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Synthetic data production for biomedical research
Yun Gyeong Lee, Mi-Sook Kwak, Jeong Eun Kim, Min Sun Kim, Dong Un No, Hee Youl Chai
Osong Public Health Res Perspect. 2025;16(2):94-99.   Published online April 22, 2025
DOI: https://doi.org/10.24171/j.phrp.2024.0335
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  • 35 Download
Graphical AbstractGraphical Abstract AbstractAbstract PDFSupplementary Material
Synthetic data, generated using advanced artificial intelligence (AI) techniques, replicates the statistical properties of real-world datasets while excluding identifiable information. Although synthetic data does not consist of actual data points, it is derived from original datasets, thereby enabling analyses that yield results comparable to those obtained with real data. Synthetic datasets are evaluated based on their utility—a measure of how effectively they mirror real data for analytical purposes. This paper presents the generation of synthetic datasets through the Healthcare Big Data Showcase Project (2019–2023). The original dataset comprises comprehensive multi-omics data from 400 individuals, including cancer survivors, chronic disease patients, and healthy participants. Synthetic data facilitates efficient access and robust analyses, serving as a practical tool for research and education. It addresses privacy concerns, supports AI research, and provides a foundation for innovative applications across diverse fields, such as public health and precision medicine.
Brief Report
Standardizing the approach to clinical-based human microbiome research: from clinical information collection to microbiome profiling and human resource utilization
Jung Wook Kim, Eun Chae Choi, Kwang Jun Lee
Received November 14, 2024  Accepted March 6, 2025  Published online April 11, 2025  
DOI: https://doi.org/10.24171/j.phrp.2024.0319    [Epub ahead of print]
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AbstractAbstract PDF
Objectives
This study presents the standardized protocols developed by the Clinical-Based Human Microbiome Research and Development Project (cHMP) in the Republic of Korea.
Methods
It addresses clinical metadata collection, specimen handling, DNA extraction, sequencing methods, and quality control measures for microbiome research.
Results
The cHMP involves collecting samples from healthy individuals and patients across various body sites, including the gastrointestinal tract, oral cavity, respiratory system, urogenital tract, and skin. These standardized procedures ensure consistent data quality through controlled specimen collection, storage, transportation, DNA extraction, and sequencing. Sequencing encompasses both amplicon and whole metagenome methods, followed by stringent quality checks. The protocols conform to international guidelines, ensuring that the data generated are both reliable and comparable across microbiome studies.
Conclusion
The cHMP underscores the importance of methodological standardization in enhancing data integrity, reproducibility, and advancing microbiome-based research with potential applications for improving human health outcomes.
Original Article
Genome Sequencing Analysis of Atypical Shigella flexneri Isolated in Korea
Nan-Ok Kim, Hae-young Na, Su-Mi Jung, Gyung Tae Chung, Hyo Sun Kawk, Sahyun Hong
Osong Public Health Res Perspect. 2017;8(1):78-85.   Published online February 28, 2017
DOI: https://doi.org/10.24171/j.phrp.2017.8.1.11
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  • 1 Crossref
AbstractAbstract PDFSupplementary Material
Objectives

An atypical Shigella flexneri strain with a plural agglutination pattern [i.e., reacting not only with serum samples containing type antigen II but also with serum samples containing group antigens (3)4 and 7(8)] was selected for genome sequencing, with the aim of obtaining additional comparative information about such strains.

Methods

The genomic DNA of atypical S. flexneri strain NCCP 15744 was sequenced using an Ion Torrent PGM sequencing machine (Life Technologies, USA). The raw sequence data were preprocessed and reference-assembled in the CLC Assembly Cell software (version 4.0.6; CLC bio, USA).

Results

Ion Torrent sequencing produced 1,450,025 single reads with an average length of 144 bp, totaling ~209 Mbp. The NCCP 15744 genome is composed of one chromosome and four plasmids and contains a gtrX gene. Among the published genome sequences of S. flexneri strains, including 2457T, Sf301, and 2002017, strain NCCP 15744 showed high similarity with strain 2002017. The differences between NCCP 15744 and 2002017 are as follows: i) NCCP 15744 carries four plasmids whereas 2002017 carries five; ii) 19 genes (including CI, CII, and cro) were lost in the SHI-O genomic island of NCCP 15744 and six genes were gained as compared with strain 2002017.

Conclusion

Strain NCCP 15744 is genetically similar to 2002017, but these two strains have different multilocus sequence types and serotypes. The exact reason is unclear, but the 19 lost genes may be responsible for the atypical seroconversion of strain NCCP 15744.

Citations

Citations to this article as recorded by  
  • Genomic and proteomic characterization of two strains of Shigella flexneri 2 isolated from infants’ stool samples in Argentina
    Mónica F. Torrez Lamberti, Lucrecia C. Terán, Fabián E. Lopez, María de las Mercedes Pescaretti, Mónica A. Delgado
    BMC Genomics.2022;[Epub]     CrossRef

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