Optical Genome Mapping: A New Frontier in Structural Genomic Variation Analysis

By Dr. Luis Vaschetto, Ph.D.Reviewed by Danielle Ellis, B.Sc.

The human genome sequencing project was completed in 2001¹, revolutionizing our understanding of biology in general and medicine in particular.

However, it also revealed limitations in our ability to analyze the genome's structure and individual genomic variations, which are mostly associated with repeats and deletion of no more than a few hundred nucleotide bases in length.

Traditional methods like karyotyping cannot accurately map these key genome characteristics, which include structural variations (SVs) and copy number variations (CNVs), being often required to understand and/or identify disease states. Fortunately, optical genome mapping (OGM) has enabled us to fill this gap.

OGM is an innovative cytogenomic technology for analyzing large eukaryotic genomes and structural chromosomal features at a high level of resolution. This technique can be used, for example, to detect chromosomal aberrations (aneuploidies, deletions, duplications, translocations). Thus, OGM, which emerged as a complementary approach, offers a unique perspective on the genome's architecture, ultimately providing critical information in genetics research.

In particular, OGM is gaining traction due to its remarkable ability to detect a broad range of structural variations, potentially simplifying workflows by replacing multiple standard cytogenetic techniques.

Principles of Optical Genome Mapping

Optical analysis of DNA fragments is based on labeling short, recurrent sequences with fluorescent tags, enabling their visualization and subsequent structural evaluation. This technique exploits the targeted labeling of DNA molecules containing recognition sequence patterns such as CTTAAG, whose prevalence may vary (intra-specifically and even intra-populationally) across genomes within a given taxon. The high-resolution fluorescence microscopy then allows a detailed examination of individual DNA fragments capable of revealing genome-specific structural and copy number variations.²

These genomic polymorphisms, namely, chromosome deletions, duplications, inversions, and translocations, constitute prevalent events with significant disease associations. Optical genome mapping is a versatile technique that offers a genome-wide assessment of such structural chromosome variants with a remarkable resolution of approximately 500 base pairs (bp), significantly exceeding the capabilities of traditional cytogenetic methods.

OGM is also a powerful tool for genome assembly, facilitating error correction, scaffolding, and validation. By integrating raw optical mapping data from the same genome, this approach can be used to develop comprehensive, chromosome-spanning consensus maps.³ OGM platforms, like Bionano Genomics, utilize nanochannel arrays and specialized chips to guide unwound DNA molecules. These channels facilitate fluorescent labeling of the DNA backbone, enabling high-resolution imaging and subsequent analysis.⁴ 

Importantly, open-source software for processing and assembling OGM data, like OptiScan and OptiMap can extract and process molecules from raw images and perform molecule-to-molecule and molecule-to-reference alignments.⁴

Importance in Structural Variation Analysis

Structural and copy number variations (SVs and CNVs, respectively) have been associated with many diseases, showing variable impacts depending on specific variant types and genomic locations. As an example, Angelman syndrome is caused by a maternal chromosome microdeletion in the region 15q11.⁵

Similarly, a microduplication of chromosome 17 (17p11.2) underlies Potocki-Lupski syndrome, which is characterized by hypotonia, feeding difficulties, cardiac anomalies, developmental delay, and autism spectrum disorder features.⁵ Microduplications have also been linked to an increased risk of suffering from attention deficit hyperactivity disorder (ADHD) and other behavioral problems.⁶

By providing a comprehensive view of structural variations across the entire genome, OGM has become an indispensable tool for researchers investigating small (very short) chromosomal rearrangements at a high resolution and thus understanding their impacts on human diseases as well as associated phenotypes.

Applications in Research and Medicine

The versatility of OGM to detect structural variations encompasses diverse applications and a wide range of research topics, including cancer research, rare disease diagnosis, and beyond. OGM has already demonstrated clinical utility in cytogenetic diagnostics of hematological neoplasms⁷, which encompass tumors arising in the blood and blood-forming tissues (bone marrow/lymphatic system). Its ability for a comprehensive assessment of chromosomal structural variants has also proven valuable in myelodysplastic syndromes.⁸

It is a method that has also enabled the deciphering of the functional significance of chromosomal translocations associated with facioscapulohumeral muscular dystrophy (FSHD), which is critical for diagnosing this condition. Its potential application in prenatal diagnostics further underscores its reach across diverse medical fields.⁹

The intersection of optical genome mapping (OGM) and personalized medicine holds immense promise for the future of healthcare. There are many associations between rare genetic diseases and specific deleterious short nucleotide variants, thereby positioning OGM as a promising tool for their detection. However, its applicability is restricted to sufficient resolution to resolve these variations within the current technical limitations.

Future Perspectives and Innovations

OGM expands its analytical reach beyond genomic structural/copy number variations. Recently, it has enabled the development of epigenetic-based mapping tools capable of detecting 5-Hydroxymethylcytosine (5-hmC), an epigenetic modification linked to gene (dys)regulation and consequently also to disease pathogenesis. OGM-based 5-hmC mapping shows a promising potential for cancer diagnostics due to its ability to identify the loss of 5-hmC marks and thus reveal epigenetic patterns across large genomic regions on single DNA molecules¹⁰, providing insights into epigenetic variability associated with particular phenotypes.

In the future, it is expected that OGM can effectively be used to detect aberrations involving single genes, dramatically enhancing diagnostic resolution. In acute lymphoblastic leukemia, for example, this technique has confirmed recurrent alterations in critical genes associated with this disease (PAX5, ETV6, VPREB1, and IKZF1), thus leading to detailed genetic diagnoses and facilitating targeted treatment approaches.¹¹

Conclusion

OGM is a technique that has revolutionized genomic structural variation analysis, providing unprecedented resolution and fidelity compared to established methods. Its potential to enhance our understanding of health and disease is immense, with implications across diverse disciplines. Although nucleotide resolution requires further refinement, OGM's power to unravel genomic complexity and decipher SV-CNV relationships holds great promise in diagnostics and personalized medicine. This transformative technique will likely be critical to shaping the transition to a new era in healthcare.

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