10 Sep Whole Genomes From Microbes to Man
Madison, WI– Optical Mapping is a new technology that will be used to discover why patients experience toxic side effects, or fail to respond to medication and to identify the causes of antibiotic resistance and virulence in pathogenic organisms. Wisconsin- based OpGen, has announced the commercial launch of its Optical Mapping(TM) system for rapid, cost-effective analysis of whole genomes, from microbes to man. The system provides a powerful tool for high-resolution genome-wide analysis of genetic variation in populations of organisms, identifying insertions, deletions, translocations and other rearrangements not readily detected by other genome analysis methods. OpGen expects to initiate its first pharmacogenomics study, analyzing cancer genome rearrangements associated with response to chemotherapy, early next year.
Optical Mapping involves the capture of multiple copies of whole genomes, as collections of long single DNA molecules isolated directly from cells without amplification or cloning, immobilized in dense arrays on Optical Chips(TM). Markers are scored simultaneously, in a single cost-effective manipulation, to produce high-resolution Optical Maps that can be used to characterize and compare genomes from any organism with no need for prior sequence information. Presence or absence of markers, and their distance apart, are scored to compare closely related genomes, to identify organisms and to detect genomic rearrangements such as indels.
Optical Mapping was developed by Dr. David Schwartz, inventor of Pulsed Field Gel Electrophoresis and Professor of Genetics and Chemistry at the University of Wisconsin in Madison. Optical Mapping has been used for identification and comparison of microbial isolates, measurement of long haplotypes directly from genomic DNA, and assessing the accuracy of DNA sequence assembly in whole genome sequencing projects.
“Optical Mapping has the potential to screen whole human genomes for genetic variation, in minutes,” said Dr. Schwartz. “This will allow genetic screening of entire populations, at low cost, providing the ultimate molecular diagnostic and pharmacogenomics system. It will revolutionize pharmacogenomics.”
Dr. Colin Dykes, OpGen’s Chief Scientific Officer, concurs, noting “This is a case of the right technology at the right time. Recent publications report that insertions and deletions (indels) appear to be more important than single nucleotide polymorphisms (SNPs) in accounting for sequence variation, evolutionary change and gene defects. Although Optical Mapping does detect SNPs, the system is primarily designed to identify genomic rearrangements, including indels, translocations and repetitive elements, in any genome. As attention shifts from SNPs to indels, Optical Mapping is perhaps the only system that can detect these events quickly, cheaply, and with high resolution, across entire genomes.”
Dr. Dykes was recruited in September 2002 as Chief Scientific Officer of OpGen. Previously, he was UK Genetics Director for Glaxo Wellcome (now GlaxoSmithKline) and led GW’s UK genetics and genomics programs from 1993-1998. Prior to joining OpGen, he was Vice President for Research and Genomics at Variagenics, Inc., the Cambridge-based pharmacogenomics company. Dr. Dykes is an internationally-recognized expert in pharmacogenetics and genomics, with more than 20 years experience in applying molecular biology, genetics and genomics to the discovery and development of human therapeutics and diagnostics.
OpGen’s has raised almost $3 million from investors including Mason Wells (Lead) as well as WARF, SWIB, and Stonehenge capital and in the process of closing an additional $5-7 million.
“We are receiving a strong reception from the VC Marketplace regarding the maturity and technology of single molecule to whole genome optical mapping and expect to close financing in the next 90 days. ” said Dan Broderick, Opgen’s Interim CEO and managing director for Mason Wells.
OpGen has said it is using its investment capital to expand its optical mapping capacity, to expedite the technology development program, and to begin marketing its technologies to to companies and organizations currently involved in sequencing entire genomes.