregional control. This is the first report presenting the association of an SCC arising from previous EV with HPV-22b infection only. © 2010 S. Karger AG, Basel.


Kim J.,Ewha Womans University | Jung D.,Ewha Womans University | Lee W.S.,BioCore Co. | Park J.-K.,Ewha Womans University
Journal of Shellfish Research | Year: 2015

The correct identification of oyster species is essential for both aquaculture and taxonomic study, but it has often been a challenging task due to enormous morphological variation in shell morphs with ecophenotypic origins. The difficulty of species identification based entirely on shell characters has raised the need for developing an accurate, rapid tool for the identification and discrimination of oyster species. In this study, a DNA microarray-based identification system was established for eight commercially important oyster species (Crassostrea ariakensis, Crassostrea gigas, Crassostrea sikamea, Crassostrea nippona, Crassostrea angulata, Ostrea circumpicta, Ostrea denselamellosa, and Saccostrea kegaki). Sixteen species-specific probes developed in this study unambiguously distinguished eight target oyster species with no false-positive or false-negative signals. Of the eight oyster species examined, three Crassostrea species, C. angulata, C. gigas, and C. sikamea, which are indistinguishable by morphology, could be precisely identified using species-specific hybridization probes. The DNA microarray-based identification system developed in this study offers a very effective and reliable tool for eight oyster species, most of which are of commercial value and/or ecological significance in the macrobenthic community of offshore marine environments.


Lim S.,Biocore Co. | Lim S.,Hanyang University | Youn J.P.,Biocore Co. | Moon S.O.,National Forensic Service | And 6 more authors.
Biochip Journal | Year: 2015

Human genomic short tandem repeats (STRs) are specific gene sequences containing base pairs that are repeatedly arranged. From the various methods available for identifying individuals, STR analysis is the method most widely used in forensic science. Conventional polymerase chain reaction (PCR) was used for STR typing, and the PCR products, consisting of amplified STR loci (amplicons) were electrophoresed with a DNA analysis device. About ten STR markers were used as standards for STR characterization and analysis of size. Extensive efforts are currently being made to explore the STR sequence diversity by analyzing multiple chromosomal loci using next generation sequencing (NGS). NGS greatly facilitates STR marker analysis for individual identification and the complete sequencing of any given sample through concurrent high-throughput sequencing of multiple loci. As a result, NGS data are more accurate and comprehensive compared to that in a conventional database. In order to overcome the limitations of the currently used size-based STR analysis method, we have typed the DNA of 13 combined DNA index system (CODIS) STR markers using Ion PGM. This kit, developed by Ion Torrent, enables the analysis of STR alleles and the sequencing of corresponding genes. We then analyzed the alleles using the HID_STR_Genotyper plugin. Through this, we determined the sequence of the allele type 15 at the D3S1358 locus in all NIST SRM 2391b samples. This allowed for the verification of the exact type of allele, which the conventional size-based STR typing methods could not resolve. © 2015, The Korean BioChip Society and Springer-Verlag Berlin Heidelberg.


Kim S.J.,BioCore Co. | Yu S.-Y.,Hanyang University | Yu S.-Y.,BioCore Co. | Yoon H.-J.,BioCore Co. | And 4 more authors.
Biochip Journal | Year: 2015

Bisphenol A (BPA), an widely used environmental chemical, is encircled to human life. However, we generally do not know whether or not it can cause negative health effects. One of the representative epigenetic changes that inhibit gene expression is DNA methylation, which has been very well studied in association with cancer and development. Gene function is changed by DNA methylation; however, its genetic code does not change. Our study hypothesized that a post-transcriptional change in DNA occurs due to exposure to BPA. These changes then cause regulation of microRNA and gene expression. To identify these successional regulations, we conducted microarraybased assays. For validation, also we conducted bisulfite sequencing, quantitative real-time PCR, miRNA inhibitor assay, and Western blotting. We found 1,751 hypo-methylation changed regions, and several micro- RNA had included methylated-regions. miR-22 was also hypomethylated (chr17:1563947-1564031) by BPA-exposure, and expression of miR-22 was up-regulated in an miRNA array and real-time PCR. miR- 22 has been reported to inhibit estrogen signaling by direct targeting of the estrogen receptor alpha mRNA. Taking notice of this point, we analyzed gene expression profiles that included its predicted targets. In the present study, we found the cause of hypomethylation of miR-22 and negative regulation of its apoptosisrelated target gene expression by BPA-exposure. These results suggests that BPA can alter sequential genomic appearances in HepG2 cells, a potentially affection of BPA toxicity. Also, the results of our study support that toxicology study need to integrated analysis of array-based assays for help in understanding of the molecular action of environmental toxicants. © 2015, The Korean BioChip Society and Springer-Verlag Berlin Heidelberg.


