Cytogenetic variation and chromosomal evolution in Palearctic white-toothed shrews (Crocidura) remain poorly understood, particularly within the Asian clade. Here, we provide the first cytogenetic characterization of Crocidura kegoensis and Crocidura dracula from Vietnam. All studied C. kegoensis individuals have stable karyotypes with 2n = 40 and FNa = 52 and are distinguished by large heterochromatic blocks on sex chromosomes. Different C. dracula specimens with equal FNa = 52 have 2n = 36-38 due to centromeric fusions. To enable comparative analysis within and beyond the genus, we generated a flow-sorted library for Crocidura sibirica and applied fluorescent in situ hybridization (FISH) to C. dracula metaphase chromosomes. Integrating our cytogenetic data with existing genetic evidence, we confirmed the presence of two distinct groups within the Asian clade of Palearctic shrews - northwestern and southeastern - that differ both genetically and karyologically. Using C. dracula as a focal taxon, we highlight ongoing, rapid speciation within the southeastern group and show that the extent level of chromosomal rearrangements in taxa correlates with their divergence time.
Karyotypes of species within the genus Equus display considerable variation in chromosome number and are characterised by numerous structural rearrangements that have played a pivotal role in their evolutionary divergence and speciation. Equus caballus (horse), 2n = 64 and Equus asinus (donkey), 2n = 62, constitute particularly interesting models for comparative studies due to the diversified morphology of their chromosomes, including acrocentric and submetacentric pairs, documented Robertsonian translocations, and centric fusions. In recent decades, widely applied molecular cytogenetic techniques, especially fluorescence in situ hybridisation (FISH), have enabled the identification of homologous regions, the determination of breakpoint locations, and the precise mapping of chromosomal fragments. Simultaneously, the rapid development of sequencing technologies has allowed for the generation of complete genomic assemblies and the detection of numerous rearrangements that were not identified by earlier methods. Despite these advances, comprehensive physical validation of the most variable chromosomal regions in both species is still lacking, which limits a full understanding of karyotype dynamics and its evolutionary significance. For this reason, further studies involving systematic BAC probe mapping and the integration of FISH data with advanced genomic techniques are warranted. Such an interdisciplinary framework would facilitate the construction of a high-resolution physical map of the genomes of Equus caballus and Equus asinus, thereby advancing our understanding of the mechanisms underlying speciation within the genus Equus.
INTRODUCTION:Most fish reproduce sexually, but some species reproduce asexually through gynogenesis. Gynogenetic species are thought to provide important insight into the evolution of sexual reproduction, and investigations into their origins are required. Clonal loaches exist in certain areas of Japan and may have resulted from a past hybridization event between the two genetically divergent groups (A and B). However, the intergroup hybrids between current groups A and B show reproduce the patterns different from those of clonal loaches, and comparisons distinguish the ancestral group within clonal loaches from the current group are needed. METHODS:We used NGS data to search for repetitive sequences that could serve as markers to reveal genetic differences between species and populations and developed new cytogenetic marker, M407. RESULTS:The karyotypes and 18S rDNA signals were conserved across all examined individuals. M407 signals were detected in group B and in the ancestral groups A and B of clonal loaches, but not in the current group A. CONCLUSION:Cytogenetic results suggest that sequences associated with group B may have been introgressed or structurally incorporated into the ancestral group A genome during hybridization events leading to the formation of clonal loaches.
