Optical Genome Mapping in Routine Human Genetic Diagnostics—Its Advantages and Limitations

Abstract

In recent years, optical genome mapping (OGM) has developed into a highly promising method of detecting large-scale structural variants in human genomes. It is capable of detecting structural variants considered difficult to detect by other current methods. Hence, it promises to be feasible as a first-line diagnostic tool, permitting insight into a new realm of previously unknown variants. However, due to its novelty, little experience with OGM is available to infer best practices for its application or to clarify which features cannot be detected. In this study, we used the Saphyr system (Bionano Genomics, San Diego, CA, USA), to explore its capabilities in human genetic diagnostics. To this end, we tested 14 DNA samples to confirm a total of 14 different structural or numerical chromosomal variants originally detected by other means, namely, deletions, duplications, inversions, trisomies, and a translocation. Overall, 12 variants could be confirmed; one deletion and one inversion could not. The prerequisites for detection of similar variants were explored by reviewing the OGM data of 54 samples analyzed in our laboratory. Limitations, some owing to the novelty of the method and some inherent to it, were described. Finally, we tested the successful application of OGM in routine diagnostics and described some of the challenges that merit consideration when utilizing OGM as a diagnostic tool.

Evaluation of optical genome mapping for detecting chromosomal translocation in clinical cytogenetics

“…We have demonstrated that Bionano OGM is an effective approach to detect balanced chromosome translocations compared with traditional methods like karyotyping and FISH. As a new method of nucleic acid sequencing and genome analysis, especially for chromosomal insertions and deletions, OGM is used to analyze multiple DNA fragments simultaneously at a scale of 500 bp as in NGS high‐throughput sequencing, other SVs need to be 30 kb or larger to be detectable (Bionano Genomics, 2018 ; Dremsek et al, 2021 ; Jeffet et al, 2021 ). It makes sure that structural variations can be detected correctly, and more information can be given about the breakpoint position in gene level.…”

“…OGM can provide more detailed information about the location of breakpoints. The DNA was labeled with a fluorophore by the methyltransferase DLE‐1 at the recognition motif CTTAAG, and generated approximately 14–15 labels per 100 kb when labeling human genomic DNA, so OGM has a theoretical resolution of 100 kb (Dremsek et al, 2021 ). In practical applications, it has a resolution of approximately 100 kb, which is 50 to 100 times higher relative to karyotype analysis.…”

“…Also the cultivation of samples can eliminates the time advantage of OGM over karyotyping. Last, the cost of OGM is much higher than traditional ways and genomic data collection and analysis also may be a limiting factor (Dremsek et al, 2021 ).…”

“…Traditional chromosome analysis techniques, such as karyotyping and fluorescence in situ hybridization (FISH), have been the basic prenatal and postnatal diagnostic methods and are capable of detecting most types of balanced and unbalanced chromosomal abnormalities, as well as numerical chromosomal aberrations in clinical genetics (Bates, 2011 ; Dremsek et al, 2021 ; MacLeod & Drexler, 2013 ; Speicher & Carter, 2005 ). Both of these techniques are not only time consuming and require a high level of manual proficiency, but also make it difficult to determine subtle changes at a relative low‐resolution level (Bates, 2011 ).…”

The Use of Genetics for Reaching a Diagnosis in XY DSD

“…Optical genome mapping (OGM) is designed to identify megabase-level complex structural variations that may occur in high repeat regions and, therefore, are difficult to be detected by short-read methods. Using fluorescently labelled sequence motifs, attached to each of the DNA strands at different density, and imaging instrument, the molecules are assembled to a reference genome with a high level of precision [Dremsek et al, 2021]. Epi- genetic modifications of histones and particularly genomic rearrangements involving CpG islands may result in aberrant methylation and subsequently transcriptional activation or repression [Jeziorska et al, 2017].…”