Qitan Tech Unveils QNome-3841, Pioneering the Era of Domestic Nanopore Sequencing

“Carbon-backbone nucleic acid molecules pass uniformly through protein nanopore channels under the influence of electric field forces.”

At the product launch event for QNome-3841, Hu Geng, Co-founder and CEO of QitanTech, provided the first comprehensive public explanation of the origin of the company’s name. This strikingly straightforward name may well reflect the focus and perseverance of these pioneers and innovators in their quest to develop nanopore-based single-molecule gene sequencers. After all, within the boundless aspirations inspired by genetic technologies, the precise decoding of life’s information remains the most fundamental prerequisite.

Hu Geng, Co-founder & CEO of QitanTech (Image from QitanTech)

Bai Jingwei, Co-founder and Chief Scientist of QitanTech, unveiled the long-awaited domestically produced nanopore gene sequencer, the QNome-3841. This marks another high-profile market move by the Qitan team, following the release of China’s first nanopore gene sequencer, the QNome-9604, last September, with the launch of its first commercial product ready for mass production and large-scale market deployment.

If nanopore sequencing also becomes an epoch-making technology like NGS, QNome-3841 will surely be written into the history of humanity’s exploration of the microscopic world.

Bai Jingwei, Co-founder & Chief Scientist of QitanTech (Image from QitanTech)

Prior to the market launch of QNome-3841, QitanTech initiated an Alpha Test in May this year. Leveraging the QNome-9604 sequencing platform, the company has collaborated with universities, research institutes, sequencing enterprises, and other organizations across fields such as pathogen research, genetic disease research, oncology, forensic science, and wildlife conservation, involving over 70 projects and more than 1,500 samples.

Compared to the stable output of 800 Gb of data, for QitanTech, the more significant meaning of the Alpha Test lies in the fact that users’ trust and expectations for domestically produced nanopore sequencers far exceeded the team’s anticipation. Therefore, in a sense, the market launch of the QNome-3841 and the dawn of the era of domestically produced nanopore sequencing are not solely matters concerning QitanTech.

In every previous interaction with VCBeat, QitanTech has shared more of its reflections on the phased limitations of its nanopore sequencing technology, such as the electrical module’s control over molecular vibrations, further optimization of nanopore structures, and enhanced plasticity of organic substrate chips, each time accompanied by corresponding solutions. When QitanTech announced its Series B financing in June this year, Bai Jingwei stated that the development of a new generation of nanopore proteins was nearing completion. In early December, the launch of a new instrument marked another product iteration for QitanTech.

With QNome-3841 by its side, Bai Jingwei’s thoughts have reached even further: QitanTech has already begun to envision a future where everything is linked and all things can be sequenced.

In China, QitanTech is virtually the earliest startup team to have devoted itself entirely to the research and development of sequencing technology based on biological nanopores, maintaining a rapid pace of iteration. Established in 2016, the team successfully developed a 16-channel proof-of-concept prototype in its second year, which was upgraded to a 64-channel engineering prototype the following year. In January 2020, QitanTech launched its minimum viable product (MVP), featuring 384 nanopores. Building on this foundation, the company officially released its first-generation QNome-9604 Nanopore Gene Sequencer, a device roughly the size of a tissue box, in September 2020. This instrument delivers sequencing throughput at the hundreds of megabases level, with a single-run accuracy rate reaching 85%.

The QNome-3841 sequencer, unveiled at the press conference, is an upgraded version of the QNome-9604. It incorporates self-developed ASIC integrated circuits and marks the first mass production of nanopore sequencers in China.

Single-molecule sequencing is regarded as the next-generation gene sequencing technology following Sanger sequencing and NGS, offering distinct generational advantages such as longer read lengths, faster sequencing speeds, and lower costs. However, its accuracy limitations have consistently constrained its application in broader scenarios.

In response, one of QitanTech’s solutions is to continuously improve nanopore proteins.

Over the past five years, QitanTech has gradually established a comprehensive system for the screening, identification, and optimization of nanopore proteins. In late 2020, leveraging rapidly advancing structural biology technologies, QitanTech discovered a new series of nanopore proteins and screened out candidates with engineering potential from hundreds of candidate scaffolds. Following in-depth research and engineering optimization, the K2 nanopore protein was developed. “This was essentially a massive protein engineering endeavor,” stated Bai Jingwei. However, the new protein scaffold yielded remarkable results: even before algorithmic optimization, sequencing accuracy surged from 90% to 95%. “This represents a qualitative leap.” Compared to its predecessor, the K1 nanopore protein, the K2 variant enables more uniform current signal distribution and a wider dynamic range of signal transitions. It is reported that QitanTech continues to optimize the structural uniformity and integrity of its nanopore proteins, aiming to further elevate the accuracy of nanopore sequencing to levels comparable to those of Next-Generation Sequencing (NGS).

QNome3841 (Image from QitanTech)

Visually, the QNome-3841 is more streamlined and compact than the QNome-9604, truly realizing the concept of a handheld sequencer. This design facilitates mobility for laboratory personnel or enables on-site deployment. In terms of read length, long reads are a hallmark of nanopore single-molecule sequencing; theoretically, there is no upper limit to read length, which depends solely on the length of the sample nucleic acids. Consequently, it offers an extensive read length range, with internal testing at QitanTech having achieved reads up to 300 kb. Regarding accuracy, the QNome-3841, equipped with its high-speed basecalling model, achieves a single-pass accuracy of 90% and a consensus accuracy (50×) of 99.9%. In terms of throughput, the QNome-3841 also demonstrates improved performance over its predecessor, generating 1–1.5 Gb of data within 8 hours.