INTRODUCTION:The identification of precise genetic etiologies is indispensable for the clinical management of monogenic disorders. However, conventional diagnostic methods and exome sequencing (ES) frequently fail to identify complex structural variations (SVs), leaving the genetic basis unexplained in approximately 30-60% of suspected cases. Optical genome mapping (OGM) emerges as a high-resolution technology capable of detecting cryptic SVs inaccessible to standard methodologies. METHODS:In this study, we evaluated the clinical utility of integrating OGM into the diagnostic algorithm for unresolved monogenic diseases. Following negative or inconclusive results from standard ES pipelines, OGM was applied to a targeted subset of patients (n=7) selected from a comprehensive clinical cohort of 1,257 individuals with suspected genetic disorders. RESULTS:The integration of OGM identified candidate SVs that may represent the second allelic alteration in two distinct cases; however, confirmation through parental segregation analysis remains pending. Specifically, OGM identified an intronic insertion in the TTLL5 gene and a deletion in a putative regulatory region approximately 400 kb upstream of the NMNAT1 gene, both of which were missed by prior diagnostic testing. CONCLUSION:Our findings suggest that OGM has potential value in investigating the missing heritability of autosomal recessive disorders. By detecting candidate SVs invisible to conventional methods, OGM may warrant consideration as a complementary diagnostic approach following inconclusive exome sequencing; however, larger cohorts and confirmatory functional studies are needed to establish its clinical utility.
Introduction: Cytogenetic findings are critical for determining prognosis, therapy and risk assessment in acute lymphoblastic leukaemia (ALL). Data on the epidemiology of cytogenetic findings in ALL from southern Asia is limited. This report documents the cytogenetic changes in ALL seen at a referral hospital in southern India and compares it with the literature. Methods: Clinical profiling and conventional cytogenetic analysis (CCA) of all patients with reverse-transcription polymerase chain reaction for detection of cryptic t(12;21). Results: Of 1,968 ALL, 1,819 (92.4%) patients aged 0.3-84 years (median 17) had successful CCA. There were 979 children (<= 18 years) and 840 adults. Abnormal karyotypes were found in 1,368 (75.2%), B-ALL-78%, and T-ALL-69%. The favourable-risk group included high hyperdiploidy (HeH, 17.4%), t(12;21) (9.8%), and t(1;19) (4.3%), with >80% of HeH and t(12;21) in children. The unfavourable-risk group included t(9;22) (11.2%, 80% adults), hypodiploidy (8.0%), MYC (8q24) translocations (2.3%), and KMT2A (11q23) translocations (1.6%). In children, the frequency of HeH (26.8%) was lower than the West (30.7%) but higher than South-East (S.E.) Asia (15.5%) while t(9;22) (4.2%) was higher than the West (2%) but lower than S.E. Asia (6.8%). In adults, frequencies again differed from S.E. Asia (HeH, 6.4% vs. 2.7% and t(9;22), 19.4% vs. 29.3%) but were comparable to the West. Conclusion: CCA effectively provides diagnostic information in over 90% of ALL cases. While the spectrum of cytogenetic changes is similar to global data, there are significant regional variations in the frequencies of specific abnormalities.
INTRODUCTION:Mosaic double aneuploidy (MDA) defines the presence of two chromosomally distinct cells lines derived from the same zygote arising from early cytogenetic events. MDA for monosomy X and trisomy 18 is a rare occurrence described in only 12 individuals in the medical literature to date. CASE PRESENTATION:Here, we present 2 individuals with MDA of monosomy X and trisomy 18 with a Turner predominant phenotype. Congruent with previous reports, the percentage of aneuploid cells is highly variable in differing tissues, without clear genotype-phenotype associations. Molecular mechanism explored in one individual suggests two independent post-zygotic events lead to this chromosomal constitution. CONCLUSION:Given the rarity of this condition and the recognition that early post-zygotic chromosomal aneuploidy events are common, additional reports of individuals with MDA are needed to expand the natural history and improve counseling for families, especially in the prenatal period, as clinical manifestations of either chromosomal condition are possible.
