Clinical Metagenomic Sequencing Reports from a Single-Center Study, 2024-2025
by Jian-min Ren·Updated 17d ago
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Description
A retrospective observational study of 1,981 clinical metagenomic next-generation sequencing (mNGS) orders from hospitalized patients between January 1, 2024, and December 31, 2025. The data, authored by Jian-min Ren and shared on figshare, compares report-interpreted positivity and pathogen detection across bronchoalveolar lavage fluid, blood, cerebrospinal fluid, and tissue specimens. Findings characterize specimen-specific differences in mNGS reporting patterns for routine inpatient practice.
Use Cases
Compare report positivity rates across different specimen types (BALF, blood, CSF, tissue) based on the described primary endpoint.
Analyze the frequency of mixed pathogen detections among positive orders based on the reported percentages.
Study the most frequently reported organisms (e.g., Epstein-Barr virus, Candida albicans) across specimen groups as described in the summary.
Contextually stratify findings by ICU association as mentioned in the description.
Strengths
Includes 1,981 specimen-specific first orders with clear counts per type: 973 BALF, 473 blood, 240 CSF, and 122 tissue.
Reports precise positivity percentages with 95% confidence intervals for each primary specimen group.
Provides data on mixed detections, quantifying orders with at least 2 distinct pathogens (e.g., 76.7% for BALF).
Includes a subset of 277 orders (14.0%) that underwent PMseq-RNA testing for RNA virus analysis.
Limitations
Column-level documentation is absent; field semantics must be inferred after download.
Row count for the underlying data tables is unknown, which may limit suitability assessment.
Data is from a single-center study, which may reflect institutional bias in testing and reporting practices.
Provenance
Source
figshare, author Jian-min Ren.
Collection Method
Single-center retrospective observational study using routine clinical mNGS data.
Time Range
January 1, 2024, to December 31, 2025.
Freshness
Last updated 2026-05-20 10:44:12; freshness should be verified.
Primary data file is a DOCX document (255.2 KB), which is a tiny dataset; actual tabular data may be embedded within the document and require extraction.