• 한국동물위생학회지
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• 제46권1호
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• pp.93-106
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• 2023

Emerging and re-emerging zoonotic viruses become critical public health, economic, societal, and cultural burdens. The Coronavirus disease-19 (COVID-19) pandemic reveals needs for effective preparedness and responsiveness against the emergence of variants and the next virus outbreak. The targeted next-generation sequencing (NGS) significantly contributes to the acquisition of viral genome sequences directly from clinical specimens. Using this advanced NGS technology, the genomic epidemiology and surveillance play a critical role in identifying of infectious source and origin, tracking of transmission chains and virus evolution, and characterizing the virulence and developing of vaccines during the outbreak. In this review, we highlight the platforms and preparation of targeted NGS for the viral genomics. We also demonstrate the application of this strategy to take advantage of the responsiveness and prevention of emerging zoonotic viruses. This article provides broad and deep insights into the preparedness and responsiveness for the next zoonotic virus outbreak.

• Journal of Genetic Medicine
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• 제5권2호
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• pp.89-93
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• 2008

"Personalized medicine," the goal of which is to provide better clinical care by applying patient's own genomic information to their health care is a global challenge for the $21^{st}$ century "genomic era." This is especially true in Korea, where provisions for clinical genetic services are inadequate for the existing demand, let alone future demands. Genomics-based knowledge and tools make it possible to approach each patient as a unique biological individual, which has led to a paradigm-shift in medical practice, giving it more of a predictive focus as compared with current treatment oriented approach. With recent advancements in genomics, many genetic tests, such as susceptibility genetic tests, have been developed for both rare single gene diseases and more common multifactorial diseases. Indeed, genetic tests for presymtomatic individuals and genetic tests for drug response have become widely available, and personalized medicine will face the challenge of assisting patients who use such tests to make appropriate and wise use of genetic risk assessment. A major challenge of genomic medicine lies in understanding and communicating disease risk in order to facilitate and support patients and their families in making informed decisions. Establishment of a health care system with provisions for genetic counseling as an integral part of health care service, in addition to genomic literacy of health care providers, is vital to meet this growing challenge. Realization of the promise of personalized medicine in the era of genomics for improvement of health care is dependent on further development of next generation sequencing technology and affordable sequencing test costs. Also necessary will be policy development concerning the ethical, legal and social issues of genomic medicine and an educated and ready medical community with clinical practice guidelines for genetic counseling and genetic testing.

• 경영정보학연구
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• 제23권3호
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• pp.97-125
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• 2021

블록체인은 유전자분석 서비스의 한계점인 개인정보 유출, 데이터 관리 이슈 등을 해결하고 이를 활성화할 핵심기술로 주목받고 있다. 유전자분석 서비스는 지속적 비용 감소와 규제환경 변화로 인해 시장규모가 증대해 왔으며, 뛰어난 보안과 다양한 서비스와 연결이 가능한 블록체인이 결합될 경우, 잠재성이 더욱 커질 것으로 예상된다. 이 연구에서는 기술수용모델(TAM)과 혁신저항이론을 결합해 연구 모형을 제작, 블록체인 속성 중 차세대 유전자분석 서비스의 수용의도와 혁신 저항에 영향을 미치는 요인들을 분석한다. 이러한 분석을 위해 블록체인 및 유전자분석 서비스에 대한 잠재적 사용자가 될 150여 명을 대상으로 설문조사를 진행하였다. 수용의도 및 저항에 영향을 줄 것이라고 추론하는 블록체인의 4자기 속성 즉, 보안성, 투명성, 가용성, 다양성 등을 연구변수로 설정하여 분석을 진행했다. 기술수용 및 혁신저항 변수에는 인지된 유용성, 인지된 위험, 인지된 복잡성 등을 설정하여, 블록체인의 특성이 매개변수를 통해 수용의도와 혁신저항에 미치는 영향을 분석했다. 이러한 분석을 통해 차세대 유전자분석 정보플랫폼의 저항을 줄이고 수용의도를 높이기 위해 중요하게 고려해야할 핵심변수를 가려낸다. 이 연구는 블록체인 기반의 새로운 유전자분석 정보플랫폼을 준비하는 업체에서 서비스 고도화를 위해 고려해야 할 혁신요인을 제시한다는 점에서 의의가 있다.

• International Journal of Contents
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• 제14권1호
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• pp.34-38
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• 2018

With the rapid growth of genomic data, new requirements have emerged that are difficult to handle with big data storage and analysis techniques. Regardless of the size of an organization performing genomic data analysis, it is becoming increasingly difficult for an institution to build a computing environment for storing and analyzing genomic data. Recently, cloud computing has emerged as a computing environment that meets these new requirements. In this paper, we analyze and compare existing distributed and parallel NGS (Next Generation Sequencing) analysis based on cloud computing environment for future research.

• 한국동물위생학회지
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• 제39권1호
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• pp.41-49
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• 2016

In the present study, fast and robust methods for the next generation sequencing (NGS) were developed for analysis of PRRSV full genome sequences, which is a positive sensed RNA virus with a high degree of genetic variability among isolates. Two strains of PRRSVs (VR2332 and VR2332-R) which have been maintained in our laboratory were used to validate our methods and to compare with the sequence registered in GenBank (GenBank accession no. EF536003). The results suggested that both of strains had 100% coverage with the reference; the VR2332 had the coverage depth from minimum 3 to maximum 23,012, for the VR2332-R from minimum 3 to maximum 41,348, and 22,712 as an average depth. Genomic data produced from the massive sequencing capacities of the NGS have enabled the study of PRRSV at an unprecedented rate and details. Unlike conventional sequence methods which require the knowledge of conserved regions, the NGS allows de novo assembly of the full viral genomes. Therefore, our results suggested that these methods using the NGS massively facilitate the generation of more full genome PRRSV sequences locally as well as nationally in regard of saving time and cost.

