Search Results (152)

Background/Objectives: Chromosomal microarray analysis (CMA) is an essential tool in modern cytogenetics for detecting copy number alterations and copy-neutral loss of heterozygosity (CN-LOH). As optical genome mapping (OGM) emerges as a potential replacement for traditional cytogenetic methods, the extent to which CMA remains necessary in routine diagnostic workflows remains to be elucidated. Methods: We retrospectively reviewed 53 primary neoplastic cases, selected from a larger cohort of 327 hematologic malignancy specimens, in which CMA identified one or more CN-LOH events. Event size, genomic content, and correlation with next-generation sequencing (NGS) findings were assessed. A separate cohort of newly diagnosed B-cell acute lymphoblastic leukemia (B-ALL) was analyzed to evaluate disease-specific CN-LOH frequency. Results: Nearly half of CN-LOH events detected were <25 Mb, below the current detection threshold of OGM inferred from published benchmarks and validated workflows. Many encompassed clinically relevant genes, including FLT3, JAK2, TET2, TP53, and RUNX1. Additionally, two-thirds of cases harbored pathogenic or likely pathogenic variants by NGS within the corresponding CN-LOH regions, further underscoring the clinical value of detecting these copy-neutral events. In contrast, CN-LOH was uncommon in B-ALL, and most alterations identified by CMA would be detectable by OGM. Many of these patients also harbored complex structural rearrangements that required multiple conventional assays for full characterization; these could be resolved by OGM in a single analysis. Conclusions: Our findings indicate that although OGM excels at resolving complex structural variants, CMA remains essential for detecting copy-neutral events. Until OGM achieves improved sensitivity for CN-LOH, an integrated approach utilizing conventional cytogenetics, CMA, NGS, and OGM provides the most reliable framework for comprehensive genomic assessment across cancer types. Full article

Background: Upland cotton (Gossypium hirsutum) is a major natural fiber crop and an important model for studying genome evolution and gene function in polyploid plants. However, its large and highly redundant genome presents substantial challenges for efficient and coordinated multiplex genome editing. Methods: Here, we developed a high-efficiency CRISPR/Cas12a-based multiplex genome editing system in cotton by integrating a tRNA–crRNA polycistronic expression strategy with a Bean yellow dwarf virus (BeYDV)-derived replicon. Results: This platform enabled coordinated expression of multiple crRNAs and simultaneous targeting of 16 loci within a centromere-proximal region of chromosome D03 (18.65–24.47 Mb). In individual transgenic lines, up to 10 target sites were edited concurrently, with nine targets exhibiting editing efficiencies above 56% and the highest efficiency reaching 96.46%. High-density multiplex editing predominantly induced small insertions and deletions at target loci. Notably, edited plants exhibited reduced growth and pronounced cytological abnormalities, including chromosome bridges, lagging chromosomes, and abnormal meiotic products. Transcriptome analysis revealed widespread dysregulation of genes involved in chromosome segregation and cell cycle regulation. Despite these functional perturbations, HiFi long-read sequencing detected no large-scale chromosomal rearrangements, indicating that genome instability arises from cumulative local perturbations rather than global structural alterations. Conclusions: Together, our results establish an efficient multiplex genome editing platform in cotton and highlight potential constraints of high-density editing on genome stability in complex plant genomes. Full article

