Comparing the performance of targeted next-generation sequencing and metagenomic next-generation sequencing in
Yangguang Cao1, Ya Xu2, Chengrui Yan3
1Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230000, Anhui, China; Clinical College of Anhui Medical University, Hefei, Anhui, China; Department of Rheumatology and Immunology, The Second Hospital of Anhui Medical University, Anhui, China; Anhui Medical University, School of Public Health, Department of Epidemiology. and Biostatistics, Center for Big Data and Population Health of IHM, Hefei, Anhui, China.
Background:
In terms of diagnosing pneumonia, there is currently limited evidence for a direct comparison of the performance of targeted next-generation sequencing (tNGS) and metagenomic next-generation sequencing (mNGS), and is no comprehensive conclusion yet. This systematic review and network meta-analysis (NMA) aimed to comprehensively compare the diagnostic performance of tNGS and mNGS in patients with pneumonia.
Methods:
A systematic literature search was conducted across PubMed, Embase, the Cochrane Library, and Web of Science. From the establishment of the database to September 10, 2025. Studies providing diagnostic data (true positive, false positive, false negative, true negative) for tNGS and/or mNGS in patients suspected of pneumonia were included. We conducted a frequency theory random effects network meta-analysis, and calculate pooled odds ratios (ORs) with 95 % confidence interval (CI) for sensitivity and specificity, and to rank diagnostic performance using surface under the cumulative ranking curve (SUCRA) values. Subgroup analyses based on sample type and patient status were conducted.
Results:
The NMA revealed no statistically significant differences in overall sensitivity (OR = 1.54, 95 % CI [0.47-5.06]) or specificity (OR = 1.29, 95 % CI [0.39-4.28]) between tNGS and mNGS. SUCRA rankings indicated that tNGS had the highest cumulative probability for sensitivity (91.9 %), followed by mNGS (74.6 %), and the cumulative specificity probability of tNGS (37.8 %) is higher than that of mNGS (17.1 %). In subgroup analysis, when multiple sample types were used, tNGS showed significantly higher specificity than mNGS (OR = 4.95, 95 % CI [1.13-21.75]).
Conclusion:
These findings suggest tNGS may be a more specific and potentially cost-effective option for the etiological diagnosis of pneumonia, particularly when multi-sample testing is employed.
Insights
Targeted next-generation sequencing (tNGS) may offer higher specificity for diagnosing pneumonia compared to metagenomic next-generation sequencing (mNGS). This finding is particularly relevant when multiple sample types are utilized for etiological diagnosis.
Area of Science:
- Medical Diagnostics
- Genomic Sequencing Technologies
- Infectious Disease Research
Background:
- Limited direct comparative evidence exists for targeted next-generation sequencing (tNGS) versus metagenomic next-generation sequencing (mNGS) in pneumonia diagnosis.
- A comprehensive conclusion on the diagnostic performance of tNGS and mNGS is lacking.
Purpose of the Study:
- To conduct a systematic review and network meta-analysis (NMA) comparing the diagnostic performance of tNGS and mNGS in pneumonia patients.
- To evaluate sensitivity, specificity, and diagnostic ranking of tNGS and mNGS.
Main Methods:
- Systematic literature search across major databases (PubMed, Embase, Cochrane, Web of Science) up to September 10, 2025.
- Inclusion of studies with diagnostic data for tNGS and/or mNGS in suspected pneumonia cases.
- Network meta-analysis using random effects model to calculate pooled odds ratios (ORs) for sensitivity and specificity, and Surface Under the Cumulative Ranking Curve (SUCRA) for performance ranking.
Main Results:
- No statistically significant overall difference in sensitivity (OR=1.54) or specificity (OR=1.29) between tNGS and mNGS.
- tNGS ranked higher in cumulative probability for sensitivity (91.9%) and specificity (37.8%) compared to mNGS (74.6% and 17.1%, respectively).
- Subgroup analysis revealed significantly higher specificity for tNGS when multiple sample types were used (OR=4.95).
Conclusions:
- tNGS emerges as a potentially more specific diagnostic option for pneumonia etiology.
- The findings suggest tNGS could be a more cost-effective choice, especially with multi-sample testing.
- Further research may validate tNGS's role in optimizing pneumonia etiological diagnosis.
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