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Cho S.,Seoul National University | Shin E.S.,DNA Link | Yu H.J.,DNA Link | Lee J.H.,Seoul National University | And 3 more authors.
Forensic Science International: Genetics | Year: 2017

The usefulness of single nucleotide polymorphism (SNP) loci for kinship testing has been demonstrated in many case works, and suggested as a promising marker for relationship identification. For interpreting results based on the calculation of the likelihood ratio (LR) in kinship testing, it is important to prepare cutoffs for respective relatives which are dependent on genetic relatedness. For this, analysis using true pedigree data is significant and reliable as it reflects the actual frequencies of markers in the population. In this study, the kinship index was explored through 1209 parent-child pairs, 1373 full sibling pairs, and 247 uncle-nephew pairs using 136 SNP loci. The cutoffs for LR were set up using different numbers of SNP loci with accuracy, sensitivity, and specificity. It is expected that this study can support the application of SNP loci-based kinship testing for various relationships. © 2017 Elsevier B.V.

News Article | November 14, 2016
Site: www.prnewswire.com

SEOUL, South Korea, Nov. 14, 2016 /PRNewswire/ -- DNA Link, Inc. and Amplicon Express announced that they established an agreement today for a strategic partnership for the delivery of the best quality genomics solutions. This strategic partnership will further strengthen the cooperative...

News Article | November 14, 2016
Site: www.prnewswire.com

SEOUL, South Korea, Nov. 14, 2016 /PRNewswire/ -- DNA Link, Inc. and Amplicon Express announced that they established an agreement today for a strategic partnership for the delivery of the best quality genomics solutions. This strategic partnership will further strengthen the cooperative...

News Article | November 14, 2016
Site: en.prnasia.com

SEOUL, South Korea, Nov 14, 2016 /PRNewswire/ -- DNA Link, Inc. and Amplicon Express announced that they established an agreement today for a strategic partnership for the delivery of the best quality genomics solutions. This strategic partnership will further strengthen the cooperative relationship between two companies, which have developed over the past several years. DNA Link and Amplicon Express have agreed to cooperate in areas including nucleic acid extraction, library preparation, and PacBio sequencing. Under the terms Amplicon Express will extract HMW DNA samples of NGS-quality from crude materials such as bacteria, plants, animals and humans. These samples will be then forwarded to DNA Link to be made into a long-inserted library ideal for PacBio sequencing for genome or transcriptome analysis by the fleet of PacBio sequencers including Sequel and RSII units at DNA Link. Jongeun Lee, CEO and the founder of DNA Link said, "Amplicon Express is an expert in nucleic acid extraction and library preparation with a long proven track of success, and DNA Link is one of the best sequencing facility that has the most experience with PacBio sequencers. This partnership will bring a tremendous synergy, and the researchers will enjoy the best quality of sequence data using the third-generation sequencers." Robert Bogden, President and founder of Amplicon Express remarked, "DNA Link is one of the few PacBio service providers that can fully realize the added value of having very long starting DNA fragments. PacBio data from DNA Link maximizes the long reads from our HMW DNA preps in 20Kb or 30Kb libraries." DNA Link, Inc. is a genomics company who is a certified service provider for Pacific Bioscience, Illumina, Ion Torrent and Affymetrix. As one of the first companies that adopted Pacific Bioscience RS II system, DNA Link has become one of the world's leading expert in NGS and Bioinformatics, capable of providing an integrated genome analysis service using various platforms. Incorporated in 2000, DNA Link has accumulated profound experiences in various types of projects for sequencing and analysis of diverse organisms such as bacteria, fungi, plants, animals, and human. Headquartered in Seoul, Republic of Korea, it has a branch office and lab in San Diego, US. Amplicon Express Inc since 1996 has made 2,500+ custom BAC libraries, picked 55+ million BAC clones, and made thousands of quality HMW gDNA preps from practically every organism imaginable. The Amplicon Express distribution network includes: Japan, Singapore, Malaysia, Taiwan, Mainland China, India, and offices in the EU. Amplicon is privately held, based in Washington State. To view the original version on PR Newswire, visit:http://www.prnewswire.com/news-releases/dna-link-and-amplicon-express-announce-joint-partnership-for-genomics-services-300361245.html

Yoon K.-A.,Research Institute and Hospital | Park J.H.,Research Institute and Hospital | Han J.,Research Institute and Hospital | Park S.,National Cancer Control Research Institute | And 9 more authors.
Human Molecular Genetics | Year: 2010