• Asian-Australasian Journal of Animal Sciences
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• 제19권8호
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• pp.1065-1070
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• 2006

The avian uncoupling protein (avUCP) is a member of the mitochondrial transporter superfamily that uncouples proton entry in the mitochondrial matrix from ATP synthesis. The sequencing analysis method was used to identify nucleotide polymorphisms within the avUCP gene in Korean native chicken (KNC). This study identified ten single nucleotide polymorphisms (SNPs) in the avUCP gene. We analyzed the SNPs of the avUCP gene to investigate whether polymorphism in the gene might be responsible for quantitative variations in economic traits in KNC. Three significant polymorphic sites for economic traits were avUCP C+282T (mean body weight, p<0.05), avUCP C+433T (daily percent lay, p<0.05), and avUCP T+1316C (daily percent lay, p<0.05). The frequency of each SNP was 0.125 (C+282T in avUCP gene exon 1 region), 0.150 (C+433T in avUCP gene intron 1 region), and 0.15 (T+1316C in avUCP gene exon 3 region), respectively. Among the identified SNPs, one pair of SNPs (genotype CC, C+282T and TT, avUCP C+433T) showed the highest daily percent lay (p<0.05) and mean body weight (p<0.05) and the frequency was 0.067. This study of the avUCP gene could be useful for genetic studies of this gene and selection on economic traits for KNC.

• Parasites, Hosts and Diseases
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• 제58권2호
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• pp.191-194
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• 2020

Free-living amoebas (FLAs) can cause severe disease in humans and animals when they become infected. However, there are no accurate survey reports on the prevalence of FLAs in Korea. In this study, we collected 163 tap water samples from buildings, apartments, and restrooms of highway service areas in 7 Korean provinces with high population density. All these buildings and facilities have water storage tanks in common. The survey was separated into categories of buildings, apartments, and highway service areas. Five hundred milliliters of tap water from each building was collected and filtered with 0.2 ㎛ pore filter paper. The filters were incubated in agar plates with heated E. coli at 25℃. After axenization, genomic DNA was collected from each FLA, and species classification was performed using partial 18S-rDNA PCR-sequencing analysis. We found that 12.9% of tap water from buildings with storage tanks in Korea was contaminated with FLAs. The highway service areas had the highest contamination rate at 33.3%. All of the FLAs, except one, were genetically similar to Vermamoeba vermiformis (Hartmannella vermiformis). The remaining FLA (KFA21) was very similar to Acanthamoeba lugdunensis (KA/E26). Although cases of human infection by V. vermiformis are very rare, we must pay attention to the fact that one-third of tap water supplies in highway service areas have been contaminated.

• Journal of Animal Science and Technology
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• 제63권5호
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• pp.1207-1210
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• 2021

Lactobacillus amylovorus are known to exist in the intestinal flora of healthy cattle or pigs. The L. amylovorus strain 1394N20 was isolated from the feces of the Hanwoo calf (Bos taurus coreanae). The genome of strain 1394N20 consists of a single circular chromosome (2,176,326 bp) with overall guanine + cytosine content of 37.8 mol%. Moreover, 2,281 protein-coding sequences, 15 rRNAs, and 65 tRNAs genes were identified in the chromosome based on the results of annotation. The bacterium has a gene encoding endoglucanase, an enzyme that hydrolyzes the 1,4-β-D-glycosidic linkages in cellulose, hemicellulose, lichenin, and cereal β-D-glucans. Genomic sequencing of L. amylovorus strain 1394N20 reveals the immense potential of the strain as a probiotic with nutrient digestibility.

• Genomics & Informatics
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• 제18권1호
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• pp.8.1-8.10
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• 2020

The explosive growth of next-generation sequencing data has resulted in ultra-large-scale datasets and ensuing computational problems. In Korea, the amount of genomic data has been increasing rapidly in the recent years. Leveraging these big data requires researchers to use large-scale computational resources and analysis pipelines. A promising solution for addressing this computational challenge is cloud computing, where CPUs, memory, storage, and programs are accessible in the form of virtual machines. Here, we present a cloud computing-based system, Bio-Express, that provides user-friendly, cost-effective analysis of massive genomic datasets. Bio-Express is loaded with predefined multi-omics data analysis pipelines, which are divided into genome, transcriptome, epigenome, and metagenome pipelines. Users can employ predefined pipelines or create a new pipeline for analyzing their own omics data. We also developed several web-based services for facilitating downstream analysis of genome data. Bio-Express web service is freely available at https://www. bioexpress.re.kr/.

• Genomics & Informatics
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• 제12권4호
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• pp.151-155
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• 2014

In November 2013, the US Food and Drug Administration (FDA) sent a warning letter to 23andMe, Inc. and ordered the company to discontinue marketing of the 23andMe Personal Genome Service (PGS) until it receives FDA marketing authorization for the device. The FDA considers the PGS as an unclassified medical device, which requires premarket approval or de novo classification. Opponents of the FDA's action expressed their concerns, saying that the FDA is overcautious and paternalistic, which violates consumers' rights and might stifle the consumer genomics field itself, and insisted that the agency should not restrict direct-to-consumer (DTC) genomic testing without empirical evidence of harm. Proponents support the agency's action as protection of consumers from potentially invalid and almost useless information. This action was also significant, since it reflected the FDA's attitude towards medical application of next-generation sequencing techniques. In this review, we followed up on the FDA-23andMe incident and evaluated the problems and prospects for DTC genetic testing.