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Future Directions: Integration of Optical Mapping into Healthcare Systems for Precision Genomics

NextEdge Admin

30 Jan 2024

3 min 49 sec

short-read sequencing,Biosciences (PacBio)

Genomic research has witnessed significant advancements in recent years, particularly with the advent of short-read sequencing (SRS) technologies that made genomic and genetic studies more affordable. However, the inherent limitation of short read lengths poses challenges in spanning repetitive and complex genomic regions, leading to fragmented and collapsed genome assemblies. This issue compromises the accuracy of downstream analyses, especially in the detection of genomic variations.

To address these limitations, long-read sequencing technologies from companies like Pacific Biosciences (PacBio) and Oxford Nanopore have emerged, offering more complete genome assemblies. However, their average read lengths, while substantial, still fall short in covering large repetitive and complex genomic regions. Additionally, achieving chromosome-level assembly remains a challenge.

Various technologies, such as short-read long-insert, linked-read sequencing, Hi-C, and optical mapping, have been employed to tackle assembly problems. Among these, optical mapping stands out as a promising solution. Optical mapping uses light microscope-based techniques to physically locate specific enzymes or sequence motifs, producing DNA sequence fingerprints. With an average molecule length of approximately 225 kb, optical maps can span genomic regions that are difficult for traditional sequencing methods to resolve.

Companies like OpGen, Bionano Genomics, and NABsys have played crucial roles in advancing optical mapping technologies. Bionano Genomics, in particular, dominates the market with platforms like Irys and Saphyr, offering improved accuracy, throughput, and contiguity.

The workflow of optical mapping involves experiment design, DNA extraction, labelling, loading, image capture, data conversion, bioinformatics analyses, and validation. Optical mapping has proven valuable in improving genome assembly contiguity, detecting structural variations, and facilitating strain typing. It has been extensively used in genomic studies across microorganisms and human diseases.

However, challenges persist, including the relatively low resolution of optical mapping, making it unsuitable for shorter maps, and the dependence on the distribution of enzyme recognition motifs. Efforts to address these challenges include the development of alternative labelling methods and exploration of epigenetic applications.

Looking ahead, optical mapping is expected to play a crucial role in genomic studies, particularly in the healthcare system. Despite its current limitations, ongoing technological advancements, including refined labelling methods, improved algorithms, and enhanced data visualization, are anticipated. The integration of optical mapping into healthcare systems is likely to contribute significantly to more accurate genome assemblies, enabling better understanding of genotype-phenotype associations and aiding in the detection of disease-related variations.