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Fusion Genomics Developing Infectious Disease Dx Using Synthetic Oligonucleotide Probes, NGS

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NEW YORK (GenomeWeb) – Canadian company Fusion Genomics aims to change the way infectious disease is diagnosed using a platform that it claims can capture and identify the genomes of more than 1,400 known human pathogens.

The assay, called OneTest PathoGenome, is currently in clinical utility studies and is being designed to perform sensitive and multiplexed pathogen identification using a combination of universal sample prep, DNA/RNA capture probes, and next-generation sequencing. OneTest can capture pathogen nucleic acids from a variety of human biological samples such as blood, nasal washes, sputum, and biopsies, in addition to environmental sources like mud and air.  

Founded in 2014, the Vancouver, British Columbia-based firm originally developed its capture probes — synthetic, non-reference-based oligonucleotides that it calls QuantumProbes — to diagnose childhood sarcomas through gene fusion assays. Fusion now sees the biggest application for its technology in infectious disease detection.

Fusion Genomics CSO and President Mohammad Qadir explained in an interview that in pediatric cancer, whole-genome sequencing is addressing the inadequacies that exist in molecular diagnostic modalities such as PCR-based assays and fluorescence in-situ hybridization.  

"As the price of whole-genome sequencing continues to fall, and a rapid turnaround time ... is not critical, it is emerging as the diagnostic modality of choice for many cancers, including pediatric sarcomas," he said.

On the other hand, Qadir believes that Fusion's technology could be used to detect sources of human idiopathic infections.

The OneTest assay, which Qadir expects to release a version of the test for research use only in Q4 2018, comprises three major components: UniPrep, QuantumProbes, and FusionCloud.

A researcher initially collects samples using UniPrep, which contains standard sample prep reagents and the QuantumProbes. The probes bind to target pathogen genetic material using magnetic beads and synthetic oligonucleotides to separate the substance, enabling researchers to prepare fully enriched sequenceable libraries of genetic data within five to six hours. NGS is then performed on the sample using any platform, either in the researcher's lab or at Fusion Genomics. 

Qadir said in an email that OneTest's quantum probes "provide up to a 9000x target enrichment over metagenomic sequencing and a 1000x sensitivity over PCR assays." In addition, the firm claims that because the quantum probes can collapse all diversity, they can target viral genomes, which can mutate up to 20 percent of their genetic code.

NGS data is then transferred to the FusionCloud bioinformatics platform to match the genetic sample to one of more than 1 million infectious disease genomes. The database's bioinformatics and machine learning tools employ pattern matching and statistical rankings to expedite analysis of sequencing data for pathogen identification.  

Fusion recently partnered with IBM to employ its cloud service for secure and stable pathogen data storage. Qadir explained that Fusion chose IBM because of its ability to rapidly scale up or down while guaranteeing protection of sensitive genetic data.

"From day one, when we started, we knew that we wanted to be cloud-based, hence the partnership with IBM, since it brings a lot to the table in terms of healthcare delivery," Qadir added.

According to Qadir, the overall sample to result time for OneTest is 10 to 12 hours. The firm plans to use microfluidic technology to automate library preparation, further reducing the overall time for results to eight hours.   

Reference testing with early users from European and Canadian reference labs that test for seasonal influenza demonstrated that OneTest provides a sensitivity of approximately 1,000 times that of PCR-based assays.

Fusion is currently conducting clinical utility studies for OneTest PathoGenome, with each sample run costing the user $200 to $300.

Fusion has also developed industrial partnerships over the past few years, but did not disclose them at this time.

Using sequencing to diagnose idiopathic infections is not a novel concept, as competitors like Karius sequence circulating cell-free microbial DNA to diagnose infection. In addition, Karius' bioinformatics tools also match pathogenic sequences to microbial sequences in a reference database consisting of publicly viewable genomes and the company's internally curated samples.  

While Qadir admits that any company using whole metagenome sequencing for infectious disease are possible competitors, he believes that the firm's "OneTest pathogen-enrichment technology will produce a higher clinical sensitivity in a shorter period of time and at a lower cost.

Qadir envisions Fusion's platform in pharmaceutical companies and research laboratories, in addition to frontline tertiary hospitals and care centers.

Fusion, which has 12 full-time employees, recently finished a financing round of $2 million through a combination of angel funding, sales, and government funding. Qadir said that the firm is planning a Series A funding round with a target of $10 million.

Qadir said that he believe that the platform's biggest advantage is that it is not exclusively restricted to pathogens. Using the same set of tubes, researchers "can also interrogate other [bodily pathways], for example, immune response pathways." In addition, Qadir said that a researcher can perform massive population studies using the platform.

"We want to try and attempt 'deleting' undiagnosed infection, and in the future, we want to provide end-to-end solutions for human health, animal health, and the environment," Qadir added.

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