Molecular Cytogenetics最新文献

Background: Xq28 duplications are a significant cause of X-linked intellectual disability (XLID). While the postnatal features of distal Xq28 duplication syndrome are well characterized, the prenatal phenotypes remain poorly defined due to limited data, posing challenges for genetic counseling.

Case presentation: We identified three fetuses carrying 454-558 kb distal Xq28 microduplications through chromosomal microarray analysis (CMA) from 13,084 prenatal cases at our center. The primary indications for diagnosis were abnormal ultrasound findings. Case 1 (male) and case 3 (female) exhibited nasal bone hypoplasia. Case 2 (male) showed increased nuchal translucency (NT) and a persistent right umbilical vein. After genetic counseling, two couples chose to terminate their pregnancies, while one couple continued the pregnancy and delivered a healthy child.

Conclusion: Distal Xq28 duplications would present diverse prenatal phenotypes, ranging from normal to abnormal. Skeletal anomalies are the most common prenatal features in symptomatic fetuses with this duplication. Prenatal diagnosis and genetic counseling are essential for providing clinical guidance to the affected families. The correlation between prenatal ultrasound findings and the distal Xq28 duplications requires further investigation in larger cohorts.

Background: Intrachromosomal insertion is a rare form of structural chromosomal rearrangement that often cannot be accurately delineated by conventional G-banding, making it difficult to predict reproductive outcomes. In clinical practice, such insertions are often misinterpreted as inversions or remain undetected, leading to recurrent segmental imbalances in offspring. We aimed to characterize an unresolved structural rearrangement identified in a family and to clarify its reproductive implications through advanced cytogenetic and molecular analyses.

Methods: Cytogenetic and molecular studies were conducted in a family where the proband exhibited a 17.8 Mb duplication at 9q21.31-q22.33. Although G-banding suggested a parental structural abnormality, its configuration could not be precisely defined. Subsequent preimplantation genetic testing for structural rearrangements (PGT-SR) using shallow whole-genome sequencing was performed on embryos, and further structural characterization was achieved through fluorescence in situ hybridization (FISH) and nanopore long-read sequencing.

Results: PGT-SR identified recurrent segmental imbalances involving the same region as in the proband, including four duplications and one deletion among 13 embryos. FISH and long-read sequencing demonstrated that the paternal rearrangement represented an intrachromosomal inverted insertion, described as ins(9)(q34.13q22.33q21.31). The father was phenotypically normal but transmitted unbalanced gametes generated by recombination between the insertion and original sites, leading to recurrent chromosomal abnormalities.

Conclusions: This case highlights the potential of intrachromosomal insertions, although balanced in carriers, to cause recurrent segmental duplications or deletions in offspring. Comprehensive analysis using FISH and long-read sequencing is essential for accurate diagnosis, appropriate genetic counseling, and informed reproductive decision-making.

Background: Expanded non-invasive prenatal testing (E-NIPT) extends traditional screening for trisomies 21, 18, and 13 to sex-chromosome aneuploidies (SCAs), rare autosomal aneuploidies (RAAs), and 92 pathogenic subchromosomal copy-number-variations (CNV) regions. However, the clinical performance of E-NIPT in large Chinese cohorts has not been fully characterized. This study aimed to assess the diagnostic performance of E-NIPT in a real-world cohort of nearly ten thousand pregnancies.

Methods: In this retrospective cohort study, we reviewed 9,708 consecutive pregnancies screened with E-NIPT at Xuzhou Maternity and Child Health Care Hospital between March 2021 and August 2024. All 192 screen-positive pregnancies were counseled for invasive diagnostic confirmation; 158 underwent chromosomal microarray analysis. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) for each anomaly category were calculated.

Results: Among 9,708 pregnancies, 192 (1.98%) were screen-positive; overall PPV among confirmed cases was 32.3%. Category-level results were: T21, 28 screen-positive with 26 confirmations and 23 true positives (sensitivity 100%, specificity 99.97%, PPV 88.5%, NPV 100%); T18, 11/10/3 (100%, 99.93%, 30.0%, 100%); T13, 15/13/2 (100%, 99.89%, 15.4%, 100%); SCAs, 37/26/15 (100%, 99.89%, 57.7%, 100%); RAAs, 43/5/1 (100%, 99.96%, 20.0%, 100%); CNVs, 58/48/7 with one false negative (sensitivity 87.5%, specificity 99.58%, PPV 14.6%, NPV 99.99%).

Conclusions: E-NIPT showed excellent apparent sensitivity and high specificity for common trisomies and SCAs, with modest PPV for CNVs and low PPV for RAAs. Positive findings should undergo invasive diagnostic confirmation and genetic counseling to guide management.

Background: Optical genome mapping (OGM) has demonstrated significant potential in detecting structural variations (SVs) and has been comprehensively evaluated both retrospectively and prospectively in prenatal diagnosis. However, obtaining an adequate volume of amniotic fluid (AF) samples for OGM remains challenging due to the diverse detection techniques currently employed in prenatal diagnosis, which can limit the applicability of OGM in this setting. This study seeks to explore enhancements in cell culture techniques and quality control processes for prenatal samples when utilizing OGM in prenatal diagnosis.

Results: OGM successfully analyzed 188 AF samples with a minimum input of 0.225 million cells for ultra-high-molecular-weight DNA extraction. The study provides a comprehensive overview of the mass of chorionic villus samples, the volume of AF used for cell culture, the duration of culture, and the cell yields obtained for OGM. It was demonstrated that reducing the number of cells used for DNA isolation may not significantly decrease DNA quality for OGM with optimal cell viability and may even yield better results than those achieved with recommended cell amounts. This suggests that the current QC standards may be overly stringent, and that variant analysis remains feasible for some samples that do not meet these criteria. Based on the variant data analysis of these samples, standards appropriate for prenatal samples were summarized.

Conclusions: The findings of this study indicate that a reduced volume of AF sample or a shortened cell culture duration can be achieved in prenatal OGM, thereby enhancing the feasibility of employing OGM in prenatal diagnosis and potentially benefiting patients. Furthermore, data QC metrics suitable for prenatal samples may be more tolerant than previously recommended, necessitating further investigation with larger cohorts to establish specific QC standards for prenatal samples.

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.