According to QitanTech’s vision, the QNome-3841 sequencer will be a tool designed for diverse users that fully leverages the advantages of strand sequencing technology, enables real-time analysis during sequencing, and facilitates comprehensive understanding of genes and discovery of disease mechanisms. In other words, they aim to empower people to gain deeper insights into life through the QNome-3841. Therefore, accessibility and ease of use are the most fundamental requirements.

Xie Dan, co-founder of QitanTech, told VCBeat that the company’s production base located in the Chengdu Tianfu International Bio-town has been completed and is poised to commence operations. Spanning over 4,000 square meters, this facility marks China’s first production base dedicated to nanopore sequencers. It houses manufacturing workshops for protein reagents, biochips, and sequencers, thereby achieving full-scale production of nanopore sequencing instruments along with their complementary chips and reagents. In terms of capacity, the base can readily produce 2,000 nanopore sequencers annually, as well as one million sets of supporting chips and reagent kits.

“Nanopore proteins are the most critical core components. Over the past five years, we have primarily focused on their screening, development, and the establishment of manufacturing processes. Our fully independent R&D capabilities enable fully autonomous production, thereby facilitating entry into mass production. This constitutes our most stable guarantee for meeting capacity demands,” stated Xie Dan.

As a core component of nanopore sequencers, QitanTech has developed two types of fluidic chips: organic substrate-based and silicon substrate-based. The former presents significant development challenges and is entirely an innovative, independently developed solution by QitanTech, offering substantial cost advantages; the latter leverages traditional semiconductor manufacturing processes, providing greater maturity in mass production accessibility and enhanced stability.

In terms of the operating system, QNome-3841 also offers two options: a standalone sequencing system based on high-performance computing and a sequencing system based on distributed computing, thereby meeting users’ application needs in different scenarios as much as possible and ensuring ease of use.

Specifically, under the standalone sequencing system, users can choose between high-speed or high-precision algorithm modes, allowing them to flexibly balance efficiency and accuracy requirements. Furthermore, the standalone sequencing platform supports cross-platform operations, covering both PC and mobile ends, thereby facilitating multi-scenario usage. The software platform adopts a microservices architecture with modular design, ensuring that optimization or upgrades of individual modules do not disrupt the operation of others. In contrast, the distributed computing-based sequencing platform is cloud-enabled, allowing users to choose between public or private clouds. This meets the need for unified management of multiple sequencing platforms in large-scale application scenarios such as major hospitals and sequencing centers. Meanwhile, QitanTech provides necessary technical support across key stages, including sample collection, nucleic acid extraction, library preparation, and bioinformatics analysis.

“Our goal is to ensure that domestically produced nanopore sequencers truly serve application-oriented needs, ushering in an era of localized nanopore sequencing in China,” pointed out Xie Dan.

When asked when and how domestically produced nanopore sequencers would achieve widespread adoption across multiple application scenarios, including scientific research, clinical practice, forensics, and industry, Xie Dan stated that this is also a question QitanTech has been contemplating. “Just as the development of nanopore sequencers themselves is driven by the combined advances in electrochemistry, structural biology, genomics, and other technologies, the construction of an application ecosystem for nanopore sequencers will not result from a single variable,” Xie Dan said. “What we can accurately grasp at present are the clear demands for nanopore sequencers across various application scenarios and their capability to meet specific needs. Our task is to promote the flourishing of nanopore sequencers in each of these application areas.”

During the Alpha Test phase, QNome-9604 was applied to multiple research areas, including microbial metagenomic testing, species identification, small-scale genome assembly, clinical pathogen detection, and viral genotyping. Records across various performance metrics were continuously broken, while QitanTech’s internal product design and manufacturing processes were steadily refined.

Xie Dan, Co-founder of QitanTech (Image from QitanTech)

In collaboration with Beijing Tsinghua Changgung Hospital, a study on metagenomics of bloodstream infections was conducted. Leveraging the unique features of the nanopore sequencing platform, the partners co-developed an efficient method for host nucleic acid depletion. Using the QNome-9604 sequencing platform, metagenomic sequencing was performed on a peripheral blood sample from a clinical patient with fever. While conventional microbial culture yielded negative results, the QitanTech sequencing platform detected trace amounts of pathogenic bacteria in the sample. In another collaborative project with Peking University Third Hospital, which focused on metagenomic testing of lower respiratory tract infection samples, researchers utilized the QNome-9604 sequencing platform to obtain a more comprehensive profile of infectious bacteria in patients.

Xie Dan pointed out that the Alpha Test validated QitanTech’s product logic for developing nanopore sequencers. This sequencing approach, characterized by significantly longer read lengths and faster speeds compared to mainstream next-generation sequencing (NGS) methods, has provided new insights and replicable solutions in a series of scenarios where no effective sequencing strategies had previously been identified. “In the future, as nanopore sequencing technology becomes more refined and widely adopted, we believe that gene technology can address a broader range of human challenges.”

It is understood that during the upcoming promotional period, QitanTech will adopt a dual-pronged approach. On one hand, the company will leverage events, conferences, and collaborative research initiatives to increase awareness of nanopore sequencing technology among researchers. On the other hand, recognizing nanopore sequencing as a cutting-edge technology, QitanTech is actively establishing a nationwide network of local service teams to provide timely technical support aligned with users’ learning curves. “The most critical task at this stage is to facilitate the faster and more effective deployment of nanopore sequencers in scenarios where there is demand,” stated Xie Dan.

Humanity’s exploration of the mysteries of life is delving ever deeper into the microscopic realm, moving from the human body to organs, and from tissues to cells. Each advancement brings a more accurate understanding of ourselves and the world. With the aid of genetic technologies, we can now observe life at the molecular level. If next-generation sequencing presents a smoothed-out version of the central dogma, nanopore sequencing undoubtedly offers richer details—details that may well hold the answers we have long sought.