Lung cancer is one of the most common cancers and the major cause of cancer death, both in Korea and worldwide, with non-small cell lung cancer (NSCLC) as the predominant histologic type. To identify genetic risk factors, we here conducted a genome-wide association study (GWAS) and a replication study in 1425 patients with NSCLC and 3011 controls from Korea. From the data for 2162 participants analyzed using the Affymetrix Genome-wide Human SNP array 5.0K, 168 single nucleotide polymorphisms (SNPs) were selected for validation. In the second stage, we were able to genotype 168 SNPs in 804 patients and 1470 controls to confirm the results of the GWAS. In the meta-analysis, rs2131877 at the chromosome 3q29 region was the most significant biomarker of lung cancer susceptibility in Koreans (P = 2.43 × 10-8). Four markers that were located within the chromosome 3q29 region were also associated with lung cancer susceptibility (trend P < 1.2 × 10-4), along with markers on 5p15 that were previously reported in populations of European descent. This high-density large-scale GWAS carried out in the Korean population suggests that 3q29 is a novel susceptibility region associated with lung cancer susceptibility in Koreans. © The Author 2010. Published by Oxford University Press. All rights reserved.

Ko S.-Y.,University of Ulsan | Oh H.-B.,University of Ulsan | Park C.-W.,University of Ulsan | Lee H.C.,University of Ulsan | Lee J.-E.,DNA Link
Clinical Microbiology and Infection | Year: 2012

Direct sequencing and reverse hybridization are currently the main methods for detecting drug-resistance mutations of hepatitis B virus (HBV). However, these methods do not enable haplotype analysis so they cannot be used to determine whether the mutations are co-located on the same viral genome. This limits the accurate identification of viral mutants that are resistant to drugs with a high genetic barrier. In our current study, ultra-deep pyrosequencing (UDPS) was used to detect HBV drug-resistance mutations in 25 entecavir-treated and five treatment-naive patients. Of the 25 entecavir-treated patients, 18 had experienced virological breakthrough and two exhibited reduced susceptibility to entecavir. The results obtained by UDPS were compared with those of direct sequencing, and the haplotypes of the drug-resistant HBV mutants were analysed. The average number of reads per patient covering the region in which drug-resistance mutations are located was 1735 (range 451-4526). UDPS detected additional drug-resistance mutations not detected by direct sequencing in 19 patients (mutation frequency range 1.1-23.8%). Entecavir-resistance mutations were found to be co-located on the same viral genome in all 20 patients displaying virological breakthrough or reduced susceptibility to entecavir. In conclusion, UDPS was not only sensitive and accurate in identifying drug-resistance mutations of HBV but also enabled haplotype analysis of the mutants. This method may offer significant advantages in explaining and predicting the responses of patients with HBV to antiviral therapy. © 2012 The Authors. Clinical Microbiology and Infection © 2012 European Society of Clinical Microbiology and Infectious Diseases.

Ryu J.-S.,Inha University | Shin E.-S.,DNA Link | Nam H.-S.,Inha University | Yi H.-G.,Inha University | And 4 more authors.
Journal of Thoracic Oncology | Year: 2011

To determine whether genetic variations in CMPK1 or RRM1, which impact the pharmacodynamics of gemcitabine, differentially affect the outcomes of non-small cell lung cancer (NSCLC) patients treated with gemcitabine or taxane/cisplatinum. Methods: We conducted retrospective study evaluating the associations between overall survival in 298 NSCLC patients at stages IIIA/IIIB (140) and IV (158), treated with gemcitabine (139) or taxane (159)/cisplatinum and 14 tagging single-nucleotide polymorphisms (tSNPs): 4 in CMPK1 and 10 in RRM1. Results: The wild-type genotypes of CMPK1 IVS1+1057 and IVS1-928 were associated with shorter overall survival in patients treated with the gemcitabine/cisplatinum (adjusted hazards ratio = 1.97 and 1.89; Cox p Bonferroni = 0.008 and 0.020), whereas this effect was not observed in patients treated with taxane/cisplatinum. No associations were observed for the other 2 CMPK1 or 10 RRM1 tSNPs. Analysis of the interaction between the CMPK1 and RRM1 genes showed that the survival of patients with CMPK1 IVS1+1057 CC and RRM1 IVS1-2374 TT, IVS7+25 AA, IVS7-425 AA, or IVS8+287 TT was significantly shorter when they were treated with the gemcitabine/cisplatinum (adjusted hazards ratio = 3.00, 2.89, 3.14, and 3.00; Cox p Bonferroni = 0.007, 0.012, 0.006, and 0.007). However, these effects were not observed in patients treated with taxane/cisplatinum. Conclusions: These findings suggest that polymorphisms of CMPK1 and their combination with those of RRM1 are helpful in identifying patients who will benefit less from a gemcitabine/cisplatinum as the first-line regimen. Copyright © 2011 by the International Association for the Study of Lung Cancer.