Langer–Giedion syndrome (LGS), also known as trichorhinophalangeal syndrome type II (TRPS II; OMIM #150230), is a contiguous-gene deletion disorder caused by haploinsufficiency of TRPS1 and EXT1. Cornelia de Lange syndrome (CdLS) is genetically heterogeneous; heterozygous variants in RAD21 cause the milder CdLS type 4 phenotype (OMIM #614701). Because RAD21 lies between TRPS1 and EXT1, overlapping phenotypes may arise when all three genes are deleted. We report a unique case of a 4-year-old female presenting with a blended phenotype of Langer–Giedion Syndrome (LGS) and Cornelia de Lange Syndrome (CdLS) type 4. This case is distinct from previously reported 8q deletions in three key aspects: (1) Complex Genomic Architecture: Chromosomal microarray revealed a novel complex rearrangement consisting of a 13.01 Mb mosaic interstitial deletion at 8q23.1–q24.12, flanked by two large duplications (21.5 Mb at 8q11.23–q23.1 and 25.78 Mb at 8q24.12–q24.3). (2) Rare Mosaicism: This represents only the second reported case of mosaicism affecting this contiguous gene region. Notably, the patient demonstrates a “mosaic rescue” effect, where the mosaicism appears to have mitigated the neurodevelopmental phenotype (the patient is bilingual and ambulatory) while failing to protect the skeleton. (3) First Bone-Specific Therapy: The patient suffered from severe, recurrent fractures due to a synergistic “double hit” of TRPS1-related osteopenia and EXT1-related exostoses. We report the first successful use of bisphosphonate therapy (pamidronate) in this specific mosaic profile, which resulted in a complete cessation of fractures during a 12-month follow-up. This case underscores the utility of detailed microarray analysis in complex phenotypes and suggests bisphosphonates as a viable rescue therapy for refractory syndromic osteoporosis. Full article

Background: Optical genome mapping (OGM) detects genome-wide structural variants (SVs), including balanced rearrangements and complex copy-number alterations beyond standard-of-care cytogenomic assays. In chronic lymphocytic leukemia (CLL), cytogenetic and genomic risk stratification is traditionally based on fluorescence in situ hybridization (FISH), karyotyping, targeted next-generation sequencing (NGS), and immunogenetic assessment of immunoglobulin heavy chain variable region (IGHV) somatic hypermutation status, each of which interrogates only a limited aspect of disease biology. Methods: We retrospectively evaluated fifty patients with CLL using OGM and integrated these findings with cytogenomics, targeted NGS, IGHV mutational status, and clinical time-to-first-treatment (TTFT) data. Structural variants were detected using OGM and pathogenic NGS variants were derived from a clinical heme malignancy panel. Clinical outcomes were extracted from the electronic medical record. Results: OGM identified reportable structural variants in 82% (41/50) of cases. The most frequent abnormality was del(13q), observed in 29/50 (58%) and comprising 73% (29/40) of all OGM-detected deletions with pathologic significance. Among these, 12/29 (42%) represented large RB1-spanning deletions, while 17/29 (58%) were focal deletions restricted to the miR15a/miR16-1 minimal region, mapping to the non-coding host gene DLEU2. Co-occurrence of adverse lesions, including deletion 11q/ATM, BIRC3 loss, trisomy 12, and deletion 17p/TP53, were recurrent and strongly associated with shorter TTFT. OGM also uncovered multiple cryptic rearrangements involving chromosomal loci that are not represented in the canonical CLL FISH probe panel, including IGL::CCND1, IGH::BCL2, IGH::BCL11A, IGH::BCL3, and multi-chromosomal copy-number complexity. IGHV data were available in 37/50 (74%) of patients; IGHV-unmutated status frequently co-segregated with OGM-defined high-risk profiles (del(11q), del(17p), trisomy 12 with secondary hits, and complex genomes whereas mutated IGHV predominated in OGM-negative or structurally simple del(13q) cases and aligned with indolent TTFT. Integration of OGM with NGS further improved genomic risk classification, particularly in cases with discordant or inconclusive routine testing. Conclusions: OGM provides a comprehensive, genome-wide view of structural variation in CLL, resolving deletion architecture, identifying cryptic translocations, and defining complex multi-hit genomic profiles that tracked closely with clinical behavior. Combining OGM and NGS analysis refined risk stratification beyond standard FISH panels and supports more precise, individualized management strategies in CLL. Prospective studies are warranted to evaluate the clinical utility of OGM-guided genomic profiling in contemporary treatment paradigms. Full article

