A whole lot of data compression goin' on: SD startup Edico Genome targets big bottleneck in genome sequencing http://t.co/0xqLp03ZQP
— Bruce V. Bigelow (@BVBigelow) April 17, 2014
"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. (...) 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. (...) The company already is moving its design to a
standard ASIC (Application Specific Integrated Circuit) processor, which
typically can be mass-produced at low cost. (...) Van Rooyen’s commercialization plan calls for mounting the Dragen
processor on cards that have been customized to work with specific
genome sequencing machines, such as Illumina’s HiSeq X Ten. (...) By using Edico’s technology, van Rooyen says a facility using
Illumina’s HiSeq X Ten machines to sequence 150 human genomes every
three days would be able to save $6 million over a four-year period. (...) That would make it easier for hospitals and other healthcare
providers to use genome sequencing to better diagnose heart disease,
inflammatory disease, prenatal disease, and other conditions." |
| https://twitter.com/EdicoGenome |
At the same time, though, it’s becoming clear that generating genomic data for thousands of cancer patients involves working with very large numbers—and that means a wave of new opportunities for innovation are emerging as genomics and Big Data come together. One startup moving to catch this wave is Edico Genome, a San Diego startup founded last year to fix a bottleneck in the way the data being generated by the HiSeq X Ten and other next-generation sequencing machines is processed.
Edico has developed a specialized computer processor for ordering the readout of nucleotides—A, C, T, or G—from short segments of DNA generated by next-generation sequencing technology so they align with a reference genome. It’s a process that genomics specialists refer to as 'mapping.'
It is a Big Data problem. The human genome consists of roughly 3.2 billion nucleotide base pairs (made of that four-letter alphabet of DNA) that encode between 20,000 and 25,000 genes."
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