Optical Mapping

What’s optical imaging all about and what is its relevance to healthcare?

Optical mapping is a single-molecule technology for analyzing entire genomes. The system is unique in that it allows imaging and analysis of long single DNA molecules, isolated directly from test organisms, without amplification or cloning, and retaining the native molecules’ patterns of DNA modification. This approach differs significantly from current methods that compare chemical copies of short stretches of an organism’s genome to a reference sequence, and which are therefore unlikely to identify the presence of unsuspected or ‘foreign’ gene sequences, or changes in patterns of DNA modification. Furthermore, whereas other technologies are primarily intended to identify point mutations and deletions, optical mapping is designed to detect a range of different genome rearrangements including deletions, insertions of foreign DNA (e.g. as in lateral gene transfer), translocations and duplications (as in gene amplification).

This is particularly important for the study and treatment of infectious diseases, where, because of the plasticity of microbial genomes, identifying and characterizing genome rearrangements is critical to understanding and combating the threat from new pathogenic strains.

Researchers can now perform studies comparing dozens of microbial isolates at the genome level to detect differences associated with clinically relevant phenotypes such as pathogenicity, antibiotic resistance, and host range. OpGen’s goal is to make this technology available to scientists and clinicians, worldwide, to facilitate such studies.

Imaging at the molecular level is having a huge impact on healthcare today. What trends have you seen in demand for and interest in your technologies and products in this area?

The re-emergence of infectious disease as the single greatest threat to human health is driving increased efforts and resources into the study of human pathogens. More and more organisms are being sequenced. Because shuffling of elements within microbial genomes is commonplace, and important for the emergence of new pathogenic strains, researchers are also searching for technologies capable of performing whole-genome comparisons of multiple isolates of the ‘reference strains’. Optical mapping is having a significant impact on this research both by reducing the costs and time for sequencing microbial genomes and also by allowing rapid, cost-effective comparisons of unsequenced organisms.

Although there have been many significant improvements in DNA sequencing technologies, whole genome sequencing is still expensive and labor intensive. Assembling ‘finished sequence’ from shotgun sequence data can be difficult, and in some cases impossible. Optical mapping addresses the assembly problem by producing a map, or blueprint, showing how the genome is organized, allowing partial sequences produced by ‘shotgun sequencing’ programs to be placed in the correct order and orientation relative to each other, and identifying the location and size of gaps to be completed. Optical maps also allow mistakes in sequence assembly to be identified and corrected early in a sequencing program, significantly reducing the time, labour and reagent costs required to produce the finished sequence. This effectively means that available funding can be used to sequence more human pathogens, more rapidly.

Establishing the genome sequence of a pathogen provides useful information, but even more valuable information can be obtained by comparing multiple isolates with different phenotypes. Increasingly, optical mapping is being used to compare multiple strains and isolates and to identify differences in genome structure associated with phenotypes such as pathogenicity, antibiotic resistance and host range. Optical mapping does not require DNA sequence information, so the system can also be used to compare strains of less-well studied pathogens for which little or no sequence information is available.

In what key ways is the technology changing the way that drugs are developed?

The system is being used primarily as a research tool, rather than in clinical drug development. However, it has the potential to be used during clinical trials, for example, to identify changes in microbial populations in patients undergoing antibiotic therapy.

What’s next for these technologies and their application in healthcare? Do you have any developments or plans of your own that you would like to talk about?

Optical mapping is currently available as a service, but plans are in place to sell integrated optical mapping instruments for research and clinical applications. This will broaden the range of applications for the technology to include the analysis of human populations as well as human pathogens. Although microarray systems, especially the mega-SNP arrays now being developed, will provide cost-effective screening tools for the human genome, most are not designed to directly detect genomic rearrangements, e.g. as found in various cancers and other human diseases. Optical mapping can provide unique and complementary data, particularly in its ability to detect novel structural mutations and may be used for in-depth characterization of loci identified by high-throughput SNP scans.

What other impact do you see for optical mapping, for example in the way that patients are being treated?

This technology has the potential to radically alter the treatment of infectious diseases. Current practice in hospital clinical microbiology laboratories requires infectious bacteria to be cultured from clinical samples, followed by isolation of individual colonies and then a battery of tests to identify the causative organism. Many organisms (e.g. Legionella) are difficult to culture and the entire process can take from 48-72 hours, thus precluding choice of therapy based on identification of the organism. Optical Mapping allows identification of organisms down to the sub-strain level, usually from fewer than 100 cells. The ability to rapidly identify the causative agents of bacterial infections, without having to perform cell culture and colony isolation, will make it possible for physicians to select the most cost-effective therapy within a few hours of seeing their patient. This will lead to better treatment for the patients, more efficient use of hospital facilities, and substantial savings for the payors responsible for reimbursing costs of medical treatment.