Chromosomal inversions and copy-number variants (CNVs) drive genomic and phenotypic diversification in birds by reshaping recombination, gene expression, and genome architecture. Here, we report a complex structural polymorphism on great tit (Parus major) chromosome 1A that occurs in the Siberian population with a 19% heterozygote frequency. Using cytogenetic and genomic approaches, we show that this rearrangement combines a ~55 Mb paracentric inversion in the long arm with a dramatic (>30 Mb) expansion of the short arm driven by extensive amplification of multiple genomic loci. These include a region homologous to the poorly characterized FAM118A gene, whose paralog FAM118B has been recently shown to play a pivotal role in innate immune activation. This region is missing from the current reference genome assembly while present in ~20 copies on wild-type 1A chromosome and nearly twentyfold amplified in the rearranged variant. It contains a nested 630 bp tandem repeat, encompassing the entire exon 3, which has burst to a total of ~50,000 copies in the rearranged chromosome. While functional analyses are required to uncover the biological effects of the genomic features linked to this rearrangement, our results offer a unique framework for studying how complex structural polymorphisms drive genome innovation and adaptive diversity. Full article

Background/Objectives: Chromosomal inversions play an important role in the evolution of insects by forming genetic barriers between closely related species and facilitating local adaptation. Polymorphic inversions in malaria mosquitoes of the Maculipennis subgroup have been studied for over 50 years, yet the evolutionary ancestry of the gene orders remains unknown. In this study, we mapped the genes flanking the breakpoints of two polymorphic X-chromosome inversions in the cryptic species Anopheles messeae and Anopheles daciae of the Maculipennis subgroup. Methods: We used an iterative mapping approach to define the breakpoint regions, selecting flanking markers based on the genome assembly of the reference species, Anopheles atroparvus. To identify the ancestral X chromosomal arrangement in An. messeae and An. daciae, we developed and implemented the genomic inversion calculator (GIC), which uses greedy heuristics to determine the shortest evolutionary scenario of rearrangements. Results: Our knowledge of the relative genomic positions of the inversion breakpoints in An. daciae and An. messeae enabled us to use the An. atroparvus genome as an outgroup and the GIC tool to show that the X0 and X2 arrangements emerged independently along the evolutionary lineages of An. daciae and An. messeae, respectively, based on the X1 arrangement. Conclusions: These results refine the structure and boundaries of the X chromosome rearrangements and reconstruct the sequence of evolutionary events in the cryptic complex An. messeae–An. daciae, demonstrating that the X1 arrangement is ancestral. This study lays the groundwork for analyzing the molecular organization of breakpoints, the mechanisms of inversion formation, and their role in speciation. Full article

Hemophilia A (HA) is an X-linked recessive bleeding disorder that predominantly affects males but rarely manifests clinically in females. We report an unusual case of a woman with HA carrying a de novo heterozygous F8 variant, skewed X chromosome inactivation (XCI), and mosaic monosomy X without the Turner syndrome phenotype. DNA was extracted from whole blood. After excluding F8 inversions and large rearrangements, Sanger sequencing of coding regions was performed. XCI was assessed by STR analysis of the AR gene. Haplotypes were identified by fragment analysis of three polymorphic sites. Karyotyping was performed using G-banding. A heterozygous missense variant in the F8 gene, c.6545G>A (p.Arg2182His), was detected with allelic imbalance. STR analysis confirmed ~93% skewed XCI. Karyotyping revealed mosaicism: 45,X [7]/46,XX [14]. Neither parent carried the c.6545G>A variant or karyotype aberrations. We suggest that 46,XX cells carried c.6545G/A with preferential inactivation of the normal X chromosome, whereas 45,X0 cells carried the mutant allele only. The limited proportion of active normal X chromosomes led to a mild rather than severe phenotype. This case highlights complex genetic mechanisms underlying HA in females and underscores the importance of comprehensive molecular and cytogenetic testing for accurate diagnosis, clinical management, and genetic counseling. Full article

