51Optical Mapping
Optical Mapping™ (OpGen Inc) involves the capture of multiple copies of whole
genomes, as collections of long single DNA molecules isolated directly from cells
without amplifi cation or cloning, immobilized in dense arrays. Shotgun optical
mapping approach can directly map genomic DNA by the random mapping of sin-
gle molecules. Markers are scored simultaneously, in a single cost-effective manip-
ulation, to produce high-resolution Optical Maps that can be used to characterize
and compare genomes from any organism with no need for prior sequence informa-
tion. This is a case of the right technology at the right time. Insertions and deletions
(indels) appear to be more important than SNPs in accounting for sequence varia-
tion, evolutionary change and gene defects. Although Optical Mapping does detect
SNPs, the system is primarily designed to identify genomic rearrangements, includ-
ing 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.
Presence or absence of markers, and their distance apart, are scored to compare
closely related genomes, to identify organisms and to detect genomic rearrange-
ments such as indels. Optical Mapping has the following advantages over other
methods for whole genome genetic analysis:
- The process involves only a single addition of reagents directly to native DNA,
with no requirement for PCR, primers or probes, providing massively parallel,
low cost marker analysis. - It effi ciently fi nds insertions, deletions, duplications, inversions, translocations,
which are not readily detected by other methods such, SNP assays, and shotgun
DNA sequencing. - It can detect completely new and unsuspected genetic variation whereas probe-
based systems are limited to measuring differences that have been found previ-
ously in other samples. - It can survey entire human genomes for insertions/deletions, which account for a
signifi cantly greater proportion of genetic variation between closely-related
genomes as compared to SNPs, and are a major cause of gene defects.
The advantage of Optical Mapping platform’s freedom from dependence on
sequence for de novo variant discovery has a downside to it, i.e. lower resolution
than sequence-based approaches. The endpoints of any individual event can only be
resolved to the nearest restriction site. This limitation is being addressed by devel-
oping alternative enzyme-based methods that increase marker density and add
sequence information to mapped molecules. Algorithms are being developed to take
advantage of the additional information for separating multiple genotypes at a sin-
gle genomic locus. With further advances it will be possible to elucidate complex
sequence-level events such as the somatic rearrangements that are a hallmark of
cancer genomes.
Biochips and Microarrays