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Advances of Optical Genome Mapping in Human Genetics
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Advances of Optical Genome Mapping in Human Genetics

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Technologies and Resources for Genetics".

Deadline for manuscript submissions: 20 September 2024 | Viewed by 2317

Special Issue Editors

Dr. Paul Dremsek

E-Mail Website
Guest Editor
Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, 1090 Vienna, Austria
Interests: cytogenomics; optical genome mapping; clinical genetics; prenatal diagnostics
Dr. Anna Schachner

E-Mail Website
Guest Editor
Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, 1090 Vienna, Austria
Interests: cytogenomics; optical genome mapping; clinical genetics; stem cell research

Special Issue Information

Dear Colleagues,

Optical genome mapping (OGM) is a relatively young technology for the genome-wide detection and characterization of all types of chromosomal structural variants. It is able to encompass a wide range of variant sizes, with up to 1000× greater resolution compared to karyotyping, which is accomplished by analyzing ultra-long DNA molecules.

The number of users of this promising technique has grown rapidly in recent years and includes members of the fields of constitutional genetics, cancer genomics and basic research. So far, OGM has been successfully introduced in cancer diagnostics. Furthermore, it was shown to be a promising tool in constitutional genetics, mainly for complementing existing analytical workflows, although several stand-alone findings have been reported as well.

The most topical questions in the community are whether and to what extent OGM competes with existing technologies, in what indications and areas of applications the use of OGM is the most effective, and the technology's current limitations. Additionally, for the clinical realm, questions regarding reproducibility and standardized mode of interpretation arise.

This Special Issue intends to compile the insights, results and knowledge of the small but ever-growing community of researchers and clinical laboratories utilizing OGM. This should help to define more clearly the viable applications of OGM and its prospective role in the toolkit of cytogenomics.

In this Special Issue, original research articles, case studies and reviews are welcome.

We look forward to receiving your contributions.

Dr. Paul Dremsek
Dr. Anna Schachner
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • optical genome mapping
  • cytogenomics
  • chromosomal structural variation
  • clinical genetics
  • cancer genetics
  • prenatal diagnostics
  • population genetics

Published Papers (2 papers)

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11 pages, 4894 KiB  
Article
Optical Genome Mapping as a Potential Routine Clinical Diagnostic Method
by Hayk Barseghyan, Doris Eisenreich, Evgenia Lindt, Martin Wendlandt, Florentine Scharf, Anna Benet-Pages, Kai Sendelbach, Teresa Neuhann, Angela Abicht, Elke Holinski-Feder and Udo Koehler
Genes 2024, 15(3), 342; https://doi.org/10.3390/genes15030342 - 07 Mar 2024
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Abstract
Chromosome analysis (CA) and chromosomal microarray analysis (CMA) have been successfully used to diagnose genetic disorders. However, many conditions remain undiagnosed due to limitations in resolution (CA) and detection of only unbalanced events (CMA). Optical genome mapping (OGM) has the potential to address [...] Read more.
Chromosome analysis (CA) and chromosomal microarray analysis (CMA) have been successfully used to diagnose genetic disorders. However, many conditions remain undiagnosed due to limitations in resolution (CA) and detection of only unbalanced events (CMA). Optical genome mapping (OGM) has the potential to address these limitations by capturing both structural variants (SVs) resulting in copy number changes and balanced rearrangements with high resolution. In this study, we investigated OGM’s concordance using 87 SVs previously identified by CA, CMA, or Southern blot. Overall, OGM was 98% concordant with only three discordant cases: (1) uncalled translocation with one breakpoint in a centromere; (2) uncalled duplication with breakpoints in the pseudoautosomal region 1; and (3) uncalled mosaic triplication originating from a marker chromosome. OGM provided diagnosis for three previously unsolved cases: (1) disruption of the SON gene due to a balanced reciprocal translocation; (2) disruption of the NBEA gene due to an inverted insertion; (3) disruption of the TSC2 gene due to a mosaic deletion. We show that OGM is a valid method for the detection of many types of SVs in a single assay and is highly concordant with legacy cytogenomic methods; however, it has limited SV detection capabilities in centromeric and pseudoautosomal regions. Full article
(This article belongs to the Special Issue Advances of Optical Genome Mapping in Human Genetics)
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8 pages, 992 KiB  
Brief Report
Evaluation of Optical Genome Mapping in Clinical Genetic Testing of Facioscapulohumeral Muscular Dystrophy
by Anja Kovanda, Luca Lovrečić, Gorazd Rudolf, Ivana Babic Bozovic, Helena Jaklič, Lea Leonardis and Borut Peterlin
Genes 2023, 14(12), 2166; https://doi.org/10.3390/genes14122166 - 30 Nov 2023
Viewed by 1078
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is the third most common hereditary muscular dystrophy, caused by the contraction of the D4Z4 repeats on the permissive 4qA haplotype on chromosome 4, resulting in the faulty expression of the DUX4 gene. Traditional diagnostics are based on Southern [...] Read more.
Facioscapulohumeral muscular dystrophy (FSHD) is the third most common hereditary muscular dystrophy, caused by the contraction of the D4Z4 repeats on the permissive 4qA haplotype on chromosome 4, resulting in the faulty expression of the DUX4 gene. Traditional diagnostics are based on Southern blotting, a time- and effort-intensive method that can be affected by single nucleotide variants (SNV) and copy number variants (CNV), as well as by the similarity of the D4Z4 repeats located on chromosome 10. We aimed to evaluate optical genome mapping (OGM) as an alternative molecular diagnostic method for the detection of FSHD. We first performed optical genome mapping with EnFocus™ FSHD analysis using DLE-1 labeling and the Saphyr instrument in patients with inconclusive diagnostic Southern blot results, negative FSHD2 results, and clinically evident FSHD. Second, we performed OGM in parallel with the classical Southern blot analysis for our prospectively collected new FSHD cases. Finally, panel exome sequencing was performed to confirm the presence of FSHD2. In two patients with diagnostically inconclusive Southern blot results, OGM was able to identify shortened D4Z4 repeats on the permissive 4qA alleles, consistent with the clinical presentation. The results of the prospectively collected patients tested in parallel using Southern blotting and OGM showed full concordance, indicating that OGM is a useful alternative to the classical Southern blotting method for detecting FSHD1. In a patient showing clinical FSHD but no shortened D4Z4 repeats in the 4qA allele using OGM or Southern blotting, a likely pathogenic variant in SMCHD1 was detected using exome sequencing, confirming FSHD2. OGM and panel exome sequencing can be used consecutively to detect FSHD2. Full article
(This article belongs to the Special Issue Advances of Optical Genome Mapping in Human Genetics)
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