INTRODUCTION:Robertsonian translocations resulting from the fusion of two acrocentric chromosomes are the most common chromosomal rearrangements in healthy individuals. Female carriers of a Robertsonian 14;21 translocation have a 10% risk for a liveborn with trisomy 21. METHODS:The study is based on a large family from Oman with eight offspring with translocation trisomy 21 (rob(14;21)(q10;q10),+21). The core family had nine live births, of which five were affected by translocation trisomy 21, two are monozygotic twins. The meiotic recombination pattern was analyzed by microsatellite markers covering chromosomes 21 and 14. For comparison, meiotic recombination was studied in an Arab family with three offspring with trisomy 21. In addition, in the mother of the core family whole-genome sequencing (WGS) was performed to look for possible variants involved in this process. RESULTS:Apart from the core family, there are three other related families with one affected child each. The increased risk for a child with translocation trisomy 21 in the core family is significant. In all cases, the nondisjunction took place at the first meiotic division (MI). Crossovers along chromosome 21 were observed in all affected children, in 2 cases a double crossover in the proximal part of chromosome 21. This pattern is completely different to that of the family with free trisomy 21. WGS did not reveal known pathogenic/likely pathogenic variants related to meiotic dysfunction. CONCLUSION:To the best of our knowledge, such a chromosomal transmission ratio distortion has not been reported so far. In addition, meiotic recombination between the translocation chromosome and free chromosome 21 showed an unusual pattern.
INTRODUCTION:Radiotherapy (RT) outcome is governed by radiosensitivity and DNA repair capacity of tumour cells and their interaction with surrounding normal tissues and vice versa. As radiosensitivity varies with the origin and genetic makeup of the cell, this study compares direct and bystander responses in directly targeted to X-rays and non-targeted (bystander) tumour (MCF-7 and PC3) and normal (MCF10A and HPrEC) epithelial cells of breast and prostate origin. METHODS:Cells were exposed to X-rays (0, 2, and 4 Gy) by a clinical linear accelerator and co-cultured with corresponding unirradiated cells. Micronucleus (MN) and clonogenic assays were adopted to quantify the DNA damage and survival fraction (SF), respectively, in all cells and multicolour fluorescence in situ hybridization (m-FISH) in MCF-7 and PC3 cells to identify the chromosomes frequently involved in translocations. RESULTS:Directly targeted tumour and normal cells showed a significant increase in MN frequency and decrease in SF. MN frequency increased from 0.023 ± 0.004 (control) to 0.076 ± 0.008 (2 Gy) and 0.177 ± 0.013 (4 Gy) in MCF-7 cells. MCF10A showed MN frequency of 0.049 ± 0.007 (control), 0.128 ± 0.011 (2 Gy), and 0.219 ± 0.014 (4 Gy). SF was significantly higher in MCF-7 (0.39 ± 0.03 and 0.15 ± 0.02) cells than MCF10A (0.30 ± 0.02 and 0.12 ± 0.01). MN frequency in PC3 cells increased from 0.056 ± 0.007 (control) to 0.168 ± 0.012 (2 Gy) and 0.378 ± 0.019 (4 Gy). HPrEC exhibited MN frequency of 0.018 ± 0.004 (control), 0.058 ± 0.007 (2 Gy), and 0.147 ± 0.012 (4 Gy). SF was higher in HPrEC (0.72 ± 0.03 and 0.40 ± 0.02) cells than PC3 (0.22 ± 0.01 and 0.09 ± 0.004). Similarly, a significant increase in MN frequency was observed in the non-targeted cells when compared to that of control, confirming occurrence of radiation-induced bystander effect. Thus, the results indicate radiation sensitivity differs among the cell types. The m-FISH results reveal a non-random distribution of X-irradiation-induced breaks and translocation. In directly targeted cells, chromosomes 7, 16, 17, 20, 21, 22 (MCF-7) and 3, 4, 6, 14, 17 (PC3) showed frequent involvement in translocations. Chromosomes 17 and 20 (MCF-7) and 10, 11, and 18 (PC3) were frequently involved in non-targeted cells. CONCLUSION:The present study results indicate that the tumour cells demonstrated higher radiosensitivity and a stronger bystander response than normal cells. Intrinsic molecular factors and genome organization affect both targeted and non-targeted responses, emphasizing their relevance for optimizing RT strategies.
