- Whole genome sequence analyses of thermotolerant Bacillus sp. isolates from food
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Sornchuer P, Saninjuk K, Tingpej P
- KMID: 2547069
- Genomics Inform.
- 2023 Sep;21(3):e35.
- doi: 10.5808/gi.23030
The Bacillus cereus group, also known as B. cereus sensu lato (B. cereus s.l.), is composed of various Bacillus species, some of which can cause diarrheal or emetic food poisoning.... -
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- Multi-omics techniques for the genetic and epigenetic analysis of rare diseases
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Choi Y, Choi DWY, Lee S
- KMID: 2544151
- J Genet Med.
- 2023 Jun;20(1):1-5.
- doi: 10.5734/JGM.2023.20.1.1
Until now, rare disease studies have mainly been carried out by detecting simple variants such as single nucleotide substitutions and short insertions and deletions in protein-coding regions of disease-associated gene... -
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- pncA Large Deletion is the Characteristic of Pyrazinamide-Resistant Mycobacterium tuberculosis belonging to the East Asian Lineage
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Kim NY, Kim DY, Chu J, Jung SH
- KMID: 2544443
- Infect Chemother.
- 2023 Jun;55(2):247-256.
- doi: 10.3947/ic.2023.0037
Background: Pyrazinamide (PZA) is often used as an add-on agent in the treatment of multidrug-resistant tuberculosis, regardless of phenotypic drug susceptibility testing (pDST) results. However, evaluating the effectiveness of PZA... -
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- New Horizons in the Diagnosis of Tuberculosis of the Spine: The Role of Whole Genome Sequencing
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Ngcelwane M, Omar SV, Said M, Bida M
- KMID: 2543158
- Asian Spine J.
- 2023 Jun;17(3):511-517.
- doi: 10.31616/asj.2022.0247
Study Design: Prospective study. Purpose: To evaluate the utility of whole genome sequencing (WGS) in drug resistance testing, lineage of the organisms, and organism- related factors responsible for bacilli settling in... -
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- Predicting Phenotypic Antimicrobial Resistance in Escherichia coli Isolates, Using Whole Genome Sequencing Data
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Kim H, Kim YA, Seo YH, Lee H, Lee K
- KMID: 2537137
- Ann Clin Microbiol.
- 2022 Dec;25(4):127-132.
- doi: 10.5145/ACM.2022.25.4.2
Background: The application of genotypic antimicrobial sensitivity tests (ASTs) is dependent on the reliability of the predictions of phenotypic resistance. In this study, routine AST results and the presence of... -
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- Metagenomic analysis of viral genes integrated in whole genome sequencing data of Thai patients with Brugada syndrome
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Chitcharoen S, Phokaew C, Mauleekoonphairoj J, Khongphatthanayothin A, Sutjaporn B, Wandee P, Poovorawan Y, Nademanee K, Payungporn S
- KMID: 2540172
- Genomics Inform.
- 2022 Dec;20(4):e44.
- doi: 10.5808/gi.22047
Brugada syndrome (BS) is an autosomal dominant inheritance cardiac arrhythmia disorder associated with sudden death in young adults. Thailand has the highest prevalence of BS worldwide, and over 60% of... -
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- Evaluation of Five User-Friendly Whole Genome Sequencing Software for Mycobacterium tuberculosis in Clinical Application
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Kim N, Seok KH, Shin S, Kim B, Park H, Roh EY, Yoon JH, Shin S
- KMID: 2536135
- J Korean Med Sci.
- 2022 Nov;37(46):e328.
- doi: 10.3346/jkms.2022.37.e328
Background: Whole genome sequencing (WGS) is an increasingly useful tool for tuberculosis (TB) diagnosis and disease management. In this study, we evaluated the utility of userfriendly WGS tools in reporting... -
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- A Case of Whole Genome Analysis of SARSCoV-2 Using Oxford Nanopore MinION System
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Kim JS, Chung SH, Kim JM, Kim HS, Kim HS, Song W
- KMID: 2523568
- Ann Clin Microbiol.
- 2021 Dec;24(4):135-140.
- doi: 10.5145/ACM.2021.24.4.4
The application of whole genome sequencing on SARS-CoV-2 viral genome is essential for our understanding of the molecular epidemiology and spread of viruses in the community. The portable whole genome... -
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- Analysis of genome variants in dwarf soybean lines obtained in F6 derived from cross of normal parents (cultivated and wild soybean)
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Roy NS, Ban YW, Yoo H, Ramekar RV, Cheong EJ, Park NI, Na JK, Park KC, Choi IY
- KMID: 2517580
- Genomics Inform.
- 2021 Jun;19(2):e19.
- doi: 10.5808/gi.21024
Plant height is an important component of plant architecture and significantly affects crop breeding practices and yield. We studied DNA variations derived from F5 recombinant inbred lines (RILs) with 96.8%... -
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- Epidemiologic Linkage of COVID-19 Outbreaks at Two University-affiliated Hospitals in the Seoul Metropolitan Area in March 2020
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Park K, Lee J, Lee K, Jung J, Kim SH, Lee J, Chalita M, Yoon SH, Chun J, Hur KH, Sung H, Kim MN, Lee HK
- KMID: 2511636
- J Korean Med Sci.
- 2021 Jan;36(4):e38.
- doi: 10.3346/jkms.2021.36.e38
Background: Coronavirus disease 2019 (COVID-19) outbreaks emerged at two universityaffiliated hospitals in Seoul (hospital A) and Uijeongbu City (hospital S) in the metropolitan Seoul area in March 2020. The aim... -
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- Clonal Distribution of Clindamycin-Resistant Erythromycin-Susceptible (CRES) Streptococcus agalactiae in Korea Based on Whole Genome Sequences
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Takahashi T, Maeda T, Lee S, Lee DH, Kim S
- KMID: 2502567
- Ann Lab Med.
