Molecular Cytogenetics最新文献

Background: Optical genome mapping (OGM) is a next-generation cytogenetic technique that may be beneficial for detecting subtle structural chromosomal alterations that can go unnoticed with conventional studies in couples with recurrent pregnancy loss.

Case presentation: We report the case of a couple referred to our assisted reproduction unit due to a history of recurrent pregnancy loss. Initially, conventional cytogenetic studies were performed to identify a possible genetic cause. To this end, the karyotypes of both members of the couple were determined. The fetal tissue from the third miscarriage was analyzed using comparative genome hybridization (CGH) array. Subsequently, the cytogenetic analysis of the couple was extended with the OGM technique. Basic infertility studies revealed normal results, and the karyotypes of both partners were initially reported as normal with respect to structural abnormalities. Following the third miscarriage, an array CGH analysis of the abortive tissue detected a deletion-duplication on chromosomes 1 and 10, respectively. Moreover, OGM revealed a balanced translocation between chromosomes 1 and 10 in the male which had not been detected through conventional karyotyping. A retrospective review of the karyotype by an expert cytogeneticist identified an apparent translocation that had previously gone unrecognized.

Conclusions: Structural chromosomal abnormalities may be underestimated in couples experiencing multiple miscarriages because they are not always accurately recognized by conventional cytogenetic techniques. OGM offers a valuable complement to these traditional methods by identifying chromosomal alterations that may have been overlooked by karyotyping, precisely characterizing the nature of the structural rearrangements. While OGM cannot currently replace karyotyping due to limitations such as the inability to detect certain translocations (e.g., Robertsonian translocations), it can enhance diagnostic accuracy and provide additional insights into the genetic causes of repeated pregnancy loss. Therefore, OGM may serve as a useful supplementary tool for improving diagnosis and management in affected couples.

Hematologic malignancies (HMs) encompass a diverse spectrum of cancers originating from the blood, bone marrow, and lymphatic systems, with myeloid malignancies representing a significant and complex subset. This review provides a focused analysis of their classification, prevalence, and incidence, highlighting the persistent challenges posed by their intricate genetic and epigenetic landscapes in clinical diagnostics and therapeutics. The genetic basis of myeloid malignancies, including chromosomal translocations, somatic mutations, and copy number variations, is examined in detail, alongside epigenetic modifications with a specific emphasis on DNA methylation. We explore the dynamic interplay between genetic and epigenetic factors, demonstrating how these mechanisms collectively shape disease progression, therapeutic resistance, and clinical outcomes. Advances in diagnostic modalities, particularly those integrating epigenomic insights, are revolutionizing the precision diagnosis of HMs. Key approaches such as nano-based contrast agents, optical imaging, flow cytometry, circulating tumor DNA analysis, and somatic mutation testing are discussed, with particular attention to the transformative role of machine learning in epigenetic data analysis. DNA methylation episignatures have emerged as a pivotal tool, enabling the development of highly sensitive and specific diagnostic and prognostic assays that are now being adopted in clinical practice. We also review the impact of computational advancements and data integration in refining diagnostic and therapeutic strategies. By combining genomic and epigenomic profiling techniques, these innovations are accelerating biomarker discovery and clinical translation, with applications in precision oncology becoming increasingly evident. Comprehensive genomic datasets, coupled with artificial intelligence, are driving actionable insights into the biology of myeloid malignancies and facilitating the optimization of patient management strategies. Finally, this review emphasizes the translational potential of these advancements, focusing on their tangible benefits for patient care and outcomes. By synthesizing current knowledge and recent innovations, we underscore the critical role of precision medicine and epigenomic research in transforming the diagnosis and treatment of myeloid malignancies, setting the stage for ongoing advancements and broader clinical implementation.

Background: Copy number variants (CNVs) are an important source of normal and pathogenic genome variations. Microduplication of 15q21.3 is rare and is associated with an increased risk of developmental retardation, corpus callosum hypoplasia, microcephaly, cardiomyopathy, optic nerve hypoplasia and so on. Microduplication of 16p11.2 is associated with 16p11.2 microduplication syndrome (OMIM: 614671). The main clinical manifestations are low birth weight, microcephaly, mental retardation, language retardation, abnormal behavior, attention deficit, schizophrenia, affective disorder, loneliness spectrum disorder and so on. Individuals who carry these two microduplications are even more rare.

Materials and methods: In this research, a 32-year-old woman (gravida 1, para 0) underwent amniocentesis at 20 weeks' gestation because the results of ultrasound showed that one of the twins was smaller than the other.

Results: Copy number variation sequencing (CNV-seq) from this family revealed two types of microduplication (420 kb microduplication on chromosome 15q21.3 and 560 kb microduplication on chromosome 16p11.2) in both fetuses. Trio whole-exome sequencing (WES) showed that the two types of microduplication both originated from the father. After genetic counselling and being informed of the unfavourable prognosis, the parents decided to continue the pregnancy.