INTRODUCTION:Cytogenetic findings are critical for determining prognosis, therapy and risk assessment in acute lymphoblastic leukaemia (ALL). Data on the epidemiology of cytogenetic findings in ALL from southern Asia is limited. This report documents the cytogenetic changes in ALL seen at a referral hospital in southern India and compares it with the literature. METHODS:Clinical profiling and conventional cytogenetic analysis (CCA) of all patients with reverse-transcription polymerase chain reaction (RT-PCR) for detection of cryptic t(12;21). RESULTS:Of 1968 ALL, 1,819 (92.4%) patients, age 0.3-84 years, (median 17) had successful CCA. There were 979 children (<18 years) and 840 adults. Abnormal karyotypes were found in 1368 (75.2%), B-ALL-78% and T-ALL-69%. Favorable-risk group included high hyperdiploidy (HeH, 17.4%), t(12;21) (9.8%), and t(1;19) (4.3%), with > 80% of HeH and t(12;21) in children. The unfavorable-risk group included t(9;22) (11.2%, 80% adults), hypodiploidy (8.0%), MYC (8q24) translocations (2.3%), and KMT2A/MLL(11q23) translocations (1.6%). In children, the frequency of HeH (26.8%) was lower than the West (30.7%) but higher than S.E. Asia (15.5%) while t(9;22) (4.2%) was higher than the West (2%) but lower than S.E. Asia (6.8%). In adults, frequencies again differed from S.E. Asia (HeH, 6.4% vs. 2.7% and t(9;22), 19.4% vs. 29.3%) but were comparable to the West. CONCLUSION:CCA effectively provides diagnostic information in over 90% of ALL cases. While the spectrum of cytogenetic changes is similar to global data, there are significant regional variations in the frequencies of specific abnormalities.
INTRODUCTION:Homoeologous chromosomes within the grass tribe Triticeae have largely retained their cross-species colinearity. However, prior studies suggest that the karyotype of Aegilops uniaristata, a diploid wild relative of wheat (genome NN, 2n = 2x = 14), is noticeably different from most of the Triticeae species. METHODS:We used fluorescence in situ hybridization with a large collection of probes hybridizing to repetitive and coding regions of the Triticeae genomes to perform comparative cytogenetic analysis and establish the macrostructure of Ae. uniaristata chromosomes. RESULTS:Compared to wheat, all chromosomes of Ae. uniaristata, with the exception of 5N, were found significantly rearranged due to multiple inter- and intrachromosomal translocations and inversions. CONCLUSION:The N-genome structure revealed in our study is useful for understanding karyotype evolution and facilitating introgression from Ae. uniaristata and the N-genome of polyploid Aegilops species for wheat improvement.
Introduction: Robertsonian translocations (ROBs) or centric fusions of acrocentric chromosomes are the most common structural chromosomal rearrangements in mammals. ROBs are of medical and veterinary concern because of associated subfertility and congenital disorders but are also of interest as a mechanism of chromosome and karyotype evolution. While ROBs are well documented in humans, mice, and cattle/bovids, they are extremely rare in horses, despite the 18 acrocentric chromosomes in the horse karyotype. Methods: We characterize the case using conventional and molecular cytogenetic approaches and DNA analysis. Results: We report the first case of ROB between nonhomologous chromosomes in the horse, whereas the carrier was 50/50 mosaic for two different ROB cell lines - 63,XX,rob(17;27) and 63,XX,rob(17;29) and had no cells with normal karyotype. Both derivative ROB chromosomes had retained two structural centromeres which is also a typical feature of human and bovine ROBs. The clinical phenotype of the mare included small ovaries, irregular estrus, and two pregnancy losses - all consistent with ROB. Discussion: We discuss the role of centromeric satellite sequences in the formation of ROBs but also differences in the prevalence of ROBs in different species, regardless of the number of acrocentric chromosomes. In this context, further molecular studies of the presented case may provide additional clues about the features of centromeric satellite repeats that facilitate or prevent ROBs in general. Robertsonian translocations (ROBs), also known as centric fusions, are chromosomal rearrangements where two chromosomes fuse by centromeres, giving rise to a large two-armed derivative chromosome. ROBs are the most common structural chromosomal rearrangements in mammals and pose medical and veterinary concern because of associated subfertility and congenital disorders, though ROBs are also of interest as a mechanism of chromosome and karyotype evolution. Robertsonian fusions are well documented in humans, mice, and cattle, but are extremely rare in horses, even though the horse karyotype has 18 acrocentric (one-armed) chromosomes, which all can potentially undergo ROB. Here, we report about the first case of ROB in the horse, whereas the affected animal was 50/50 mosaic for two different ROB cell lines: one with ROB between chromosome (Chr)17 and Chr27, another between Chr17 and Chr29, and had no cells with normal karyotype. The mare had several reproductive issues, including small ovaries, irregular estrus, and two pregnancy losses - clinical features which are consistent with ROBs in other species. Besides presenting the first ROB in the horse and mosaicism for two different ROBs, which is extremely rare in any species, we also discuss why ROBs are frequent rearrangements in some species and extremely rare in others, regardless of the number of acrocentric chromosomes.