Observations of the processes of oogenesis, fertilization, and the earliest embryonic development have given us the opportunity to estimate the importance of chromosomal distribution errors for the success of mammalian reproduction. It is now known that in the large volume of oocytes, zygotes and the first embryonic cells, the rearrangement of chromatin is associated with a complex rearrangement of cytoskeletal structures, which creates specific problems. This review discusses two main issues critical to the success of early embryos: Why oocyte meiosis is too frequently wrong in chromosomal segregation? Why the first zygotic mitoses are too frequently wrong in chromosomal segregation? We concluded the following: (1) The main cytoskeletal defects that disturb oocyte meiosis are a problematic connection between cytoskeleton and nucleoskeleton, unsuccessful movement of the spindle to the oocyte periphery, unstable anchoring of the spindle to oolemma, and deviations in meiotic spindle morphology; (2) The main cytoskeletal defects that disturb pronuclear unification are nonfunctional male centriole, unsuccessful forming of microtubule aster around the sperm centrosome, problematic movement of the two pronuclei towards each other and inappropriate contacts between centrosomes, microtubules and nuclear pore complexes; (3) Cytoskeletal defects that disturb zygote mitosis are unsuccessful forming of bipolar mitotic spindle, non-synchronized congression of maternal and paternal chromosomes, and unsuccessful attachment of kinetochores to microtubules. Full article

KMT2A-rearranged (KMT2A-r) acute lymphoblastic leukemia (ALL), particularly in infants, represents one of the most aggressive pediatric hematological malignancies with a historically dismal prognosis. While KMT2A-AFF1 (t(4;11)) is the most prevalent fusion, a diverse array of partner genes exists, each conferring distinct biological and clinical features. This review focuses on the rare but clinically significant KMT2A-AFF3 subtype, which arises from the t(2;11)(q11.2;q23) chromosomal translocation. This review summarizes the molecular pathogenesis driven by the KMT2A-AFF3 fusion oncoprotein, which functions as an aberrant transcriptional complex. This complex hijacks essential epigenetic machinery, including the recruitment of DOT1L and interaction with Menin, leading to pathogenic histone modifications (e.g., H3K79 hypermethylation) and the subsequent upregulation of critical target genes, notably the HOXA cluster and MEIS1, thereby enforcing a B-lymphoid differentiation arrest at the pro-B/pre-B stage. Clinically, KMT2A-AFF3 ALL is characterized by high-risk features, including infant onset, hyperleukocytosis, central nervous system (CNS) involvement, and a distinct CD10-negative immunophenotype. This review highlights the evidence defining its poor prognosis, which is primarily driven by profound chemoresistance to conventional therapies, including glucocorticoids. Finally, we discuss the rapidly evolving therapeutic landscape, detailing the limitations of standard intensive chemotherapy and the immense promise of novel targeted strategies, such as Menin inhibitors (e.g., Revumenib), DOT1L inhibitors, and immunotherapies (e.g., CAR-T cells, Blinatumomab), which hold the potential to revolutionize outcomes for this high-risk leukemia subtype. Full article

Background: Intellectual disability (ID) is a heterogeneous condition caused by diverse genetic factors, including single-nucleotide variants (SNVs) and copy number variants (CNVs). Whole-exome sequencing (WES) and clinical exome sequencing (CES) have become essential tools for identifying pathogenic variants; however, their relative diagnostic performance in ID has not been fully characterized. Methods: Children diagnosed with ID or related neurodevelopmental disorders underwent WES or CES. Identified variants were classified according to ACMG/AMP and ClinGen guidelines, with segregation analysis performed when parental samples were available. Diagnostic yields were compared across demographic, prenatal, and phenotypic subgroups. A multidimensional semi-quantitative scoring system encompassing 15 clinical domains (e.g., age at onset, neuro-motor function, seizures, MRI findings, vision, and dysmorphic features) was developed. Z-scores were calculated for each parameter, followed by hierarchical cluster analysis (HCA) and correlation modeling to define genotype–phenotype associations and pathway-level clustering. Results: A broad spectrum of pathogenic and likely pathogenic variants across multiple genes and biological pathways was identified in our study. CNV-associated cases frequently exhibited prenatal anomalies or multisystem phenotypes associated with large chromosomal rearrangements. Monogenic variants and their corresponding phenotypic profiles were identified through clinical exome sequencing (CES) and whole-exome sequencing (WES). Phenotypic HCA based on Z-scores revealed three major biological groups of patients with coherent genotype–phenotype relationships: Group 1, severe multisystem neurodevelopmental disorders dominated by transcriptional and RNA-processing genes (POLR1C, TCF4, HNRNPU, NIPBL, ACTG1); Group 2, intermediate epileptic and metabolic forms associated with ion-channel and excitability-related genes (SCN2A, PAH, IQSEC2, GNPAT); and Group 3, milder or focal neurodevelopmental phenotypes involving myelination and signaling-related genes (NKX6-2, PLP1, PGAP3, SMAD6, ATP1A3). Gene distribution significantly differed among these biological categories (χ² = 54.566, df = 34, p = 0.0141), confirming non-random, biologically consistent grouping. Higher Z-scores correlated with earlier onset and greater neurological severity, underscoring the clinical relevance of the multidimensional analytical framework. Conclusions: This study highlights the genetic complexity and clinical heterogeneity of intellectual disability and demonstrates the superior diagnostic resolution of WES and CES. Integrating multidimensional phenotypic profiling with genomic analysis enhances genotype–phenotype integration and enables data-driven phenotype stratification and pathway-based re-analysis. This combined diagnostic and analytical framework offers a more comprehensive approach to diagnosing monogenic ID and provides a foundation for future predictive and functional studies. Full article

