Qitan Technology Accelerates Commercialization of Domestic Nanopore Sequencers: What Has It Done Right?

“Currently, more than 100 institutions are using the QitanTech QNome sequencing platform.”

At the new product launch held on June 28, Dr. Xie Dan, co-founder of QitanTech, reviewed the company’s initial achievements in its commercialization efforts. The QNome-3841, the first commercially available nanopore sequencer developed in China by QitanTech, was officially launched in December 2021 and has since been rapidly applied to research in various fields, including disease control and prevention, pathogen research, animal epidemic prevention and control, and environmental monitoring and protection.

In its sixth year, QitanTech has finally completed the technological accumulation for its fully domestically produced nanopore sequencer, marking the inaugural year of its commercialization. According to Dr. Xie Dan, multiple research teams from scientific research institutes, universities, hospitals, and centers for disease control and prevention are currently conducting research and exploring applications across various fields based on QitanTech’s QNome sequencing platform, resulting in the publication of five high-impact papers in SCI-indexed journals. Furthermore, the company has made rapid progress in its intellectual property (IP) layout; to date, it has accumulated nearly 200 IP achievements, including over 80 invention patents.

From theoretical exploration to engineering prototypes, and finally to commercial products, the stability, core performance, and empirical data of QNome-3841 have all gained market recognition. As China enters an era of domestically produced nanopore sequencers, certain cutting-edge research paradigms are being transformed by efficient, high-precision domestic instruments.

QitanTech’s Fully Independently Developed Generations of Nanopore Gene Sequencers | Image Source: Provided by the Interviewee

Meanwhile, QitanTech is rapidly iterating its products and gradually building a diversified product portfolio. On June 28, the company officially launched QNome-3841hex, an upgraded sequencer to its QNome-3841 model. Reportedly, this product was developed to meet users’ needs for greater flexibility and higher-throughput sequencing. Specifically, the QNome-3841hex can generate 18 GB of data per run, allowing flexible sequencing by enabling different samples to be processed at different times using single or multiple chips. This aims to help a growing number of research, clinical, and industrial users explore new genetic questions with nanopore sequencers.

In fact, for QitanTech, the phased success of its initial commercialization attempt represents both accumulated experience and favorable timing.

In China, QitanTech was among the first teams to engage in and explore the development of nanopore sequencers, witnessing the tortuous growth of this industry.

For a long time after its invention, the advantages of nanopore sequencing technology in gene sequencing, such as long read lengths and real-time sequencing, remained an elusive dream for most scientific research practices. Due to high per-run costs and inconsistent accuracy, this technology was confined to a few top-tier research laboratories. In recent years, with leapfrog advancements in multidisciplinary technologies including structural biology, bioinformatics, and electronics, the performance and efficiency of nanopore sequencing have improved significantly, leading to the emergence of key research findings based on these platforms.

In a sense, after more than a decade of exploration, nanopore sequencing technology is now entering a window period for widespread application.

In late March of this year, Science published six articles in succession, presenting the first complete, gap-free sequence of the human genome. This milestone came 20 years after the announcement of the renowned Human Genome Project reference map. Yet few are aware that 8% of human bases were left as gaps in that earlier map—a testament to the wisdom and years of effort by the world’s leading scientists at the time—because their highly repetitive sequences made assembly exceedingly difficult.

“Sequencing the entire human genome is an attempt to uncover the last unknowns of the human genome, and the reason it had never been successfully accomplished before was the immense difficulty involved.” This is how the lead researcher described the missing 8% of the human genome. According to the subsequent interpretive article on the sequencing work, nanopore sequencing technology played a crucial role in this study.

The underlying reason is that, in the past, widely used second-generation sequencers required splitting complete gene sequences into small fragments for decoding and subsequent reassembly into sequence maps. While this approach enabled sequencing of the majority of base sequences, it failed to identify short stretches of long repetitive genomic sequences. This is why 8% of the genome sequencing effort was forced to be shelved. The principle of nanopore sequencing technology mentioned earlier involves passing intact DNA molecules through nanoscale pores to obtain base information from very long sequences.

In China, an increasing number of researchers are employing nanopore sequencers to explore the unknown.

Researchers conducting experiments. Image credit: Provided by the interviewee

At QitanTech’s new product launch, Professor Li Ruichao from the College of Veterinary Medicine at Yangzhou University, an early user of QitanTech’s nanopore gene sequencer, stated that previous studies had demonstrated the clear advantage of the QNome platform in terms of sequencing read length. He expressed his expectation for Chinese-made nanopore gene sequencing technology to become more mature and stable. Professor Wang Hui, Director of the Clinical Laboratory at Peking University People’s Hospital, and Researcher Yang Hang from the Wuhan Institute of Virology, Chinese Academy of Sciences, also shared their experiences and insights regarding the practical testing and application exploration of nanopore gene sequencers in microbiological research. In their view, domestic nanopore sequencing platforms have already demonstrated technical advantages in areas such as bacterial genome assembly, metagenomic sequencing, and detection of drug-resistant bacteria.

In the early stages of commercialization, nanopore sequencers became a powerful complement to next-generation sequencing instruments.

Currently, although second-generation sequencers remain the mainstream sequencing technology platform, their significant limitations—such as short read lengths (75 bp–300 bp), bulky instrumentation, and high capital investment—restrict their applicability in many scenarios. In contrast, nanopore gene sequencers offer longer read lengths (up to 2 Mb), faster speed, real-time data output, streamlined operation, compact portability, and lower instrument costs, thereby providing more efficient solutions across diverse application scenarios.