INTRODUCTION:Reproductive failure has been associated with various chromosomal abnormalities, including small supernumerary marker chromosomes (sSMCs). In rare cases, uniparental disomy (UPD) may also contribute to reproductive problems, particularly when involving imprinted regions or in cases of isodisomy where autosomal recessive disorders may manifest. UPD involving chromosome 1 (UPD1) is rare and has not been linked to a consistent phenotype. CASE PRESENTATION:We present a 27-year-old woman with a 5-year history of reproductive difficulty, including one biochemical pregnancy loss and one clinically recognized miscarriage at 8 weeks of gestation. Cytogenetic analysis revealed mosaicism for a small sSMC derived from chromosome 1. SNP microarray identified complete UPD1 without copy number changes. Fluorescence in situ hybridization (FISH) confirmed centromeric material of chromosome 1 in the marker chromosome. CONCLUSION:To the best of our knowledge, this is the first reported case combining mosaic sSMC(1) and complete UPD1 in a phenotypically healthy woman with reproductive failure. The coexistence of these abnormalities likely reflects a postzygotic chromosomal rescue mechanism. These findings underscore the diagnostic value of integrated cytogenomic analyses in unexplained reproductive failure and subfertility.
INTRODUCTION:Induced pluripotent stem (iPS) cells share key features with embryonic stem (ES) cells, including similar limitations such as the accumulation of (epi)genetic and genomic alterations. However, sex chromosome instability in mouse iPS cells remains poorly understood. This retrospective study aimed to investigate this phenomenon by analyzing mouse iPS cell clones. Specifically, we examined whether factors such as passage number, cell sex, founder cell type, or reprogramming method influence the presence or absence of sex chromosome abnormalities. METHODS:Sex chromosome stability was evaluated in 26 independent male and female mouse iPS cell clones using standard karyotyping techniques. Additionally, we analyzed an artificially generated XXY iPS cell model, in which an extra X chromosome was introduced into a normal XY cell line. Statistical analyses were conducted on the karyotyping results and correlated with both continuous variables (e.g., passage number) and categorical variables (e.g., cell sex, founder cell type, and reprogramming method). RESULTS:Female iPS cell clones displayed significantly higher levels of sex chromosome instability compared to their male counterparts, regardless of the founder cell type or reprogramming strategy. A similar pattern of X chromosome instability was also observed in the XXY iPS cell model. CONCLUSION:Our findings demonstrate that sex chromosome instability occurs in mouse iPS cells, as previously reported in mouse ES cells, suggesting a conserved phenomenon across pluripotent stem cell types. Importantly, the presence of multiple X chromosomes in the pluripotent state appears to contribute to this instability. Further studies are required to elucidate the underlying molecular mechanisms.