- 2020 Sep;40(5):370-381.
- doi: 10.3343/alm.2020.40.5.370
Background: The clindamycin-resistant erythromycin-susceptible (CRES) phenotype is rare in Streptococcus agalactiae (group B streptococci). We aimed to determine the molecular characteristics of CRES S. agalactiae using whole genome sequencing (WGS). Methods:... -
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- Functional annotation of de novo variants from healthy individuals
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Lee J, Hong SE
- KMID: 2468872
- Genomics Inform.
- 2019 Dec;17(4):e46.
- doi: 10.5808/GI.2019.17.4.e46
The implications of germline de novo variants (DNVs) in diseases are well documented. Despite extensive research, inconsistencies between studies remain a challenge, and the distribution and genetic characteristics of DNVs... -
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- Analysis of unmapped regions associated with long deletions in Korean whole genome sequences based on short read data
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Lee Y, Park K, Koh I
- KMID: 2468866
- Genomics Inform.
- 2019 Dec;17(4):e40.
- doi: 10.5808/GI.2019.17.4.e40
While studies aimed at detecting and analyzing indels or single nucleotide polymorphisms within human genomic sequences have been actively conducted, studies on detecting long insertions/deletions are not easy to orchestrate.... -
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- Rapid Whole-genome Sequencing of Zika Viruses using Direct RNA Sequencing
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Kim JH, Kim J, Koo BS, Oh H, Hong JJ, Hwang ES
- KMID: 2468031
- J Bacteriol Virol.
- 2019 Sep;49(3):115-123.
- doi: 10.4167/jbv.2019.49.3.115
Zika virus (ZIKV) is one of the pathogens which is transmitted world widely, but there are no effective drugs and vaccines. Whole genome sequencing (WGS) of viruses could be applied... -
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- Generation and protective efficacy of a cold-adapted attenuated genotype 2b porcine epidemic diarrhea virus
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Won H, Lee DU, Jang G, Noh YH, Lee SC, Choi HW, Yoon IJ, Yoo HS, Lee C
- KMID: 2453894
- J Vet Sci.
- 2019 Jul;20(4):e32.
- doi: 10.4142/jvs.2019.20.e32
The recent emergence and re-emergence of porcine epidemic diarrhea virus (PEDV) underscore the urgent need for the development of novel, safe, and effective vaccines against the prevailing strain. In this... -
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- Genomic analysis of Korean patients with advanced prostate cancer by use of a comprehensive next-generation sequencing panel and low-coverage, whole-genome sequencing
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Kang M, Cho E, Jang J, Lee J, Jeon Y, Jeong BC, Seo SI, Jeon SS, Lee HM, Choi HY, Jeon HG
- KMID: 2450539
- Investig Clin Urol.
- 2019 Jul;60(4):227-234.
- doi: 10.4111/icu.2019.60.4.227
PURPOSE: To analyze the characteristics of somatic mutations and copy number alterations (CNAs) in Korean patients with advanced prostate cancer (PCa) by use of the Oncomine Comprehensive Panel (ThermoFisher Scientific)... -
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- Comparing Two Mycobacterium tuberculosis Genomes from Chinese Immigrants with Native Genomes Using Mauve Alignments
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Ryoo S, Lee J, Oh JY, Kim BK, Kim Y, Kim JH, Shin C, Lee SH
- KMID: 2414563
- Tuberc Respir Dis.
- 2018 Jul;81(3):216-221.
- doi: 10.4046/trd.2017.0091
BACKGROUND: The number of immigrants with tuberculosis (TB) increases each year in South Korea. Determining the transmission dynamics based on whole genome sequencing (WGS) to cluster the strains has been... -
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- Phenotypic and Genomic Characterization of AmpC-Producing Klebsiella pneumoniae From Korea
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Palmieri M, Schicklin , Pelegrin A, Chatellier S, Franceschi C, Mirande C, Park YJ, van Belkum A
- KMID: 2408077
- Ann Lab Med.
- 2018 Jul;38(4):367-370.
- doi: 10.3343/alm.2018.38.4.367
The prevalence of multidrug-resistant gram-negative bacteria has continuously increased over the past few years; bacterial strains producing AmpC β-lactamases and/or extended-spectrum β-lactamases (ESBLs) are of particular concern. We combined high-resolution... -
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- Phenotypic and genotypic analyses of an attenuated porcine reproductive and respiratory syndrome virus strain after serial passages in cultured porcine alveolar macrophages
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Lee SC, Lee S, Yoo GW, Choi HW, Noh YH, Park CE, Shin JH, Yoon IJ, Kang SY, Lee C
- KMID: 2412126
- J Vet Sci.
- 2018 May;19(3):358-367.
- doi: 10.4142/jvs.2018.19.3.358
The porcine reproductive and respiratory syndrome virus (PRRSV) is a globally ubiquitous swine viral pathogen that causes major economic losses worldwide. We previously reported an over-attenuated phenotype of cell-adapted PRRSV... -
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- Estimation of the Genetic Substitution Rate of Hanwoo and Holstein Cattle Using Whole Genome Sequencing Data
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Lee YS, Shin D
- KMID: 2413247
- Genomics Inform.
- 2018 Mar;16(1):14-20.
- doi: 10.5808/GI.2018.16.1.14
Despite the importance of mutation rate, some difficulties exist in estimating it. Next-generation sequencing (NGS) data yields large numbers of single-nucleotide polymorphisms, which can make it feasible to estimate substitution... -
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