QitanTech QNome Sequencing Platform Image source: Provided by the interviewee

At this stage, QitanTech’s nanopore sequencing technology is most maturely applied in scientific research and clinical innovation for pathogenic microorganism detection.

Specifically, on one hand, in terms of bioinformatics methods for pathogenic microorganism detection, QitanTech has established a complete set of standards and procedures for constructing pathogen databases. Through quality control, removal of redundant data, and screening of pathogen subtypes that infect humans, combined with microbiological and epidemiological characteristics of pathogens, data features are defined and structured to establish representative reference sequence libraries and infection knowledge bases for pathogens.

On the other hand, QitanTech has developed a pathogen sequence identification algorithm and analysis pipeline tailored to the characteristics of nanopore sequencing data—specifically its long read lengths and inherent error rates in raw instrument output—to meet the demands of real-time analysis. By employing methods such as rapid alignment-based identification, precise alignment verification, and cross-alignment to eliminate species misclassification, this approach enhances the sensitivity and specificity of pathogen detection. Furthermore, through precise alignment with antimicrobial resistance (AMR) gene databases and leveraging the direct association between AMR genes and species enabled by long-read data, it accurately identifies potential drug-resistant bacteria in samples, thereby providing evidence to guide clinical treatment.

“Compared with the second-generation sequencing mNGS approach, the method we have developed significantly reduces turnaround time, meeting the diagnostic needs for respiratory tract infections,” said Dr. Xie Dan. “These features also make it more readily acceptable to primary-care hospitals and laboratories, and enable its application in point-of-care sequencing settings.”

In addition, leveraging the nanopore sequencing platform’s ability to directly sequence genetic material—thereby avoiding amplification and GC bias—and its capacity for read lengths exceeding 2 Mb, QitanTech is exploring a wide range of applications, including mutation detection, small genome assembly, fusion gene detection, and structural variant detection. The company is also working to unlock the platform’s potential for detecting epigenetic modifications and other small molecules, such as proteins.

In the future, nanopore sequencing technology may reshape the landscape of the sequencing industry, driving an upgrade from centralized, capital-intensive models to distributed, grassroots-level technologies.

At the end of last year, coinciding with QitanTech’s release of the QNome-3841, its manufacturing base in the Chengdu Tianfu International Bio-Town was completed and commenced operations. From QitanTech’s perspective, nanopore gene sequencers represent the trend toward miniaturization and portability in in vitro diagnostic equipment, and domestic production is a critical milestone for the large-scale adoption of this technology.

On one hand, in the field of nanopore gene sequencers, only two companies worldwide—Oxford Nanopore Technologies from the UK and QitanTech—have launched commercial products. From a customer experience perspective, domestically produced products offer shorter logistics cycles, lower transportation costs, and eliminate the need for long-distance overseas shipping, thereby ensuring better shelf life and stability of reagents and chips. Furthermore, QitanTech has established professional pre-sales and after-sales service teams across China, enabling timely responses to user needs, which is crucial for the early adoption of technologically innovative products.

On the other hand, biosafety data security has risen to the level of national strategy; domestically produced sequencers can better ensure the information security of genetic big data. The cost is lower due to the complete localization of components, avoiding supply chain constraints imposed by foreign countries.

“The prerequisites for domestic substitution of nanopore sequencers are achieving internationally leading key performance indicators, localizing core components, and ensuring pricing aligns with national market demands,” pointed out Dr. Xie Dan. “On this basis, we will promote the translation of cutting-edge technologies into grassroots applications.”

VCBeat has learned that QitanTech’s newly launched QNome-3841hex retains the features of its predecessor, maintaining a single-read accuracy of 90% and a consensus accuracy of 99.9%. The sequencing read lengths range from 200 bp to over 2 Mbp. In terms of application performance, QitanTech conducted performance tests with various chip combinations on the QNome-3841hex to address diverse scenario requirements. Application testing was carried out in multiple areas, including pathogen identification, microbial assembly, tumor fusion gene detection, forensic identification, and low-depth human genome sequencing, all yielding results or metrics that exceeded expectations. These outcomes demonstrate the broad applicability and reliability of the QNome-3841hex. By continuously launching supporting products such as automated library preparation systems, ultra-long library preparation reagents, various application-specific kits, and bioinformatics analysis tools, QitanTech is steadily lowering the barrier to entry for nanopore sequencing platforms.

QNome-3841hex Nanopore Gene Sequencer

“Next, we will initiate the application for QitanTech’s first Class III medical device certification from the NMPA, which will also be the first such application for a nanopore gene sequencer in China,” stated Dr. Xie Dan. He indicated that within 2022, QitanTech plans to finalize the design of the instrument intended for registration and commence regulatory testing. “Although the process from application to approval for a Class III medical device certificate is lengthy, obtaining this certification is a prerequisite for accessing the vast clinical market.” Furthermore, QitanTech is actively promoting the development of relevant standards for the domestic sequencing industry.

Beyond commercializing nanopore gene sequencing, QitanTech is also working to build awareness and understanding of next-generation sequencing concepts among broader audiences. The company aims to engage more people in exploring the unknowns of life, leveraging this fascinating nanopore sequencing technology to answer more fundamental biological questions.