Ahn J.J.,Hanyang University | Kim J.-H.,Bio Core Co. | Kim Y.,Hanyang University | Hong J.Y.,Hanyang University | And 3 more authors.
Analytical Biochemistry | Year: 2015

Locked nucleic acid (LNA) is a modified RNA nucleotide that can be incorporated at specific positions to generate probes with the desired length, melting temperature (TM), and specificity. Here, we describe a method of multiplex genotyping based on dramatic shifts in the TM of a single dual-labeled LNA probe. Using this method, two varieties of the hairtail fish Trichiurus lepturus can be distinguished from each other, as well as from Trichiurus japonicus, based on a 1- to 2-bp difference in a fragment of mitochondrial cytochrome oxidase subunit 1. The shift in TM was 15 °C for a 1-bp mismatch and 27 °C for a 2-bp mismatch, indicating remarkable specificity. We anticipate that the method will be widely useful in applications such as species identification that require accurate, multiplex, and efficient detection of DNA polymorphisms. © 2015 Elsevier Inc.


Kim E.Y.,Yonsei University | Cho E.N.,Yonsei University | Park H.S.,Yonsei University | Kim A.,Yonsei University | And 5 more authors.
BMC Cancer | Year: 2016

Background: Biopsy for lung cancer diagnosis is usually done at a single site. But it is unclear that genetic information at one biopsy site represents that of other lesions and is sufficient for therapeutic decision making. Methods: Non-synonymous mutations and insertions/deletions of 16 genes containing actionable mutations, and intron 2 deletion polymorphism of Bcl2-like11 were analyzed in 41 primary tumor and metastatic lymph node (L/N) matched, pStage IIA ~ IIIA non-small cell lung cancer (NSCLC) samples using a next generation sequencing based technique. Results: A total of 249 mutations, including 213 non-synonymous mutations, 32 deletions, and four insertions were discovered. There was a higher chance of discovering non-synonymous mutations in the primary tumors than in the metastatic L/N (138 (64.8%) vs. 75 (35.2%)). In the primary tumors, 106 G > A:C > T transitions (76.8%) of 138 non-synonymous mutations were detected, whereas in the metastatic L/N, 44 (58.7%) of 75 were discovered. A total 24 (11.3%) out of 213 non-synonymous mutations were developed in the context of APOBEC signature. Of those, 21 (87.5%) was detected in the primary tumors and 4 (16.7%) was detected in the metastatic L/N. When the mutation profiles between primary tumor and metastatic L/N were compared, 13 (31.7%) of 41 cases showed discrepant mutation profile. There were no statistically significant differences in disease free survival and overall survival between groups showing identical mutation profiles and those with discrepancy between primary and metastatic L/N. Conclusions: Genetic heterogeneity between the primary and L/N metastatic lesions is not infrequent finding to consider when interpreting genomic data based on the result of one site inspection. A large prospective study may be needed to evaluate the impact of genetic heterogeneity on the clinical outcomes of NSCLC patients. © 2016 Kim et al.


PubMed | Bio Core Co. and Hanyang University
Type: | Journal: Analytical biochemistry | Year: 2015

Locked nucleic acid (LNA) is a modified RNA nucleotide that can be incorporated at specific positions to generate probes with the desired length, melting temperature (TM), and specificity. Here, we describe a method of multiplex genotyping based on dramatic shifts in the TM of a single dual-labeled LNA probe. Using this method, two varieties of the hairtail fish Trichiurus lepturus can be distinguished from each other, as well as from Trichiurus japonicus, based on a 1- to 2-bp difference in a fragment of mitochondrial cytochrome oxidase subunit 1. The shift in TM was 15C for a 1-bp mismatch and 27C for a 2-bp mismatch, indicating remarkable specificity. We anticipate that the method will be widely useful in applications such as species identification that require accurate, multiplex, and efficient detection of DNA polymorphisms.


