Advances in optical mapping for genomic research

Abstract

Recent advances in optical mapping have allowed the construction of improved genome assemblies with greater contiguity. Optical mapping also enables genome comparison and identification of large-scale structural variations. Association of these large-scale genomic features with biological functions is an important goal in plant and animal breeding and in medical research. Optical mapping has also been used in microbiology and still plays an important role in strain typing and epidemiological studies. Here, we review the development of optical mapping in recent decades to illustrate its importance in genomic research. We detail its applications and algorithms to show its specific advantages. Finally, we discuss the challenges required to facilitate the optimization of optical mapping and improve its future development and application.

The Impact of Modern Technologies on Molecular Diagnostic Success Rates, with a Focus on Inherited Retinal Dystrophy and Hearing Loss

“…Although LRS techniques are rapidly developing and show a great ability to identify SVs, their routine application in clinical diagnostics still requires several improvements in terms of sequencing and variant interpretation; it also requires a cost reduction. In addition, despite the fact that these technologies can provide substantial read length, the reads can only be assembled to the scaffold level and not to the chromosome level [ 195 ]. Complementary approaches to identify SVs can be offered by cytogenetics [ 193 ].…”

“…However, for the analysis of SVs, optical mapping can be used in a complementary manner to sequencing techniques [ 193 ]. With the ability to map ultra-long dsDNA molecules at a low cost, optical mapping has facilitated SV detection, haplotype phasing, and genome assembly [ 195 ]. In a recent study, researchers utilized optical mapping to identify a 48-kb duplication at the LAMA1 locus that causes Poretti–Boltshauser syndrome (OMIM: 615960).…”

Expanding the conservation genomics toolbox: incorporating structural variants to enhance functional studies for species of conservation concern

“…On average, optical maps span~225 kb, providing information on the physical distance and relationship among genomic traits. Optical mapping utilises a technique based on light-microscopy to identify specific sequence motifs (such as restriction enzyme cut sites), which are then used to generate images of fluorescently-labeled DNA molecules (Schwartz et al, 1993), enabling the characterisation of large, complex rearrangements missed by long-reads alone (Yuan et al, 2020). Besides being used to improve the scaffolding of genome assemblies (e.g., Howe & Wood, 2015;J.…”

Single-molecule optical genome mapping in nanochannels: multidisciplinarity at the nanoscale

“…Optical DNA mapping has emerged in recent years as a valuable technique for unraveling long-range information along the genome [1][2][3]. The method incorporates a multi-disciplinary approach ( Figure 1) for extraction of long-range single-molecule genomic data, and provides an indispensable complementary perspective to DNA sequencing.…”

“…Optical mapping is a vibrant field [1,2,8], and is currently the go-to method for detecting and validating large-scale genomic rearrangements, such as structural and copy number variations (SVs, CNVs respectively) [9][10][11][12][13] ( Figure 1D). With Mbp read lengths, optical mapping reveals such large-scale variations from the reference genome, while conventional short-read next-generation sequencing (NGS) is blind to them.…”