INTRODUCTION:The influence of X/Y-autosomal translocations on reproductive competence is determined by both the cytogenetic positioning of translocation breakpoints and the potential disruption of critical genomic regions essential for reproductive physiology, particularly gene-dense Y-chromosomal segments or X-chromosome loci associated with ovarian folliculogenesis. This investigation examined 4 cases of cytogenetically balanced X/Y-autosomal translocations through the single-nucleotide polymorphism (SNP) and preimplantation genetic testing for structural rearrangements (SNP-based PGT-SR), enabling concurrent assessment of embryonic chromosomal integrity and precise differentiation between euploid embryos and balanced translocation carriers. CASES PRESENTATION:Cases 1-2 exhibited Y-autosomal translocations with breakpoints localized to the azoospermia factor critical region, while cases 3-4 demonstrated X-autosomal translocations where breakpoints mapped outside ovarian functional domains (Xq13-q28). Embryo selection utilizing SNP-based PGT-SR achieved clinical transfer of euploid embryos lacking the parental translocation in cases 2 and 4. Case 3, following multidisciplinary counseling, opted for transfer of a balanced translocation carrier euploid embryo with conserved genomic architecture. Prenatal diagnostic evaluations demonstrated complete concordance with PGT-SR outcomes. CONCLUSION:The impact of chromosomal translocation on reproduction is contingent upon whether the breakpoint location influences critical functional regions. SNP-based PGT-SR can accurately determine the genetic status of embryos exhibiting balanced X/Y-autosomal translocations by systematically evaluating the integrity of the embryo's genetic material. This approach enhances detection accuracy and mitigates the risk of transmitting the translocation to subsequent generations.
INTRODUCTION:Satellite DNA (satDNA) is an important component of eukaryotic genomes that influences chromosomal organization and evolution. This study investigates the sequence diversity, chromosomal distribution, and copy number variation of the CLA-SAT-149 satDNA family (149 bp) in four clariid catfish species, Clarias macrocephalus, C. gariepinus, C. batrachus, and C. nieuhofii, as well as in F1 hybrids and backcross (BC) progeny. METHODS:Fluorescence in situ hybridization (FISH) was used to map CLA-SAT-149 on metaphase chromosomes. Quantitative PCR (qPCR) quantified copy number variation. Amplicon sequencing was applied to characterize sequence variants, and Bayesian clustering analysis was used to assess genetic relationships among subfamilies. RESULTS:Chromosome mapping showed species-specific signals present in C. macrocephalus and F1 hybrids but absent in C. gariepinus and C. nieuhofii. qPCR revealed significantly higher copy numbers in C. macrocephalus. Two sequence variants were identified: the canonical 149-bp (subfamily A) and an 85-bp derivative (subfamily B). Bayesian analysis indicated multiple genetically distinct subgroups among species. F1 hybrids and BC progeny exhibited unique sequence profiles and copy number patterns, while C. nieuhofii lacked CLA-SAT-149 entirely. CONCLUSION:The results support lineage-specific expansion, amplification, and loss of CLA-SAT-149 in clariid catfish, consistent with the satDNA library model. These patterns provide insights into satDNA evolution and have potential applications in aquaculture genetics, hybrid identification, and species differentiation.
INTRODUCTION:MECOM rearrangements are frequently observed in myeloid neoplasms and associated with poor prognosis. Among the genomic alterations leading to MECOM rearrangements, t(2;3)(p13∼p25;q26.2) accounts for approximately 13% of reported cases. However, the precise DNA breakpoints of this translocation have not been previously reported, nor has the mechanism by which it alters MECOM expression been fully elucidated. In this report, we describe two cases with myelodysplastic syndromes (MDS) and t(2;3)(p23;q26.2). Our genomic characterization of these two t(2;3) translocations provided insights into the molecular mechanism of MECOM activation. CASE PRESENTATION:Case 1 is a 44-year-old female who presented with new anemia and thrombocytopenia. She was treated with azacitidine. After two allogeneic stem cell transplants, her disease relapsed with rapid progression to acute myeloid leukemia (AML). The patient passed away 1 year after progression to AML and 8 years after initial diagnosis. Case 2 is a 75-year-old female who was incidentally found to have macrocytic anemia with rare circulating blasts. She remained asymptomatic from anemia and did not require transfusions or treatment. Her disease progressed to MDS with excess blasts 3 years later. Patient was treated with azacitidine. Fifteen months later, her disease further progressed to AML. She passed away 5 months later and four and a half years after initial diagnosis. DNA sequencing analysis of these two cases revealed that the t(2;3)(p23;q26.2) breakpoints were within the regulatory regions of ZFP36L2 and THADA on chromosome 2 and the proximity of MECOM on chromosome 3, creating a novel regulatory configuration for MECOM. Notably, the translocation breakpoints differed by 270 kb on chromosome 2 and 93 kb on chromosome 3, resulting in distinct translocated regulatory elements with varying sizes and proximities to MECOM. These structural differences may influence the level of MECOM upregulation and contribute to variation in disease severity and progression. CONCLUSION:Our findings highlighted that, despite cytogenetic similarity, different t(2;3) translocations may exert distinct regulatory effects depending on the precise breakpoint locations. Thus, molecular characterization of MECOM rearrangements is critical for understanding disease pathogenesis and prognosis in myeloid neoplasms and may lead to the development of novel treatment.