Acute myeloid leukemia (AML) is an aggressive clonal hematopoietic malignancy, characterized by marked biological heterogeneity and variable clinical outcomes. Among its rarer genetic subsets is AML with rearrangements of the MDS1 and EVI1 complex locus (MECOM), occurring in fewer than 2% of newly diagnosed cases. This review examines the biology and clinical significance of MECOM-rearranged AML, with a focus on its diverse mechanisms of leukemogenesis, including chromosomal inversion and translocation involving 3q26. We discuss how aberrant EVI1/MECOM activity alters gene expression networks and drives malignant transformation. Current therapeutic approaches—including intensive chemotherapy, hypomethylating agents in combination with venetoclax, and allogeneic stem cell transplantation—are evaluated with particular emphasis on inv(3) and other t(3q26) subtypes. Despite these treatment strategies, outcomes remain poor, underscoring the urgent need for novel, more effective therapies for this high-risk form of AML. Full article

In Lolium perenne, a novel growth habit mutant, named VIROIZ, was recovered following colchicine treatment, and it was confirmed to maintain the diploid chromosome number (2n = 2x = 14). The mutation affected the stem morphology by inducing prolific axillary shoot formation at nodal zones, resulting in a spreading growth habit that can extend to ~70 cm in width. Inheritance analysis based on single-plant evaluations in crosses with wild-type plants (F₁, n = 285; F₂, n = 380) and in selfed progeny (S₁, n = 255) consistently showed ~40% expression of the spreading phenotype, deviating from classical Mendelian ratios and indicating complex genetic control. Phenotypic selection further distinguished divergent classes: positively selected lines (C1⁺) averaged 3.90 axillary tillers per stem, whereas negatively selected lines (C1⁻) averaged only 0.22. Partial sequencing of 11 candidate genes implicated in shoot architecture, covering 40–90% of full-length DNA, did not provide a conclusive explanation for the altered stem growth. Notably, a single point mutation was observed in CRT3 (an endoplasmic reticulum chaperone that interacts with brassinosteroid signaling) highlighting it as a primary target for future studies. Cytological analysis of meiosis in F₁ hybrids between VIROIZ and wild-type plants revealed irregular chromosome pairing with persistent univalents (2–4 per cell), supporting the presence of structural chromosomal rearrangements that may disrupt gene organization and function in VIROIZ. The non-Mendelian segregation of the spreading phenotype, together with the observed meiotic irregularities, suggests that the mutation affects regulatory genes responsive to hormonal signals controlling axillary meristem initiation. The mutant represents a valuable resource for turf-type L. perenne breeding and for studying hormonal regulation of shoot morphogenesis in Poaceae. Full article

