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Edico Genome Makes First Sale of NGS Processor


By Laurel Oldach 

September 4, 2014 | The year of the thousand-dollar genome just got a little more interesting as Edico Genome, which makes a data processor called the DRAGEN for next generation sequencing (NGS) data, made its first sale to Sequenom, Inc.

According to its designers at Edico, the DRAGEN, short for Dynamic Read Analysis of GENomes, reduces the time to map a complete human genome to reference by sixty-fold. At present the mapping, sorting, deduplication and variant calling that are required to turn 200 GB of raw massively parallel sequences into an interpretable genome takes, by Edico’s estimate, about twenty hours on an industry standard server. The marketing team at Edico Genome likes to compare the task to piecing together a telephone book that’s been put through an industrial shredder. This poses a considerable threat of backlog given that a high-throughput sequencer like Illumina’s HiSeq X Ten can turn out a comparable amount of sequence every thirty minutes.

For Sequenom, a leader in noninvasive prenatal testing (NIPT) with about 40% market share, faster analysis at lower cost is of the essence. In contrast to more established methods of prenatal testing, which draw DNA directly from the placenta and pose some risk of miscarriage, NIPT uses maternal blood, which contains short fragments of circulating fetal DNA. If mapping a single genome is like piecing together a telephone book, then NIPT is like putting together two telephone books, which share at least half of the constituent phone numbers, when there are a dozen copies of Mom’s phone book for every one of Baby’s. Nonetheless, Sequenom has found ways to piece together a low-coverage sequence of the fetal genome, enough to identify aneuploidy as well as some microdeletions. The company advertises diagnostic capability for a panel of fourteen genetic disorders, from Down syndrome (trisomy 21) to Prader-Willi/Angelman syndrome (deletion in 15q).

Sequenom’s flagship MaterniT21 Plus test currently has a five-day turnaround time from receipt of a maternal blood sample. To speed its data processing, Sequenom plans to use the mapping, sorting and deduplication algorithms built into the DRAGEN; although the DRAGEN pipeline also includes an algorithm for variant calling, Sequenom will continue to use its own proprietary software at this step. Neither party will comment specifically on the time or cost savings Sequenom gains from adding the DRAGEN to its pipeline, but both are reportedly significant.

The sale was sealed after Sequenom took part in an early iteration of Edico Genome’s availability program, which allowed participants to test the DRAGEN against their existing pipelines. Both parties are close-mouthed about the specifics of these trial runs, citing an upcoming poster to be presented at the American Society for Human Genetics annual meeting in October. “We’re very excited specifically because Sequenom is one of the leaders in clinical genomics. It’s also a big endorsement of our product,” says Edico CEO Pieter van Rooyen, adding, “we’ve got a fairly significant number of other customers involved in the early access program already.”

The DRAGEN’s increase in processing speed is achieved by an application-specific integrated circuit, hardware that sacrifices the flexibility of a general-purpose server for efficiency in the specific task of arranging segments of a genome. “We have the cheapest solution because we come to it from a consumer electronic perspective,” says van Rooyen, an electrical engineer by training. The concept of using reconfigurable hardware (the DRAGEN uses a field-programmable gate array, or FPGA) to speed up computationally intensive alignment is not new; however, engineering at Edico Genome has enabled them to shrink the analytical platform to just one FPGA compared to the multiple parallel FPGA chips required for tools such as the GSC XpressAlign. The DRAGEN is an external chip that can be integrated into a sequencer or server, with what Edico describes as a push-button workflow once installed.

It has been an eventful summer for Edico, which raised $10 million in venture capital in July. For now, van Rooyen says, the company will focus on scaling up, courting new customers in subfields of clinical genomics such as tumor profiling, rare disease diagnosis, and pharmacogenomics. “We’ve got awesome technology, and we’re happy to get it out into the hands of customers,” says van Rooyen. “We would like to make sequencing cheap and affordable, and get to the bottom of all these different diseases… as was promised [with the initial draft of the human genome] fourteen years ago.”

 

 

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