IIntroduction Radioiodine (131I) is commonly used for the treatment of hyperthyroidism and for differentiated thyroid cancer (DTC) as an ablative therapy. Radioiodine (131I) constitutes almost 90% of the therapies that are currently performed in the nuclear medicine field. In this study, retrospective cytogenetic follow up analysis was performed after 29 years (2023) and 30 years (2024) in a papillary thyroid cancer patient who received the second round of 131I treatment in 1994. Methods Metaphase chromosomes prepared from the in vitro culture of peripheral blood lymphocytes of the patient were utilized for the analysis of unstable (dicentrics and fragments) and stable chromosome aberrations (simple, complex and clonal). For dicentric chromosome detection, fluorescence in situ hybridization FISH) was performed using human centromere and telomere specific peptide nucleic acid probes. Chromosome translocations were detected by a cocktail of DNA probes for individual chromosomes (1, 2 and 4) and multicolor FISH probe for the entire human genome. Micronuclei were analyzed by cytokinesis block micronucleus assay. Absorbed radiation dose was estimated at 95% confidence intervals from the frequencies of chromosome aberrations (dicentric chromosomes and translocations) using correlation coefficients of the γ-rays dose response curve using the DoseEstimate_v5.1 algorithm. Results The percentage of cells with stable and unstable chromosome aberrations remained the same (~8%) in the patient during the entire retrospective study albeit variations in the frequencies of reciprocal and non-reciprocal translocations. The frequency of color junctions (chromosome exchange events) detected by the multicolor FISH technique showed a sharp increase in this study (0.33/cell) compared to our earlier study (0.19/cell). The persistence of clonal translocation involving chromosomes 14;15 was observed in 1-1.6% of the total cells analyzed. In the 29-year follow up study, one complex translocation involving chromosomes 1, 9 and 14 was detected by mFISH in a total of 200 cells. Discussion Our findings indicate that the past internal therapeutic exposure of radioiodine results in long-lasting chromosomal damage and the retrospective study of this nature will be useful for monitoring the progression of any oncogenic events driven by chromosomal instability in the hematopoietic system of 131I therapy patients.
INTRODUCTION:In birds, males have the homogametic sex chromosomes ZZ, whereas females have the heterogametic ZW. Similar to mammalians, avian Z and W chromosomes are believed to have originated from a pair of autosomes. Over evolutionary time, the W chromosome degenerated, losing many genes. The remaining W-linked genes retain homologs on the Z chromosome. One such gene is UBAP2, which participates in cellular metabolism and signaling through the ubiquitin-proteasome pathway in mammals. However, the functions of its avian homologs, UBAP2Z (Z-linked) and UBAP2W (W-linked), remain poorly understood. To investigate the functional divergence between them in birds, we analyzed their mRNA and protein expression in embryonic gonads of Japanese quail. METHODS:Using RNA-seq data of embryonic gonads of Japanese quail, contigs were generated by de novo assembly. The nucleotide sequences were predicted from the contigs by blastn analysis. Expression levels were calculated by bowtie2 and RSEM. Immunohistochemistry and Western blotting employing monoclonal antibodies specific to UBAP2Z and UBAP2W were generated to investigate protein expression and localization. Additionally, far-Western blotting was performed to examine protein-protein interactions. RESULTS:UBAP2Z and UBAP2W nucleotide and amino acid sequences showed high similarity and shared a conserved N-terminal UBA domain. However, UBAP2W expression was consistently lower than that of UBAP2Z and showed a distinct localization pattern from UBAP2Z in embryonic gonads. In males, UBAP2Z was expressed in seminiferous tubules, while in females, it localized to the medulla. By contrast, UBAP2W was exclusively observed in the cortex of female gonads, particularly at developmental stage HH38. Furthermore, UBAP2Z and UBAP2W interacted with different binding partners, indicating divergence in their molecular function. CONCLUSION:These findings indicate that UBAP2W has a distinct female-specific functional role in avian gonadal differentiation. We propose that UBAP2W contributes to ovarian development and oogenesis through the ubiquitin-proteasome pathway, while UBAP2Z is involved in general cellular regulation across sexes. This study highlights functional divergence between Z- and W-linked paralogs in birds and provides new insights into sex chromosome evolution and gonadal development.