Conclusion: We provide a detailed description of the phenotype in a rare family with 15q21.3 and 16p11.2 microduplication. Combination of karyotype analysis, CNV-seq, WES, prenatal ultrasound and genetic counselling is helpful for the prenatal diagnosis of chromosomal microdeletions/microduplications.

Clinical trial number: Not applicable.

Background: Acute lymphoblastic leukemia (ALL) is the most common childhood cancer, comprising approximately 25% of pediatric malignancies. Notably, chromosomal aberrations and genetic alterations play a central role in the pathogenesis of ALL, serving as critical diagnostic and prognostic markers. In this study, we use array-based comparative genomic hybridization (array-CGH) to explore the landscape of copy number variations (CNVs) and variants of uncertain significance (VUS) in 67 Malaysian childhood ALL patients with normal karyotype.

Results: A total of 36 pathogenic CNVs (26 gains, 10 losses) were identified in 19 (28.4%) patients which harbor genes related to the development of ALL. The genes include the MLLT3 (9p21.3), ETV6 (12p13.2), RUNX1 (21q22.12), ERG (21q22.2) and DMD (Xp21.1). On the other hand, a total of 46 variants of uncertain significance (VUS) was observed in 34 (50.7%) patients.

Conclusions: Our study indicates that array-CGH is able to identify and characterize the CNVs responsible for the pathogenesis of childhood ALL. However, further studies are required to determine the pathogenic implications of VUS in the development of childhood ALL.

Telomere in cancers shows a main impact on maintaining chromosomal stability and unlimited proliferative capacity of tumor cells to promote cancer development and progression. So, we targeted to detect telomere-related genes(TRGs) in hepatocellular carcinoma (HCC) to develop a novel predictive maker and response to immunotherapy. We sourced clinical data and gene expression datasets of HCC patients from databases including TCGA and GEO database. The TelNet database was utilized to identify genes associated with telomeres. Genes with altered expression from TCGA and GSE14520 were intersected with TRGs, and Cox regression analysis was conducted to pinpoint genes strongly linked to survival prognosis. The risk model was developed using the Least Absolute Shrinkage and Selection Operator (LASSO) regression technique. Subsequently, evaluation of the risk model focused on immune cell infiltration, checkpoint genes, drug responsiveness, and immunotherapy outcomes across both high- and low-risk patient groups. We obtained 25 TRGs from the overlapping set of 34 genes using Cox regression analysis. Finally, six TRGs (CDC20, TRIP13, EZH2, AKR1B10, ESR1, and DNAJC6) were identified to formulate the risk score (RS) model, which independently predicted prognosis for HCC. The high-risk group demonstrated worse survival outcomes and showed elevated levels of infiltration by Macrophages M0 and Tregs. Furthermore, a notable correlation was observed between the genes in the risk model and immune checkpoint genes. The RS model, derived from TRGs, has been validated for its predictive value in immunotherapy outcomes. In conclusion, this model not only predicted the prognosis of HCC patients but also their immune responses, providing innovative strategies for cancer therapy.

Lynch syndrome is an autosomal dominant disorder predisposing individuals to colorectal and other cancers, primarily caused by variants in mismatch repair genes. This study describes a novel MSH6 variant affecting transcript structure in a Taiwanese family meeting the Amsterdam II criteria for Lynch syndrome. A 67-year-old male presented with jejunal adenocarcinoma and a strong family history of colorectal cancer. Immunohistochemistry revealed loss of MSH6 expression, while next-generation sequencing performed on tumor tissue failed to detect any MSH6 variants. Comprehensive genetic analysis, including RT-PCR and Sanger sequencing of both cDNA and genomic DNA, identified a novel exon 5-6 skipping variant in the MSH6 gene transcript (NM_000179.3:r.3262_3645del), linked to a 2268 bp deletion from the 3' portion of intron 4 to the middle of intron 6 of the MSH6 gene (NC_000002.12:g.47803007_47805274del). This variant was also detected in two of the patient's asymptomatic sons, highlighting its heritability and potential cancer predisposition. The study emphasizes the limitations of capture-enrichment NGS panels in detecting certain types of variants and underscores the value of orthogonal confirmation using cDNA analysis for transcript aberrations. The identification of this novel variant expands our understanding of Lynch syndrome's mutational spectrum and has implications for genetic diagnosis and counseling. Based on these findings, the patient was treated with pembrolizumab, resulting in stable disease for 8 months. This case highlights the importance of comprehensive genetic approaches in suspected Lynch syndrome cases and the potential utility of mRNA-based screening as an additional method when NGS analysis is negative and the clinical presentation strongly suggests Lynch syndrome.

