What is Optical Genome Mapping?

Optical Genome Mapping is a technique that enables the direct visualization of long DNA molecules to detect structural variants with high accuracy. The process involves isolating high molecular weight DNA, labeling specific sequences with fluorescent markers, stretching the DNA on a solid surface, and imaging it using high-resolution microscopy. The resulting optical maps provide detailed insights into the genome’s structural organization.

(A) Schematic process of OGM (B) The different types of SVs shown by OGM (Yellow and orange bands indicate the reference genome & blue band the test sample, the black lines show the pattern and location of the CTTAAG motifs)

Advantages:

1. High Resolution and Sensitivity:

• OGM offers high-resolution maps capable of detecting structural variants as small as a few kilobases. This sensitivity is significantly better than many traditional methods, allowing for the detection of smaller SVs that might be missed otherwise.

• It excels in identifying complex rearrangements and repeat-rich regions, which are often challenging.

2. Comprehensive Detection:

• OGM can identify a wide range of SV types, including deletions, duplications, insertions, inversions, and translocations.

• It is particularly effective for de novo assembly and closing gaps in complex genomic regions, providing a more complete picture of the genome.

3. Direct Visualization: Unlike sequencing-based methods, which infer SVs indirectly, OGM allows for the direct visualization of DNA molecules. This direct approach provides more precise information about the location, size, and nature of structural variants.

4. Long-Read Capabilities: OGM utilizes long DNA molecules, often exceeding hundreds of kilobases. This long-read capability helps in spanning large repetitive regions and complex genomic structures that are difficult to analyze with short-read sequencing technologies.

Limitations:

1. High Cost and Complexity:

• OGM requires specialized equipment and expertise, making it more expensive and less accessible than some other SV detection methods. The initial setup cost and ongoing maintenance can be significant barriers for many laboratories.

• The sample preparation and imaging processes are complex and time-consuming, requiring skilled technicians and sophisticated protocols.

2. Lower Throughput:

• Compared to high-throughput sequencing technologies, OGM typically has lower throughput. This limitation can restrict its use in large-scale population studies or routine clinical diagnostics where high sample volumes are required.

• The imaging and data analysis processes are relatively slow, further limiting the number of samples that can be processed simultaneously.

3. Data Interpretation Challenges:

• The large datasets generated by OGM require advanced bioinformatics tools and expertise for interpretation. The complexity of the data can pose challenges in distinguishing true SVs from artifacts and noise.

• Integrating OGM data with other genomic datasets, such as sequencing data, can be complex and require sophisticated computational approaches.

4. Limited Availability:

• OGM technology is not as widely available as other SV detection methods. The dependence on specialized instruments and reagents restricts its accessibility to well-funded research institutions and clinical laboratories.

5. Sample Quality Requirements:

• OGM requires high-quality, high-molecular-weight DNA for optimal performance. Obtaining such DNA can be challenging, particularly from clinical samples like formalin-fixed, paraffin-embedded (FFPE) tissues.

• The quality and integrity of the DNA can significantly impact the accuracy and resolution of the optical maps, necessitating stringent quality control measures.
  

OGM vs. Array CGH:

• Detection Range: Array CGH is primarily designed for detecting copy number variations (CNVs) and may miss balanced rearrangements and smaller SVs. OGM offers a broader detection range, including all types of SVs.

• Resolution: OGM provides higher resolution and can detect smaller SVs compared to Array CGH. However, Array CGH is more widely accessible and cost-effective.

• Data Interpretation: Array CGH generates simpler data that is easier to interpret compared to the complex datasets produced by OGM. This simplicity makes Array CGH more suitable for routine clinical diagnostics.

References:

• Optical genome mapping: A ‘tool’ with significant potential from... College of American Pathologists. Available at: https://www.cap.org/member-resources/articles/optical-genome-mapping-a-tool-with-significant-potential-from-discovery-to-diagnostics (Image source)

-Written by Sohni Tagore