Edico Genome Aims at Data Processing Bottleneck in Whole Genome Sequencing
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the number of servers being used. Some companies, such as four-year-old Bina Technologies of Redwood City, CA, have developed new ways to optimize these server clusters to reduce the time, cost, and complexity of matching millions of short DNA sequences so they are in the correct order.
Edico CEO Pieter van Rooyen says his company’s technology can dramatically lower the cost of mapping a genome, and is more accurate and power-efficient than existing technologies. By mounting Edico’s proprietary Dragen processor on a standard computer expansion bus (similar to a graphics processing card) that is dedicated for genomics processing, van Rooyen says Edico’s technology could be installed in any next-generation sequencing machine—and would reduce the time needed to map a genome from 20 hours to 20 minutes.
In contrast to a computer server that operates according to a generalized set of instructions, the Dragen processor has been optimized specifically for genomic sequencing. As a result, van Rooyen says the Dragen processor can process in a single clock cycle what takes a server 4,000 clock cycles to accomplish.
“We can more than handle the data,” van Rooyen says. “This truly takes [genome sequencing] from a long process to more of a push-button sequencing, and helps address all the other issues surrounding genome sequencing, like IT staffing and data storage.”
Van Rooyen says the underlying innovation of Edico’s technology is in the way the company implemented the genome-mapping algorithm, incorporating data compression techniques into a Field Programmable Gate Array (FPGA), a processor that is configured for specialized use after it is manufactured.
“It’s not a hard problem in a sense, but it is a large problem,” said Tim Hunkapiller, a Seattle-based genomics expert who reviewed Edico’s chip design and technology. “They took a hard-core approach. It’s a really highly efficient implementation of the mapping algorithm… The secret sauce, if nothing else, is that they just did a really good job.”
Hunkapiller is a consultant for Carlsbad, CA-based Life Technologies, now part of Thermo Fisher. According to van Rooyen, he reviewed the Edicos technology on behalf of a high-profile investor who was considering backing the company.
Van Rooyen, a South African with a doctorate in electrical engineering, says he came up with the idea for Edico’s technology years ago, when he was working in South Africa as … Next Page »