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Background Monosomy 18p (MIM: 146390) is a well-known chromosomal disorder associated with intellectual disability, short stature, and non-specific craniofacial features resulting from partial or total deletion of the short arm of chromosome 18. The differential diagnosis is broad due to nonspecific and variable phenotypes. The majority of 18p monosomy cases result from de novo deletions, while the remainder are either caused by de novo translocation with loss of 18p, malsegregation of a parental translocation or inversion, or the presence of a ring chromosome or isochromosome 18q. Establishing the etiopathogenetic mechanism is essential to properly assess the risk of recurrence. Chromosomal Microarray Analysis (CMA) has enabled better genotype-phenotype correlations. Nonetheless, CMA is not appropriate for characterizing complex or balanced structural variants, which may underlie complex rearrangement, and the resolution of karyotype analysis is limited. Case presentation Here, we report the first case of a derivative 18p interstitial monosomy caused by a maternal complex intrachromosomal rearrangement, fully characterized by Optical Genome Mapping (OGM). Conclusions This rearrangement could not be fully characterized by either CMA or karyotype analyses, both of which yielded only partial and inconclusive results. The integration of OGM into routine diagnostics could enhance the understanding of complex chromosomal rearrangements, leading to improved prognostic and reproductive risk assessment.

Introduction Chromosomal structural variations (SVs) are important causes of neurodevelopmental disorders in children, but traditional detection techniques often fail to accurately resolve the precise breakpoints and pathogenic genes of complex rearrangements. To apply optical genome mapping (OGM) detects SVs across the whole genome by high-throughput labeling of ultra-long (>150 kb) DNA molecules, high-resolution fluorescence imaging, and alignment algorithms using a reference genome. Its resolution is up to 500 bp and is especially effective in finding exact breakpoints and orientations of complex rearrangements. This provides unprecedented technical support for clinical diagnosis and research. To perform genetic analysis of a family with chromosome 4 abnormalities using optical genome mapping technology, aiming to uncover the underlying pathogenic mechanisms. By integrating functional pathway enrichment analysis, this study explores the genotype-phenotype correlation in the patient and provides a theoretical basis for clinical diagnosis and treatment. Methods Karyotype analysis, multicolor fluorescence in situ hybridization (M-FISH), and OGM were performed on the proband and family members. Functional enrichment analysis was conducted using Metascape and GeneMANIA. Results The results showed that OGM technology precisely located the breakpoints, revealing that the patient carried a maternally derived derivative chromosome 4 (der(4)), with three copies of the 1q31.3, 1q31.3-q41, and 1q43 segments (totaling 20.5 Mb), involving 319 genes. Metascape analysis indicated that the genes were significantly enriched in multiple biological processes and pathways, especially in immune-related pathways and nervous system development processes, with the complement activation pathway having the highest enrichment degree, with -log10(p) reaching 13.9. Genemania showed that the candidate gene network was significantly enriched in functions related to humoral immune regulation, complement system activation, and muscle structure development, with a co-expression ratio of 98.07%. Conclusion OGM technology can identify complex chromosomal rearrangements that cannot be detected by conventional methods and provides molecular evidence for the familial pattern of disease. Combined with functional pathway enrichment analysis, the study proposes that disruption of the “complement–neurodevelopmental axis” may be the main cause of the proband’s neurodevelopmental disorder. These findings offer family-level evidence supporting the clinical application of OGM.

Background Acute myeloid leukemia-myelodysplasia related (AML-MR) is a biologically and clinically distinct subtype of AML that arises in the context of prior dysplasia. It is characterized by adverse cytogenetics and poor prognosis compared to other AML subtypes. Several genetic mechanisms underpin the pathogenesis of AML-MR; however, additional findings are likely to come to light over time with advanced genomic technologies, enhancing our understanding of their evolution. This report details a case of AML-MR involving unreported gene fusion. Case presentation A 59-year-old female with multiple comorbidities presented with slurred speech. Pathological evaluation and DNA-based next-generation sequencing results were consistent with AML-MR. AML fluorescence in situ hybridization (FISH) panel revealed an extra signal for RUNX1 . G-banding karyotype revealed a solitary rare t(X;21)(q26.1;q22.12) in 18 out of 20 cells analyzed. Optical genome mapping (OGM) was performed to precisely localize the breakpoints and identify the specific genes or gene fusions created by the translocation. OGM identified a novel fusion involving ENOX2 (Xq26.1) and RUNX1 (21q22.12), which was subsequently confirmed by a retrospective custom FISH probe targeting ENOX2 . Conclusions The identification of an ENOX2::RUNX1 fusion in AML-MR expands the spectrum of rare RUNX1 fusions. High-resolution approaches such as OGM enable precise delineation of fusion partners and breakpoints beyond the resolution of conventional cytogenetics. While the biological and clinical significance of this fusion remains to be determined, this finding highlights the value of OGM in the identification of novel and rare genomic rearrangements in leukemia and other malignancies.

