NEW YORK (GenomeWeb) – Novogene, a Beijing-based sequencing service provider that was founded in 2011, is looking to enter the clinical next-generation sequencing market with two cancer panels that it has submitted to the China Food and Drug Administration (CFDA) for approval, officials said this week.
The company currently offers two research-only tests, a hotspot panel and a larger panel that assesses mutations in just under 500 genes. It has validated both panels to run on either Thermo Fisher Scientific's Ion Proton or Illumina's NextSeq, CEO Ruiqiang Li told GenomeWeb.
The company is also working on a hereditary cancer panel and has plans to develop a noninvasive prenatal test.
Aside from the NextSeq and Proton, Novogene provides sequencing services for research on the Illumina HiSeq X Ten system, the HiSeq 4000 and 2500, and the MiSeq, Li said.
Prior to founding Novogene, Li was VP of bioinformatics at BGI, where he co-developed the SOAPdenovo assembly algorithm that BGI researchers first used to assemble the panda genome de novo from short sequence reads.
Li said he left BGI as the firm began to switch its focus away from Illumina sequencing technology and became interested in developing its own sequencing technology, for which it acquired Complete Genomics. BGI and Novogene have "different strategies and a different focus," he said, adding that he wanted to continue "developing applications for the Illumina technology."
With its recent HiSeq X Ten purchase, Li said Novogene has more Illumina sequencing capacity than any other service provider in China. Previously, BGI held that title.
Prior to delving into the clinical sequencing realm, Novogene focused on ag-bio research projects — participating in consortia to sequence the genomes of potato, the Tibetan boar, and cotton.
The firm's headquarters are in Beijing, but Novogene also has offices and personnel in Hong Kong, California, Washington D.C., New York, Singapore, the UK, and Australia, Li said.
The firm's first clinical tests will be its cancer panels. Already, it has run over 5,000 samples for its CFDA submission, Li said. Even before the tests gain approval, Novogene is able to provide them to physicians because the lab has medical certification, but they are "not for diagnosis," he said.
For its smaller hotspot panel, Novogene uses PCR amplicon-based technology for sample prep, and for the larger one, it uses Agilent's SureSelect capture-based technology. In each case, the panels are custom designed, as opposed to using manufacturers' off-the-shelf kits, Li said.
The larger, nearly 500-gene panel currently identifies actionable mutations in over half of patient samples, Li said, but he expects that percentage to increase with further improvements and experience running the panel.
The smaller panel will cost less than $1,000, while the large panel will be priced under $2,000, Li said. Turnaround time is less than one week.
Novogene chose to develop both a hotspot panel and a comprehensive panel to give patients and physicians choices. While the larger panel is more likely to identify an actionable mutation, sometimes a physician will just want to assess a specific hotspot mutation that is frequently mutated in a certain cancer type and can indicate a therapy.
The panels cover relevant genes across all solid tumor cancer types, although the vast majority of patient samples so far have been lung cancer samples, Li said.
Novogene is also developing a hereditary cancer panel that includes the BRCA1 and BRCA2 genes, as well as other genes that confer cancer risk, such as the Lynch syndrome genes.
Li said that the main hurdle in the development of the hereditary cancer panel is determining which variants are pathogenic. "To measure risk, we need more data and we are just now in the process of building up our database," he said. "We are studying and sequencing breast cancer patients that have a family history" in order to better annotate variants, he said, adding that the panel will be more useful with an improved database.
Li predicted that in the future, all patients who are diagnosed with cancer will be sequenced to determine whether they can be treated with a targeted therapy. In addition, he said, "cancer changes quickly," so technologies that "monitor the process to see how mutations change during treatment," will likely be adopted. For that, Novogene is working on an assay to sequence circulating tumor DNA. "In principle, we think it can be very useful," he said, and might eventually replace tissue-based tests. However, clinical utility has not yet been demonstrated, he added.
Outside of cancer, Novogene is looking to tap into the noninvasive prenatal testing (NIPT) market, which has been growing in China. Li estimated that over 1 million noninvasive prenatal tests have already been run. Both BGI and Berry Genomics have received CFDA approval for their respective NIPTs.
On the research side, Novogene is developing sample prep and bioinformatics technologies, Li said. The firm has a particular interest in technologies for single-cell whole-genome sequencing and single-cell transcriptome sequencing, as well as in improving bioinformatics for de novo assembly.
It also offers RNA-seq, bisulfite sequencing, lncRNA-seq, metagenomic sequencing, as well as whole-genome human, plant, animal, and microbial sequencing services.
In addition, Li said that China plans to launch a precision medicine program, similar to the one President Barack Obama announced for the US earlier this year.
"Many universities, hospitals, and research institutions are trying to prepare for the program," he said. "We're really hopeful for the field."