Molecular Cytogenetics最新文献

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.

Background: Copy number variations (CNVs) of uncertain significance (VUS) are increasingly identified through prenatal and postnatal genetic testing, yet their clinical interpretation remains challenging. We report a neonate with hematologic and genitourinary anomalies in whom a de novo duplication at chromosome 2q23.1-2q23.3 was discovered, prompting further genomic and clinical investigation.

Main body: The patient was born via cesarean section due to oligohydramnios and increased umbilical artery flow, following an otherwise normal pregnancy. Postnatal findings included anemia, thrombocytopenia, and hypospadias. Genetic analysis revealed a 1.5 Mb duplication at 2q23.1-2q23.3 (chr2:149,390,001-150,890,000, GRCh37), encompassing several protein-coding genes. Parental testing confirmed the duplication was de novo. The CNV overlaps with regions previously associated with 2q23.1 microduplication syndrome, although the phenotype in this case differs. A separate 1.02 Mb duplication at 3p26.3 was identified in the father, involving the CHL1 gene, but was not inherited and is not considered contributory. The 2q23.2 duplication was not found in population CNV databases including gnomAD-SV, DGV, and ClinGen, suggesting it is rare or novel. A detailed clinical summary and genomic analysis were performed to explore genotype-phenotype correlations.

Conclusion: This case underscores the importance of integrating clinical and genomic data to interpret de novo CNVs in neonates. The findings contribute to the understanding of rare duplications in the 2q23 region and highlight the need for cautious interpretation of incidental parental variants. Further studies are needed to elucidate the pathogenic potential of such duplications and their role in neonatal disease.

Introduction: Partial gene duplications are structural variants that are challenging to interpret, particularly in the context of neurodevelopmental disorders. The ASH1L gene, associated with autism spectrum disorders and cognitive impairment, exemplifies the complexity of such variants. This study explores the integration of Optical Genome Mapping (OGM) with traditional cytogenetic techniques and RNA sequencing to enhance the characterization of de novo partial gene duplications.

Methods: Initial detection of the duplication was performed using array comparative genomic hybridization (CGH) and exome sequencing, which were insufficient to resolve the detailed structure or predict functional impacts. OGM was employed to clarify the structural arrangement, while RNA sequencing assessed the expression profile of the ASH1L gene.

Results: OGM identified a tandem arrangement of two duplications at 1q22. One duplication resulted in a 3-exon intragenic duplication with a predicted frameshift effect, which conventional methods had misinterpreted as a single event. RNA sequencing revealed no reduction in ASH1L mRNA levels despite the frameshift, suggesting the non-activation of the nonsense-mediated decay (NMD) system.

Discussion: These findings challenge conventional views on the functional consequences of structural variants. The study demonstrates the capability of OGM to uncover complex genomic rearrangements that evade detection by traditional methods. Integrating advanced genomic tools enhances diagnostic precision and broadens our understanding of the pathogenicity of structural variants in developmental disorders.

Background: Kaufman oculocerebrofacial syndrome (KOS; OMIM #244450)is a rare autosomal recessive disorder caused by pathogenic biallelic variants in UBE3B, characterized by craniofacial dysmorphism, global developmental delay, hypotonia, and multisystem anomalies.

Case presentation: We describe a 12-month-old Jordanian girl born to consanguineous parents, who exhibited microcephaly, hypotonia, feeding difficulties, and failure to thrive. Echocardiography revealed a mild basal septal hypertrophy. Developmental evaluation confirmed moderate global delay. Whole-exome sequencing revealed a homozygous UBE3B splice site variant (c.1741 + 2T > C), previously reported as pathogenic in ClinVar and classified as pathogenic according to ACMG/AMP criteria but without a detailed phenotypic description. Family history revealed additional neonatal deaths in a consanguineous context, raising the possibility of an underlying autosomal recessive condition.

Conclusion: This case adds to the limited body of literature on KOS and provides further evidence for the pathogenicity of the c.1741 + 2T > C variant. This case highlights the importance of considering KOS in infants presenting with characteristic craniofacial features such as blepharophimosis, ptosis, preauricular tags, and developmental delay, particularly in consanguineous families.

Neutropenia has been recognized as a common feature of Cohen Syndrome, but its role as an early manifestation has not been fully elucidated. In this report, we present three patients diagnosed with Cohen Syndrome who were referred for neutropenia. All patients exhibited consistent clinical features of Cohen Syndrome, with neutropenia being the indication for genetic research. Neutropenia was the most prominent finding in all patients, and in one case, it was the earliest finding with other specific features. Additionally, we identified two novel variants, c.6107del (p.Asp2036Valfs*3) and c.5703del (p.Arg1901SerfsTer10) in the VPS13B gene, further contributing to the genetic understanding of this syndrome. Our findings emphasize the importance of early recognition of neutropenia as a key clinical sign in the diagnosis of Cohen Syndrome. Furthermore, these novel variants expand the genetic spectrum of the disorder and highlight the need for continued genetic investigation in rare syndromes.

