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Young-Suk Lee

Publications and source records attributed to Young-Suk Lee.

4 recordsLinked to original sources
PubMed2026

A portable recalibration workflow for reference-based variant calling in non-human genomes.

A key computational step in reference-based variant calling is distinguishing true genetic variants from sequencing errors. Advanced tools and workflows have been developed to handle this by computational modelling of technical errors from the sequencing machines. However, these recalibration workflows have largely been evaluated for human data only and its exact applicability for non-human data remains unknown. Here, we conducted a systematic evaluation of variant calling on human, rice, sheep, and chickpea data, and found that existing workflows introduce unexpected statistical bias, thus leading to suboptimal variant calls for non-human data. To address this problem, we present simple guidelines for constructing a "pseudo-"database (pseudoDB) of genetic variants as a scalable and portable solution for recalibration and variant calling. With human data, our pseudoDB-based workflow performs comparably to existing dbSNP-based GATK3 workflows and those using DeepVariant, Strelka2, and FreeBayes. We extend this to other non-human genomes, namely cattle, brown bear, swan goose, African oil palm, Komodo dragon, and stevia, altogether resulting in the identification of up to 242.0% unique genetic variants. The majority of newly identified variants are within the non-coding regions, hinting at the rich diversity of genome regulation in the non-human population. Our pseudoDB-based workflow is agnostic to reference genomes and modular for easy integration with other computational workflows for human and non-human resequencing data.

Humans↗
PubMed2004

Predictive comparisons of procalcitonin (PCT) level, arterial ketone body ratio (AKBR), APACHE III score and multiple organ dysfunction score (MODS) in systemic inflammatory response syndrome (SIRS).

Procalcitonin (PCT) is a newly introduced marker of systemic inflammation and bacterial infection. A marked increase in circulating PCT level in critically ill patients has been related with the severity of illness and poor survival. The goal of this study was to compare the prognostic power of PCT and three other parameters, the arterial ketone body ratio (AKBR), the acute physiology, age, chronic health evaluation (APACHE) III score and the multiple organ dysfunction score (MODS), in the differentiation between survivors and nonsurvivors of systemic inflammatory response syndrome (SIRS). The study was performed in 95 patients over 16 years of age who met the criteria of SIRS. PCT and AKBR were assayed in arterial blood samples. The APACHE III score and MODS were recorded after the first 24 hours of surgical ICU (SICU) admission and then daily for two weeks or until either discharge or death. The patients were divided into two groups, survivors (n=71) and nonsurvivors (n=24), in accordance with the ICU outcome. They were also divided into three groups according to the trend of PCT level: declining, increasing or no change. Significant differences between survivors and nonsurvivors were found in APACHE III score and MODS throughout the study period, but in PCT value only up to the 7th day and in AKBR only up to the 3rd day. PCT values of the three groups were not significantly different on the first day between survivors and nonsurvivors. Receiver operating characteristic (ROC) curves for prediction of mortality by PCT, AKBR, APACHE III score and MODS were 0.690, 0.320, 0.915 and 0.913, respectively, on the admission day. In conclusion, PCT could have some use as a mortality predictor in SIRS patients but was less reliable than APACHE III score or MODS.

APACHE↗
PubMed2004

Randomized, open-label, two-period crossover comparison of the pharmacokinetic and pharmacodynamic properties of two amlodipine formulations in healthy adult male Korean subjects.

BACKGROUND: Amlodipine, a third-generation dihydropyridine calcium antagonist, is prescribed in the management of angina and hypertension. A newly developed amlodipine formulation (amlodipine camsylate) is associated with similar physical properties, melting point, and solubility-and improved stability against long-term stability test and accelerated temperature test-compared with the conventional formulation (amlodipine besylate). OBJECTIVE: This study was performed to compare the pharmacokinetic (PK) and pharmacodynamic (PD) properties and safety profiles of a newly developed amlodipine formulation with a conventional formulation in healthy male subjects. METHODS: This randomized, open-label, 2-period crossover comparative study was conducted at the Clinical Trial Center, Gil Medical Center, Gachon Medical School (Incheon, Korea). Eighteen healthy male Korean subjects aged 20 to 40 years were enrolled. All subjects received a single oral dose (5-mg tablet) of a conventional (reference) or newly developed (test) amlodipine formulation. Blood samples for PK analysis of amlodipine were obtained during the 144-hour period after dosing. Systolic and diastolic blood pressure (BP) (SBP and DBP, respectively) and pulse rate (PR) were measured just before each blood sampling. Assessment of safety profiles, including hematology and biochemistry, electrocardiography, urinalysis, and monitoring of adverse events (AEs), was performed. RESULTS: All participants completed both treatment periods. Their mean (SD) age was 22.3 (1.5) years (range, 20-25 years) and their mean (SD) body weight was 67.9 (5.6) kg (range, 57-77 kg). The plasma concentration-time profiles of amlodipine were similar after administration of the 2 formulations. The reference and test formulations were pharmacokinetically equivalent. The 90% CIs for the mean treatment ratios of the log-transformed peak plasma concentration and the area under the plasma concentration-time curve were within the predetermined equivalence range of 80% to 125%. Despite administration of a single dose, significant maximal changes in SBP, DBP, and PR were achieved after drug administration for both formulations compared with baseline values (all, P < 0.001). No significant differences in PD profiles were found between the 2 formulations. No clinically relevant changes were observed in physical, biochemical, hematologic, electrocardiographic, or urinalysis findings during the study. Neither formulation caused any AEs during the study. CONCLUSIONS: The 2 amlodipine formulations were pharmacokinetically equivalent and showed similar PD characteristics in these healthy male subjects.

Adult↗