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China's GeneMind Biosciences Launches GenoCare 1600 Single-Molecule Sequencer


BALTIMORE – Chinese sequencing tech company GeneMind Biosciences has launched its single-molecule DNA sequencer, GenoCare 1600.

The Shenzhen-based company, which live-streamed the launch event on WeChat on Monday due to regional COVID measures in China, appears to be rolling out the platform exclusively in China for now. It did not respond to questions regarding plans to commercialize the sequencer outside of the country.

During the event, GeneMind CEO Qin Yan offered some details about GenoCare 1600. According to him, the benchtop sequencer can accommodate one flow cell with 16 independent lanes. The instrument can produce 240 million reads per run, generating 8 Gb to 12 Gb of data, with read lengths ranging from single-end 36 bases to 75 bases. In addition, the turnaround time for the platform, from sample to report, is about 24 hours.

Yan also described the key technology behind GenoCare 1600, surface-restricted fluorescence sequencing (SURFseq). It combines total internal reflection (TIRF) microscopy to identify the fluorescent signal of a base, a high-fidelity sequencing chemistry, and high-density flow cells, as well as machine learning and AI-based analysis software for signal processing.

Similar to Illumina sequencing, GenoCare 1600 uses a sequencing-by-synthesis chemistry, which comprises cycles of base incorporation, washing, imaging, and cleavage of the fluorescent tag. However, one main distinction for GenoCare is that it does not involve PCR amplification. Instead, fragmented sample DNA can be directly loaded onto the flow cell.

The PCR-free feature can help reduce sequencing errors and biases as well as ​​streamline the sample preparation workflow, Yan claimed, making the platform "especially suitable to be deployed to local hospitals" for clinical testing.

During his presentation, Yan outlined the R&D timeline for GenoCare 1600, noting that the company developed the prototype for the instrument between 2014 and 2015, followed by multiple iterations of the platform in the years after.

This timeline is congruent with that of Direct Genomics, the company that originally developed the GenoCare platform based on Helicos BioSciences’ technology. In 2019, Direct Genomics ousted its founder, He Jiankui, after he edited the germline genomes of twin girls as embryos, for which he was sentenced to prison.

Yan did not mention Direct Genomics or GeneMind’s relationship with that company during the event. The firm also did not respond to an inquiry regarding whether it is a direct successor to Direct Genomics and its single-molecule sequencing technology from Helicos. Previously, a spokesperson from GeneMind had said the company "would like to make a clarification relative to gene-editing events" but subsequently declined an interview to offer more details.

Yan said GeneMind initiated clinical validation of the GenoCare platform in 2019. In June of this year, the platform secured approval from China's National Medical Products Administration (NMPA) for noninvasive prenatal testing (NIPT) to detect trisomy 21, trisomy 18, and trisomy 13. However, the device is not approved for clinical human whole-genome sequencing, according to the agency.

During the launch event, GeneMind Chief Technology Officer Lei Sun, a former senior scientist at Pacific Biosciences according to the company's website, highlighted some applications of GenoCare 1600, including NIPT, copy number variation (CNV) detection, preimplantation genetic testing for aneuploidies (PGT-A), and RNA sequencing.

For NIPT, the typical GenoCare 1600 sequencing workflow involves 1.5 hours for DNA extraction, 1.5 hours for sequencing library preparation, and 30 minutes for priming the flow cell with an automated instrument, according to Sun. Each sequencing run can accommodate 32 samples while generating 3.5 million reads per sample.

Sun showcased a dataset where the company tested GenoCare 1600 on 2,888 NIPT samples, including several with trisomy 21, trisomy 18, and trisomy 13. The data indicated that the platform delivered results that were "highly concordant" with the traditional clinical diagnosis methods. Additionally, the absence of PCR amplification enables GenoCare 1600 to avoid GC bias, augmenting the sequencing accuracy, Sun said.

He also showed that the platform was able to detect trisomy 8 in a case at Zhejiang University Hospital that was missed by conventional next-generation sequencing.

Similarly, for CNV detection, Sun said that the platform can process 32 samples per run while delivering data with minimal GC bias. The company tested the instrument with gDNA standard samples harboring nine different CNVs and was able to identify all of these. When applying the platform to analyze 117 CNV-positive and 83 CNV-negative miscarriage samples that were previously profiled with conventional NGS, GenoCare 1600 was able to achieve 100 percent positive predictive value (PPV) and perfect negative predictive value (NPV).

Sun also highlighted a 2020 study that was coauthored by GeneMind scientists and published in BMC Medical Genomics. In that paper, researchers deployed GenoCare to sequence samples from fraternal twins with Phelan-McDermid syndrome and their parents and helped discover that the patients had a deletion that did not involve the SHANK3 gene.

Beyond clinical applications, Sun also illustrated GenoCare’s potential research use such as for single-molecule direct RNA sequencing and targeted sequencing of cancer-related genes. Specifically, Sun said RNA probes can be anchored on the GenoCare flow cell, enabling on-chip capture of mRNA for direct sequencing, eliminating the need for cDNA synthesis.

Minyue Dong, chair of reproductive genetics at the Women's Hospital of Zhejiang University School of Medicine, shared some preliminary data on GenoCare’s performance for NIPT. His team used the sequencer to analyze more than 400 samples — 195 from pregnant women of advanced maternal age, 70 from pregnancies suspected of high risk based on genetic screening, and 152 from pregnancies with abnormal embryos observed with ultrasound.

The results showed that GenoCare achieved 97 percent overall specificity for NIPT and perfect sensitivity for trisomy 21, trisomy 18, and trisomy 13. Additionally, the platform’s overall negative predictive value (NPV) was 100 percent, while the positive predictive value (PPV) for trisomy 21, trisomy 18, and trisomy 13 was 99 percent, 97 percent, and 46 percent, respectively.

When compared with another NGS platform, Dong said, GenoCare tends to show less GC bias and higher resolution than Illumina's NextSeq 550, although he did not provide more details. As such, he said that GenoCare, with its desirable throughput, speed, and cost, could augment the field of NIPT, although more large-scale clinical validation studies are still needed.

Yan said GeneMind currently holds more than 270 patents across the globe pertaining to its single-molecule sequencing technology. According to the United States Patent and Trademark Office, the company currently holds close to 20 patents in the US, issued between 2019 and October 2022.

In addition, Yan said the company currently has a manufacturing center in Shenzhen, which is capable of producing 1,000 sequencers per year. The company also manufactures its sequencing reagents, flow cells, nucleotides, fluorescent dyes, and key enzymes in house, he added.

GeneMind did not disclose any sales projections for GenoCare 1600 during the event. It also did not respond to questions about pricing for the GenoCare 1600 instrument or its sequencing cost.