Background Duchenne muscular dystrophy (DMD) is a severe disorder that primarily affects males due to its X-linked recessive inheritance. It is caused by pathogenic variants of the DMD gene, most commonly exonic deletions, duplications, or point mutations. Current routine genetic testing methods, including next-generation sequencing and multiplex ligation-dependent probe amplification, can identify pathogenic DMD variants in over 90% of clinically diagnosed patients. However, in rare cases, a molecular diagnosis cannot be established using routine methods. Case presentation We describe a follow-up genetic analysis, based on karyotyping and optical genome mapping (OGM), of a patient with clinically diagnosed DMD who initially had negative results in extensive routine genetic testing. Karyotyping revealed a paracentric X-chromosomal inversion with estimated breakpoints at p22.31 and p21.2. OGM fine-mapped this alteration as inv(X)(p22.2p21.1) and confirmed its pathogenicity by identifying the proximal breakpoint within intron 41 of DMD , thereby disrupting the gene and providing a definitive molecular genetic diagnosis. Conclusions Current results further underscore the important role of chromosomal inversions as causal in a subset of DMD patients who remain without a molecular diagnosis after routine testing. It also demonstrates the utility of OGM in providing detailed, gene-level insights into cytogenetic abnormalities observed in the diagnostics of neuromuscular disorders.

Among the human leukemia cell lines described in the literature, only the MDS-L cell line has been definitively established from a patient during the myelodysplastic syndrome (MDS) phase of the disease. However, the limited studies on its genomic complexity have restricted its applicability as an in vitro model for MDS. Here, we aimed to better characterize the chromosomal and genetic alterations of MDS-L. A comprehensive approach was employed combining conventional G banding, multicolor FISH (M-FISH), SNP arrays with the novel Optical Genome Mapping (OGM) technology. In addition, the mutational landscape was defined using targeted next-generation sequencing (NGS). G-banding revealed two karyotypically distinct cell populations, both exhibiting complex karyotypes. Using G-banding and OGM, we identified previously undescribed structural alterations, including der(1)t(1;7)(q11;q11.2), del(1)(q11), der(4)t(4;5)(p16;q11.2), i(5)(p10), der(6)t(6;15)(p21.3;q15), i(8)(q10), der(9)t(9;10)(q34;p11.21), der(19)t(6;19)(p13;p22) and i(22)(q10). Both OGM and SNP microarray analyses detected multiple copy number variants and regions of homozygosity. Chromosome breakpoints were precisely defined by OGM, allowing the identification of gene disruption events. Moreover, M-FISH technique validated the origins of additional chromosomal material observed in the karyotype, identified cryptic rearrangements, and distinguished the two clonal populations within the cell line. Finally, NGS revealed mutations in CEBPA , NRAS , TET2 and TP53 genes associated with MDS pathology. This multi-technique approach has enabled a precise characterization of the MDS-L cell line’s genomic complexity, highlighting the unique contributions of each technique in uncovering various genetic alterations and establishing a valuable resource for mechanistic studies and pre-clinical drug development.

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.

Novel treatments in chronic lymphocytic leukemia (CLL) have generated interest regarding the clinical impact of genomic complexity, currently assessed by chromosome banding analysis (CBA) and chromosomal microarray analysis (CMA). Optical genome mapping (OGM), a novel technique based on imaging of long DNA molecules labeled at specific sites, allows the identification of multiple cytogenetic abnormalities in a single test. We aimed to determine whether OGM is a suitable alternative to cytogenomic assessment in CLL, especially focused on genomic complexity. Cytogenomic OGM aberrations from 42 patients were compared with CBA, FISH, and CMA information. Clinical–biological characteristics and time to first treatment (TTFT) were analyzed according to the complexity detected by OGM. Globally, OGM identified 90.3% of the known alterations (279/309). Discordances were mainly found in (peri-)centromeric or telomeric regions or subclonal aberrations (<15–20%). OGM underscored additional abnormalities, providing novel structural information on known aberrations in 55% of patients. Regarding genomic complexity, the number of OGM abnormalities had better accuracy in predicting TTFT than current methods (C-index: 0.696, 0.602, 0.661 by OGM, CBA, and CMA, respectively). A cut-off of ≥10 alterations defined a complex OGM group (C-OGM, n = 12), which included 11/14 patients with ≥5 abnormalities by CBA/CMA and one patient with chromothripsis (Kappa index = 0.778; p < 0.001). Moreover, C-OGM displayed enrichment of TP53 abnormalities (58.3% vs. 3.3%, p < 0.001) and a significantly shorter TTFT (median: 2 vs. 43 months, p = 0.014). OGM is a robust technology for implementation in the routine management of CLL patients, although further studies are required to define standard genomic complexity criteria.

