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BioNano Genomics Ships V2 Chip for Human Genome Analysis; Anticipates Booking 25 Systems in 2014


BioNano Genomics is now offering a V2 chip for its genome analysis platform, Irys, and it anticipates orders for the system will jump to 25 in 2014 from 10 in 2013, the company said at last week's JP Morgan Healthcare Conference in San Francisco.

The company launched Irys, its nanochannel-based single-molecule DNA mapping platform last year, and the first version of its chip was geared toward mid-sized genomes such as the fruit fly, CEO Erik Holmlin said during a presentation.

A new version of its chip is available for order from new customers, and BioNano Genomics has completed upgrading its installed base with the V2 chip. Using three of the V2 chips, researchers can map an entire human genome. Holmlin said that by mid-year the company will increase throughput of the chip to enable a human genome to be mapped using two chips, and by the end of the year only one chip will be required, enabling a human genome to be mapped and scanned in one day. In 2015, the firm plans to offer a V3 chip, which will reduce the scanning time to one hour per chip for a human genome.

Holmlin said that the company anticipates its installed base will reach 35 systems in 2014, bringing in $9 million of revenue, and hit 111 systems in 2015 for $33 million. It is also currently seeking to raise between $30 million and $35 million in a Series C financing round, and it expects to break even by 2015 and be cashflow positive by 2016. By 2017, Holmlin projects the company will have revenues exceeding $100 million.

Holmlin said it is the nanochannel arrays on the chips that are key to the system. The 45-nm2 nanochannels are picked purposely because at that size a "DNA molecule will spontaneously unwind," Holmlin said.

Prior to linearizing the DNA, sequence-specific labels are applied. The DNA is then loaded onto the chip where it is stretched out, scanned, and imaged. Algorithms then convert the images into molecules; additional algorithms then align the molecules de novo and construct a consensus genome. Relative positions of labels are measured and can be compared to every other label in the genome, which enables cross-mapping across multiple samples or to a reference genome, Holmlin said.

The company is positioning the Irys system as a "bridge" between cytogenetics and next-gen sequencing. While next-gen sequencing is great at detecting small variations, it does not readily pick up mid- to large-sized structural variations. Cytogenetics, meantime, can detect very large variations, but is not good for de novo discovery — researchers must know what they are looking for.

The Irys system finds mid- to large-size variations, "and reveals the order and orientation of functionally relevant components," Holmlin said.

For instance, the company has used its technology to look for structural variations in a well-characterized trio of cell lines known as the CEPH trio. The Irys "found an abundance of structural variations missed by standard methods," Holmlin said. For each case, the company found between 1,000 and 1,300 structural variations, 90 percent of which were validated by third parties using orthogonal technology, and "most of which had never been described."

In a collaboration with Mike Rossi at Emory University, the technology was used to evaluate complex cancer rearrangements in multiple myeloma genomes. Multiple myeloma is characterized by recurrent chromosomal abnormalities and nearly half of all cases can be linked to one of five common chromosomal abnormalities. One such abnormality is a translocation between chromosome 14 and chromosome 4, which is especially difficult to detect with microarrays because there is no net loss or gain of genomic information. The abnormality is also linked to poor survival, and its presence may impact treatment decisions.

In the collaboration with Emory, Holmlin said that the Irys system readily detected that translocation, as well as another translocation involving chromosome 14 and chromosome 16, and a 44.9-kilobase deletion at the p53 locus. Comparing the data to RNA-seq data, the researchers discovered that a putative transcript fusion described in the RNA-seq data was actually a false positive. Mapping the genome indicated that the putative transcript fusion was actually a homologous region on chromosome 8.

Holmlin said that the company is positioning its system to target "unmet need in human genomics research," and said it could also have applications in applied markets like ag-bio, biofuels, bioterrorism defense, and forensics and human identification. The technology is "at the edge of transitioning from life science to clinical diagnostics," he said, and eventually the company will "develop relationships with pharmaceutical companies to use the technology in drug development."