BACKGROUND:Chromosomal microarray analysis (CMA) is a first-tier diagnostic test for children with unexplained developmental and/or congenital anomalies. This study aimed to evaluate the diagnostic contribution of CMA in a large, phenotypically diverse Turkish pediatric cohort. METHODS:CMA was performed in 1,022 children presenting with developmental delay, intellectual disability, autism spectrum disorder, epilepsy, and/or congenital anomalies. Copy number variants (CNVs) were classified as pathogenic, likely pathogenic, or variants of uncertain significance based on American College of Medical Genetics guidelines. RESULTS:CNVs were identified in 279 patients (27.3%), totaling 315 CNVs. Of these, 151 patients (14.8%) carried at least one pathogenic or likely pathogenic CNV, representing the diagnostic yield of the study. CNVs were more frequently classified as pathogenic when presenting as deletions. The diagnostic rate was higher among patients with syndromic features (20.2%) compared to those with isolated developmental delay/intellectual disability (11.8%). Among patients with CNVs, 139 (49.8%) exhibited phenotypes consistent with well-characterized genomic syndromes. In addition, rare but clinically significant CNVs were also identified, involving well-established dosage-sensitive genes. Notably, chromosomes X, 15, and 16 were among the most frequently affected, reflecting known genomic hotspots associated with neurodevelopmental and structural phenotypes. CONCLUSION:CMA is a powerful diagnostic tool in the evaluation of pediatric patients with neurodevelopmental and structural disorders. This study emphasizes the added value of high-resolution CNV detection and careful clinical phenotyping to optimize diagnostic yield and guide precision care in clinically heterogeneous pediatric populations.
BACKGROUND:Structural variants (SVs) are defined as genomic variants affecting more than 50 base pairs. They include deletions, insertions, inversions, translocations, tandem repeats, and copy number variations. These SVs contribute significantly to genetic complexity and are involved in human evolution, genetic disorders, and cancer. Over 50% of the SVs cannot be detected due to limitations in methods and technologies. The short-read sequencing technologies (SRSs) are limited in detecting single-nucleotide variants and have limited usage for analysis of complex genomic loci, repeat regions, and phasing. SUMMARY:The advent of long-read sequencing (LRS) technologies, such as Oxford Nanopore and PacBio, has revolutionized SV detection. These platforms enable the accurate characterization of diverse variant types, ranging from simple deletions to complex chromothripsis events, and support de novo assembly, haplotype phasing, and the resolution of repetitive or structurally complex genomic regions. One major outcome is the completion of the telomere-to-telomere human reference genome. This review summarizes recent advances in LRS for SV detection, including sequencing platforms, bioinformatic tools, data analysis, and validation strategies. The clinical applications, particularly in the diagnosis of rare diseases, are illustrated with two cases that were successfully resolved using both LRS approaches. KEY MESSAGE:LRS can overcome the limitations of SRS in SV detection, providing more accurate insights into genome disorders. It enables the detection of repeat and difficult-to-resolve regions of the genome and facilitates clinical diagnoses to base-level breakpoint detection. Despite challenges such as high cost, data interpretation, and clinical linking, continued advancements are elevating LRS as an invaluable tool in precision genomic medicine.