Background/Objectives: Relapsed acute myeloid leukemia (AML) is often characterized by clonal evolution and acquired genomic abnormalities, which can inform prognosis and direct therapeutic decisions. The emergence of high-risk chromosomal rearrangements during relapse is of particular significance, yet the impact of rare and complex events remains poorly understood. This report details a case of relapsed AML that demonstrated rare MYC and MECOM rearrangements and additional features that were not observed at initial diagnosis, emphasizing the clinical relevance of serial cytogenetic assessments. Case Description: A 70-year-old man was initially diagnosed with AML, exhibiting monocytic differentiation, an 11q23 deletion involving KMT2A loss, and a U2AF1 mutation. After achieving remission with azacitidine and venetoclax, the patient relapsed within ten months, necessitating reevaluation and modification of therapy. Repeat cytogenetic analysis at relapse revealed a distinct t(3;8)(q26.2;q24.3) exhibiting MYC and MECOM rearrangements, features that were absent at initial diagnosis. Conclusions: This case underscores the importance of serial cytogenetic and molecular profiling in relapsed AML. The emergence of new abnormalities upon relapse suggested underlying genomic instability and clonal evolution. MYC rearrangements are notably rare in AML, especially with concurrent MECOM rearrangements, highlighting a unique feature of this case. The identification of novel abnormalities at relapse may carry prognostic and therapeutic significance and may be used to refine risk stratification. Thus, ongoing cytogenetic monitoring is essential to adapt management approaches in evolving disease contexts. Full article

Fanconi anemia (FA) is a genetic disorder characterized by congenital anomalies, bone marrow failure, and cancer predisposition. Among other solid cancers, head and neck squamous cell carcinoma (FA HNSCC) is the most common cancer type in individuals with FA. The FA pathway is required for the complete repair of DNA interstrand crosslinks (ICLs), and unresolved ICLs result in cell cycle arrest, apoptosis, or complex chromosomal rearrangements due to chromosome breaks, ultimately leading to tumorigenesis. FA HNSCCs present earlier (median age of onset in the 30s) and exhibit a more aggressive course with frequent recurrence and second primaries, and entail a poorer survival rate compared to sporadic HNSCC. FA HNSCCs are mostly human papillomavirus (HPV)-negative and frequently carry somatic copy number variations (CNVs), which amplify oncogenes implicated in sporadic HNSCC, but single-nucleotide variants or small insertions and deletions are less frequent than in HPV-negative sporadic HNSCC. A subset of sporadic HNSCC carries pathogenic mutations or promoter methylation in FA genes, which also harbor characteristic somatic CNVs, suggesting shared molecular underpinnings with FA HNSCC. Heightened inflammation from genomic instability and transcriptional activation of retrotransposons contribute to tumorigenesis and increased invasiveness by the epithelial-to-mesenchymal transition. Due to heightened sensitivity to DNA crosslinking agents in patients with FA, platinum-based chemotherapy is generally avoided, which presents a significant hurdle for treatment and thereby leaves limited therapeutic options. Surgical management is the mainstay of therapy if possible, and targeted therapy has been increasingly studied in HNSCC in FA. Full article

Complex chromosomal rearrangements (CCRs) are rare structural abnormalities involving at least three chromosomal breakpoints and often two or more chromosomes. Owing to their inherent genomic complexity, CCRs are frequently associated with abnormal phenotypes, including developmental delay, congenital anomalies, and infertility. In this study, we report four male patients, three of them with de novo rare structural chromosomal rearrangement detected through a combination of Giemsa-Trypsin (GTG) banding, fluorescence in situ hybridization (FISH), and high-resolution microarray techniques (SNP array and array CGH). Each of the four cases turned out to be of a different type: in addition to two exceptional CCRs, an inv dup del 18q and a cluster rearrangement involving the long arm of chromosome 4 were identified. Despite the limitations of the testing methods, we performed a detailed analysis of the relationship between the most detailed genotype data and the associated phenotype. Our study provides further valuable evidence that the use of molecular cytogenetic methods is of paramount importance even in cases with abnormal karyotypes detected by light microscopy, as high-resolution data may reveal unsuspected genomic complexity, which is essential for genetic counseling in these patients. Full article