Technology: What is Whole Genome Mapping?

OpGen, Inc. has developed a unique and powerful Optical Mapping Technology for Whole Genome Mapping that rapidly generates high-resolution, ordered, whole genome restriction maps from single DNA molecules. Optical Maps are generated de novo, independent of sequence information, and provide a comprehensive view of genomic architecture. An Optical Map is displayed in the unique MapCode™ pattern below where the vertical lines indicate the locations of restriction sites, and the distance between the lines represent the fragment size.

Whole Genome Restriction Map – vertical lines represent restriction sites

Step 1. Extract

High molecular weight (HMW) DNA is recovered from microbial cells.

• Microbial cells are embedded in low melting agarose plugs and treated with lysing solutions.
• Samples are washed thoroughly, melted at 70°C, and treated with ß-agarase to release the HMW DNA.
• Sample prep procedure varies with the specific microbial sample.

Step 2. Capture & Digest

Genomic DNA is captured and immobilized as Single molecules on a charged optical substrate, then digested with a restriction endonuclease.

• Prepared HMW DNA is loaded into the channels of a microfluidics Optical Chip device.
• Genomic DNA is captured in parallel arrays as long, single DNA molecules. Immobilized molecules are retained electrostatically.
• Genomic DNA is interrogated with a restriction endonuclease. The restriction fragment order is maintained for each molecule.

Step 3. Stain & Assemble

Genomic DNA is stained, scanned, measured, and assembled into a whole genome ordered restriction map.

• Digested genomic DNA is stained with a fluorescent dye and then positioned onto an automated fluorescent microscopy system for data acquisition.
• Image analysis software measures the size and order of restriction fragments for each molecule. This process converts optical data into digital data resulting in defined single molecule restriction maps.
• Collections of single molecule maps are then assembled by overlapping fragment patterns to produce a whole genome ordered restriction map, an Optical Map.
• Single Molecule Maps are assembled to produce a high resolution consensus map covering the entire genome.

Step 4. Analyze

Using OpGen’s proprietary MapSolver™ Software Analysis Tool, Optical Maps may be analyzed and compared to discover genetic variation, perform high resolution epidemiology, or facilitate genome closure.

Learn more about specific applications — 
Comparative Genomics, Strain Typing, and Whole Genome Sequence Assembly.