Background: Patients with tendinopathy (TD) have expressed dissatisfaction with the efficacy of the first-line treatment, indomethacin. This research aims to identify key biomarkers in TD and investigate their underlying mechanisms.

Methods: Tendon samples were harvested from 5 Sprague-Dawley (SD) rats exhibiting TD and 5 healthy normal controls (NCs), destined for transcriptome sequencing. After thorough preprocessing of the RNA sequencing data, a differential expression analysis was performed to identify genes that significantly differentiated the TD group from the NCs. To identify candidate genes, an intersection analysis was performed between the differentially expressed genes (DEGs) and the key module genes obtained through weighted gene co-expression network analysis. The candidate genes underwent Mendelian randomization (MR) analysis and least absolute shrinkage and selection operator analysis to identify key genes. We conducted experimental validation and sensitivity analyses, such as pleiotropy, heterogeneity, and leave-one-out evaluations, to ensure the robustness of our findings.

Results: The findings present new evidence indicating that SLC8A1 facilitates the progression of TD. MR analysis established a causal link between SLC8A1 and TD progression (p < 0.05). The study indicated that SLC8A1 might inhibit TD progression by negatively regulating gamma-glutamylisoleucine levels. In SD rats, TD led to a disordered arrangement of collagen structures, increased infiltration of inflammatory cells, increased cell density, and thicker inflammatory hyperplasia in tendon. These results confirm the effective creation of a TD model. Analysis showed significant upregulation of SLC8A1 expression in the TD group (p < 0.05).

Conclusion: This research highlights SLC8A1 as a potential biomarker in TD development, providing novel perspectives for clinical diagnosis and treatment strategies.

Background: Chronic Myeloid Leukemia (CML) is primarily driven by the Philadelphia chromosome, producing the BCR::ABL1 fusion protein. Although imatinib significantly improved CML outcomes, resistance remains a key challenge. Resistance often leads to cytogenetic abnormalities (ACAs), indicating poor disease prognosis. This is the first study that investigates genetic profiles in imatinib-resistant Indonesian CML patients.

Method: The study included adult chronic-phase CML patients who met the criteria of treatment failure under the treatment of imatinib. Peripheral blood samples and bone marrow samples were collected and then processed for cytogenetic examination following the International System of Human Cytogenetic Nomenclature (ISCN) guidelines. BCR::ABL1 transcript levels were measured using Quantitative Real-Time PCR.

Result: Out of 27 CML patients, the mean age was 39.15 years, with a male-to-female ratio of 1:1.5. The mean BCR::ABL1 international scale (IS) value was 37.20 ± 4.56, and patients on tyrosine kinase inhibitor (TKI) therapy had a median treatment duration of 80 months. Cytogenetic analysis showed Philadelphia chromosome (Ph) positivity in 11.11% of peripheral blood and 34.78% of bone marrow samples, with Ph negativity in 25.93% and 17.93%, respectively. Peripheral blood abnormalities included trisomy 8 (11.11%), additional Ph (7.41%), trisomy 19 (3.70%), and complex karyotypes (14.81%), while bone marrow abnormalities included trisomy 8 (13.04%), additional Ph (8.69%), trisomy 21 (4.35%), monosomy 7/7q- (8.70%), and complex karyotypes (43.45%).

Conclusion: Cytogenetic anomalies such as trisomy 8, trisomy 19, and complex karyotypes may contribute to TKI resistance. Further study is needed to understand additional abnormalities observed.

Deletions in chromosome 4p can lead to two distinct phenotypes, Wolf-Hirschhorn syndrome (WHS) and proximal 4p deletion syndrome. While WHS, associated with distal deletions, has well-characterized phenotypic features, proximal 4p deletion syndrome, involving the 4p14-p 16.1 region, shows moderate manifestations, and its causative gene remains unknown with fewer reported cases. Here we report a Chinese case: a 21-year-old female with a peripheral blood chromosomal karyotype of 46,XX, del(4)(p15.3-p16). NGS-CNVA further revealed an 11.7 Mb deletion in the 4p16.2-p15.32 region and a 1.25 Mb microduplication in 16p13.13. She had ovarian dysfunction, and moderate Intellectual Disability(ID) without typical proximal 4p deletion phenotypes. Through analysis of Genecards and OMIM databases, we identified two neurodevelopmental genes DRD5 and WFS1, and four ovarian dysfunction-related genes WFS1, CC2D2A, PROM1, and QDPR, suggesting their roles in the patient's manifestations. Additionally, a review of 37 published cases of proximal 4p deletion syndrome revealed 17 cases with an overlap in the deleted region with our case. This report not only enhances the recognition of this rare syndrome among clinicians but also provides a basis for further exploration of the potential causative genes, contributing to a better understanding of the genotype-phenotype correlations in proximal 4p deletion syndrome.