PubMed | Yonsei University, Bio Core Co. and Hanyang University
Type: | Journal: BMC cancer | Year: 2016

Biopsy for lung cancer diagnosis is usually done at a single site. But it is unclear that genetic information at one biopsy site represents that of other lesions and is sufficient for therapeutic decision making.Non-synonymous mutations and insertions/deletions of 16 genes containing actionable mutations, and intron 2 deletion polymorphism of Bcl2-like11 were analyzed in 41 primary tumor and metastatic lymph node (L/N) matched, pStage IIA~IIIA non-small cell lung cancer (NSCLC) samples using a next generation sequencing based technique.A total of 249 mutations, including 213 non-synonymous mutations, 32 deletions, and four insertions were discovered. There was a higher chance of discovering non-synonymous mutations in the primary tumors than in the metastatic L/N (138 (64.8%) vs. 75 (35.2%)). In the primary tumors, 106 G > A:C > T transitions (76.8%) of 138 non-synonymous mutations were detected, whereas in the metastatic L/N, 44 (58.7%) of 75 were discovered. A total 24 (11.3%) out of 213 non-synonymous mutations were developed in the context of APOBEC signature. Of those, 21 (87.5%) was detected in the primary tumors and 4 (16.7%) was detected in the metastatic L/N. When the mutation profiles between primary tumor and metastatic L/N were compared, 13 (31.7%) of 41 cases showed discrepant mutation profile. There were no statistically significant differences in disease free survival and overall survival between groups showing identical mutation profiles and those with discrepancy between primary and metastatic L/N.Genetic heterogeneity between the primary and L/N metastatic lesions is not infrequent finding to consider when interpreting genomic data based on the result of one site inspection. A large prospective study may be needed to evaluate the impact of genetic heterogeneity on the clinical outcomes of NSCLC patients.


Suh J.H.,Chung - Ang University | Lee Y.Y.,Chung - Ang University | Lee H.J.,BioCore Co. | Kang M.,Chung - Ang University | And 4 more authors.
Journal of Pharmaceutical and Biomedical Analysis | Year: 2013

A novel dispersive liquid-liquid microextraction method based on solidification of floating organic droplets (DLLME-SFO) technique was developed for the determination of duloxetine in human plasma samples by high performance liquid chromatography with fluorescence detection (HPLC-FLD). During the extraction procedure, plasma protein was precipitated by using a mixture of zinc sulfate solution and acetonitrile. After the protein precipitation step, duloxetine in an alkaline sample solution was quickly extracted by DLLME-SFO with 50μL of 1-undecanol (extractant). Disperser was unnecessary because the small amount of remaining acetonitrile, which acts as a protein precipitating reagent, was also employed as a disperser; therefore, organic solvent consumption was reduced as much as possible. The emulsion was centrifuged and then fine droplets were floated to the top of the sample solution. The floated droplets were solidified in an ice bath and easily transferred. Various DLLME-SFO parameters such as extractant type, extractant amount, ionic strength, pH and extraction time were optimized. The chromatographic separation of duloxetine was carried out using ethanol as mobile phase. Validation of the method was performed with respect to linearity, intra- and inter-day accuracy and precision, limit of quantification (LOQ), and recovery. Calibration curves for duloxetine showed good linearity with correlation coefficients (r2) higher than 0.99. The method showed good precision and accuracy, with intra- and inter-assay coefficients of variation less than 15% (LOQ: less than 20%) at all concentrations. The recovery was carried out following the standard addition procedure with yields ranging from 59.6 to 65.5%. A newly developed environmentally friendly method was successfully applied to the pharmacokinetic study of duloxetine in human plasma and was shown to be an alternative green approach compared with the conventional solid-phase microextraction (SPME) and dispersive liquid-liquid microextraction (DLLME) techniques. © 2012 Elsevier B.V.

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