Significant Disparities in tNGS Product Performance Metrics Highlight Need for Industry Collaboration to Overcome Fragmentation – 2025 VBEF

According to Frost & Sullivan, the market size of genetic testing in China is projected to grow from RMB 48.7 billion in 2025 to RMB 153.6 billion in 2030, representing a compound annual growth rate (CAGR) of 25.8% over the next five years. Among various technologies, Next-Generation Sequencing (NGS), also known as high-throughput sequencing, has become the most widely applied and highly commercialized sequencing technology due to its advantages in high throughput, rapid detection, and relatively high accuracy. High-throughput sequencing remains the primary driver for the large-scale commercial adoption of gene sequencing technologies and is expected to maintain its position as the mainstream sequencing technology for the foreseeable future.

In addition to inheriting the research applications of first-generation sequencing, high-throughput sequencing technology plays a significant role in clinical settings. It can identify tumor mutation genes, thereby rapidly determining targeted therapies and enabling precision medicine. Furthermore, it is utilized for prenatal testing, preimplantation genetic screening in assisted reproduction, and diagnosis of genetic disorders. Moreover, in the face of emerging infectious diseases that pose major threats to global public health, high-throughput sequencing provides critical evidence for clinical treatment through broad-spectrum screening, high sensitivity, and rapid response. This facilitates pathogen diagnosis in various types of infectious diseases, including nervous system infections, respiratory tract infections, and bloodstream infections.

At the Forum on the Development of Precision Medicine and Molecular Diagnostics, part of the 2025 VBEF Top 100 Future Healthcare and Pharmaceuticals Exhibition, Zeng Xianqiu, Product Director at Dayuanqi Biotechnology, presented an industry perspective on the current applications of high-throughput sequencing in pathogen diagnosis, as well as the advantages and pain points associated with related products.

Zeng Xianqiu, Product Director at Dayuanqi Bio

In pathogen diagnosis and practical applications, high-throughput sequencing technologies are primarily categorized into three types: whole-genome sequencing, mNGS, and tNGS (Targeted Next-Generation Sequencing).

The first approach is whole-genome sequencing, a technology that played a pivotal role during the COVID-19 pandemic. Whole-genome sequencing of pathogens primarily employs next-generation sequencing (NGS) platforms to comprehensively determine the genomic sequences of pathogens. In-depth analysis of these sequences reveals genomic-level changes in pathogenic microorganisms, thereby elucidating the origins, transmission dynamics, and mutational evolution of viruses. During the pandemic, researchers leveraged this technology to identify the genetic sequence of SARS-CoV-2, providing critical technical support for subsequent epidemic control measures and vaccine development. Currently, whole-genome sequencing is mainly utilized by disease control and prevention institutions at all levels, as well as research institutes, for pathogen source tracing, surveillance, and tracking.

The second approach is metagenomic next-generation sequencing (mNGS), a technology of significant importance in pathogen discovery. In December 2019, researchers identified the novel coronavirus using mNGS and subsequently determined its genomic sequence through whole-genome sequencing. Clinically, mNGS is more frequently applied to detect pathogens in rare specimen types that are difficult to characterize using conventional diagnostic methods. mNGS has also become the preferred option for controlling outbreaks of unknown etiology.

The third type is tNGS, a clinical application technology that has developed rapidly over the past three years. Its advantages lie in its lower cost and coverage of pathogens responsible for 95%–99% of clinical infection cases, thereby enabling rapid adoption within hospitals. Furthermore, with the national healthcare insurance cost-containment measures implemented in recent years, cost-effective testing technologies such as tNGS are gaining greater popularity.

However, the rapid development of tNGS has also led to significant product heterogeneity.Evaluation data jointly compiled by the National Institutes for Food and Drug Control (NIFDC) and 11 other institutions reveal significant variations among tNGS kits from different manufacturers in key performance metrics, including sensitivity, specificity, and reproducibility. For instance, only two institutions achieved a 100% positive agreement rate when testing high-concentration reference materials, whereas some reagents exhibited false-positive rates as high as 30%, with coefficients of variation for reproducibility approaching 70%. These findings suggest to clinicians that test results may fluctuate depending on the reagent selected, necessitating cautious interpretation in conjunction with the laboratory’s quality control capabilities.

From the perspective of industrial application, Zeng Xianqiu shared how enterprises can develop high-throughput sequencing (HTS) technologies required for pathogen diagnosis. The bioinformatics analysis pipeline for HTS involves several key steps: finalization of the bioinformatics workflow, construction of standard libraries, database curation, finalization of scenario-specific databases, and in silico performance evaluation.

In the aforementioned process, extensive use of public databases is required. Zeng Xianqiu emphasized the advantages and disadvantages of these resources. While public databases offer benefits such as comprehensive data and ease of access, they also present challenges including data redundancy and informational errors.Data redundancy leads to inefficient analysis, while information errors may stem from human error or genomic contamination. To address these issues, developers need to clean the database through operations such as noise reduction, signal-to-noise ratio assessment, and removal of contaminated homologous genomes, thereby improving analytical efficiency and accuracy.

Furthermore, in clinical applications, developers also need to build an interpretation knowledge base.Zeng Xianqiu pointed out that, in addition to the need for standardization of test results, another critical issue is how to apply these results in clinical practice—specifically, how to differentiate whether a detected bacterium is a pathogen or merely a contaminant or incidental finding. This requires researchers to make judgments based on clinical context and patient case information, thereby necessitating the introduction of databases to aid in interpretation.

Of course, after the database is developed, it cannot be directly applied in clinical practice as an analytical product. Researchers need to develop corresponding tNGS and mNGS products based on the database, combined with actual clinical needs, before they can be put into use. After product development, validation and refinement are also required. During actual product validation, Zeng Xianqiu’s company found that, compared with traditional methods, tNGS demonstrated higher sensitivity and specificity in tuberculosis-related testing; for mNGS, the positivity rate was significantly increased in large-scale applications compared with traditional methods, and the product showed good quality performance in quality assessments.

Zeng Xianqiu concluded by emphasizing the importance of industry standardization. Currently, there are differing perspectives and standards within the industry regarding the application of tNGS and mNGS. However, all differentiated testing technologies and products that emerge in the early stages can gradually move toward standardization and industrialization over time. In this context, the entire industry chain must work collaboratively to jointly establish standards and address key industry pain points, thereby accelerating industry standardization as well as product optimization and iteration.

We anticipate that, with continuous technological advancements and the gradual refinement of industry standards, high-throughput sequencing technology will provide a more accurate, rapid, and reliable basis for clinical pathogen diagnosis, thereby making greater contributions to global public health.