Tak Y.K.,Seoul National University | Kim W.Y.,Seoul National University | Kim M.J.,Seoul National University | Han E.,Seoul National University | And 5 more authors.
Analytica Chimica Acta | Year: 2012

Forensic DNA samples can degrade easily due to exposure to light and moisture at the crime scene. In addition, the amount of DNA acquired at a criminal site is inherently limited. This limited amount of human DNA has to be quantified accurately after the process of DNA extraction. The accurately quantified extracted genomic DNA is then used as a DNA template in polymerase chain reaction (PCR) amplification for short tandem repeat (STR) human identification. Accordingly, highly sensitive and human-specific quantification of forensic DNA samples is an essential issue in forensic study. In this work, a quantum dot (Qdot)-labeled Alu sequence was developed as a probe to simultaneously satisfy both the high sensitivity and human genome selectivity for quantification of forensic DNA samples. This probe provided PCR-free determination of human genomic DNA and had a 2.5-femtogram detection limit due to the strong emission and photostability of the Qdot. The Qdot-labeled Alu sequence has been used successfully to assess 18 different forensic DNA samples for STR human identification. © 2012 Elsevier B.V.

PubMed | Yonsei University, DNA Link, Oxford Genetics, Glaxosmithkline and National Health Research Institute
Type: Journal Article | Journal: Heart Asia | Year: 2016

Recent genome-wide association (GWA) studies have identified and replicated several genetic loci associated with the risk of development of coronary artery disease (CAD) in samples from populations of Caucasian and Asian descent. However, only chromosome 9p21 has been confirmed as a major susceptibility locus conferring risk for development of CAD across multiple ethnic groups. The authors aimed to find evidence of further similarities and differences in genetic risk of CAD between Korean and other populations.The authors performed a GWA study comprising 230 cases and 290 controls from a Korean population typed on 490032 single nucleotide polymorphisms (SNPs). A total of 3148 SNPs were taken forward for genotyping in a subsequent replication study using an independent sample of 1172 cases and 1087 controls from the same population.The association previously observed on chromosome 9p21 was independently replicated (p=3.08e-07). Within this region, the same risk haplotype was observed in samples from both Korea and of Western European descent, suggesting that the causal mutation carried on this background occurred on a single ancestral allele. Other than 9p21, the authors were unable to replicate any of the previously reported signals for association with CAD. Furthermore, no evidence of association was found at chromosome 1q41 for risk of myocardial infarction, previously identified as conferring risk in a Japanese population.A common causal variant is likely to be responsible for risk of CAD in Korean and Western European populations at chromosome 9p21.3. Further investigations are required to confirm non-replication of any other cross-race genetic risk factors.

PubMed | DNA Link and Seoul National University
Type: Journal Article | Journal: Transfusion medicine and hemotherapy : offizielles Organ der Deutschen Gesellschaft fur Transfusionsmedizin und Immunhamatologie | Year: 2016

Kinship testing using biallelic SNP markers has been demonstrated to be a promising approach as a supplement to standard STR typing, and several systems, such as pyrosequencing and microarray, have been introduced and utilized in real forensic cases. The Affymetrix microarray containing 169 autosomal SNPs developed for forensic application was applied to our practical case for kinship analysis that had remained inconclusive due to partial STR profiles of degraded DNA and possibility of inbreeding within the population.169 autosomal SNPs were typed on array with severely degraded DNA of two bone samples, and the kinship compared to genotypes in a reference database of their putative family members.Two bone samples remained unidentified through traditional STR typing with partial profiles of 10 or 14 of 16 alleles. Because these samples originated from a geographically isolated population, a cautious approach was required when analyzing and declaring true paternity only based on PI values. In a supplementary SNP typing, 106 and 78 SNPs were obtained, and the match candidates were found in each case with improved PI values than using only STRs and with no discrepant SNPs in comparison.Our case showed that the utility of multiple SNPs on array is expected in practical forensic caseworks with an establishment of reference database.

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