Background Cell line authentication and karyotype assessment are two critical quality control tests that should be performed when using cell lines for biologic research and are expected measurements for cell therapy development. The current paradigm requires two separate measurements to assess these attributes, therefore a single straightforward approach that could assess karyotype and authenticate cell lines is beneficial. Results We have developed a new optical genome mapping based approach named OGM-ID which can authenticate cell lines utilizing the same data that has previously been demonstrated as an alternative for traditional karyotyping. OGM-ID utilizes genome wide large (> 500 bp) insertions and deletions to uniquely identify cell lines. OGM-ID can be used to determine interspecies and intraspecies contamination. Benchmarking of OGM-ID was performed using three different family lineages, where replicates were clearly identified, and the relative genetic distance between individuals could be further monitored utilizing the zygosity of variants. Additionally, the donor of wild type and edited iPSCs was correctly determined even after multiple clonal selection events. Current limitations of OGM-ID require control around the version of Bionano Solve used and similar depths of coverage between samples. Conclusions OGM-ID is a whole genome technique that produces results comparable to other cell line authentication techniques with the added benefit of obtaining a cell line’s karyotype simultaneously. OGM-ID’s ability to distinguish large insertions or deletions, which are common in genome editing, also gives it a unique ability to distinguish between multiple clonal iPSC-derived allogeneic cell product candidates derived from the same donor.

While short-read sequencing currently dominates genetic research and diagnostics, it frequently falls short of capturing certain structural variants (SVs), which are often implicated in the etiology of neurodevelopmental disorders (NDDs). Optical genome mapping (OGM) is an innovative technique capable of capturing SVs that are undetectable or challenging-to-detect via short-read methods. This study aimed to investigate NDDs using OGM, specifically focusing on cases that remained unsolved after standard exome sequencing. OGM was performed in 47 families using ultra-high molecular weight DNA. Single-molecule maps were assembled de novo, followed by SV and copy number variant calling. We identified 7 variants of interest, of which 5 (10.6%) were classified as likely pathogenic or pathogenic, located in BCL11A, OPHN1 , PHF8, SON , and NFIA. We also identified an inversion disrupting NAALADL2 , a gene which previously was found to harbor complex rearrangements in two NDD cases. Variants in known NDD genes or candidate variants of interest missed by exome sequencing mainly consisted of larger insertions (> 1kbp), inversions, and deletions/duplications of a low number of exons (1–4 exons). In conclusion, in addition to improving molecular diagnosis in NDDs, this technique may also reveal novel NDD genes which may harbor complex SVs often missed by standard sequencing techniques.

Dyskeratosis congenita (DC) is an inherited bone marrow failure syndrome characterized by defects in telomere biology and clinical manifestations such as nail dystrophy, skin pigmentation abnormalities, and mucosal leukoplakia. Here, using whole exome sequencing (WES), whole genome sequencing (WGS), optical mapping sequencing (OGM), third‐generation sequencing, and mRNA sequencing, we diagnosed a participant with PARN gene complex compound heterozygous variants. In addition, protein structure simulation, immunohistochemistry, and western blot were conducted to investigate the structure and expression level of the PARN protein. WES revealed a maternal PARN variant, c.204G>T (p.Gln68His) (NM_002582.3). An insertion variant in the PARN gene from the father was identified by OGM and mRNA sequencing. Third‐generation sequencing results determined the insertion position of the SINE‐VNTR‐Alu (SVA) transposon and its size (2537 bp), which was found to lead to a premature stop codon (p.Gly469delinsGlu∗). The PARN protein level of the parents was reduced due to complex heterozygous variants. Overall, OGM diagnosed the structural variants of the participant with DC, supplementing the disease variant spectrum of DC. This case highlights a novel disease‐causing structural variant and the importance of transposon analysis in a clinical diagnostic setting.