Background: Gestational trophoblastic neoplasms consist of complete and partial hydatidiform moles, both of which are considered aberrant conceptuses. Both conditions, complete hydatidiform mole (CHM) and partial hydatidiform mole (PHM), differ in histological characteristics, genetic origin and content and clinical features. CHM have a diploid karyotype, mostly 46,XX but lack maternal genetic contribution with all chromosomes of paternal origin. High-resolution SNP microarray testing is an efficient method used to determine the parental contribution of the genomic material in molar pregnancies and confirm the diagnosis.

Case presentation: We present a case of CHM in a 43-year-old, G3P2Ab1 who presented to the emergency department with 2 episodes of heavy bleeding. Chromosome analysis showed a normal 46,XX karyotype but with a homozygous pericentric inversion on chromosome 9. High-resolution SNP microarray studies detected whole genome uniparental isodisomy.

Conclusion: We present a case of CHM with homozygous pericentric inversion on chromosome 9 and whole genome uniparental isodisomy. This case illustrates the efficacy of high-resolution SNP microarray in confirming the diagnosis of CHM.

Background: The X chromosome is enriched with genes related to brain development, and the hemizygous state of these genes in men causes some difficulties in the clinical interpretation of copy number variations (CNVs). In this study, we present data on the frequency and spectrum of CNVs on the X chromosome in a cohort of patients with neurodevelopmental disorders (NDDs).

Methods: Chromosomal microarray analysis was performed for 1175 patients with NDDs. CNVs were confirmed by real-time quantitative PCR. X chromosome inactivation was analysed by methyl-sensitive PCR. To determine the pathogenic significance of the CNVs, several criteria, including the origin (inherited or de novo), variant type (microdeletion or microduplication), and X chromosome inactivation pattern in asymptomatic and symptomatic carriers, were considered. Additionally, the spectrum, size and molecular bases of copy number changes in genes or gene regions involved in the development of the pathological phenotype in each patient were considered.

Results: CNVs on the X chromosome were identified in 33 patients (2.8%). Duplications and triplications (27 cases) were four times more common than deletions (6 cases). In 74% of patients, CNVs were of maternal origin; in 10% they were of paternal origin; and in 16% they arose de novo. The frequency of skewed X inactivation among family members who were healthy carriers of pathogenic and likely pathogenic CNVs and variants of uncertain significance (VUSs) on the X chromosome was 23%. For the first time, we reported several CNVs, including a pathogenic microdeletion at Xq26.1q26.2 involving the ARHGAP36 gene and a microduplication at Xp22.2 involving the OFD1 gene, CONCLUSIONS: This study expands on the frequency and spectrum of CNVs in patients with NDDs. Pathogenic variants on the X chromosome were present in 15% of cases, LP in 12%, VUS in 57%, and LB in 16% of cases. Previously unreported CNVs aid in the identification of new structural variants and genes associated with X-linked intellectual disability. We propose to consider the X-chromosome inactivation status when assessing the pathogenetic significance of CNVs using the ACMG algorithm (American College of Medical Genetics).

Background: The saffron-producing Crocus sativus (L.) and its wild relative C. cartwrightianus (Herb.) are key species for understanding genetic evolution in this genus. Molecular-cytogenetic methods, especially fluorescent in situ hybridization (FISH), are essential for exploring the genetic relationships in this genus. Yet, preparing high-quality chromosomes for FISH analysis across Crocus species remains difficult. A standardized protocol for achieving clear and well-separated mitotic chromosomes is still lacking. This study aimed to assess the effectiveness of pretreatments with four chromosome synchronization methods for optimal chromosome spread preparation in Crocus. Root tips of different Crocus species were treated with four chromosome preparation methods namely hydroxyurea-colchicine (HC), nitrous oxide (NO), hydroxyquinoline (HQ), and ice water (IW) pretreatments to investigate their effectiveness in producing high-quality mitotic chromosome spreads. Metaphases obtained by the four methods were analyzed to assess their quality and metaphase index.

Results: Evaluation of 22,507 cells allowed us to confidently recommend a protocol for Crocus chromosome preparation. Among the methods, ice water pretreatment yielded the highest metaphase index (2.05%), more than doubling the results of HC (1.08%), NO (1.15%), and HQ (1.16%). Ice water-treated chromosomes exhibited better chromosome morphology, with relatively proper size, and non-overlapping chromosomes that were optimal for FISH analysis. Ice water pretreatment was also applied to C. cartwrightianus, the diploid progenitor of C. sativus, where it demonstrated similar efficacy. DAPI staining of chromosomes in both species allowed for clear visualization of intercalary and terminal heterochromatin. FISH analysis using 18S-5.8S-25S and 5S rDNA probes confirmed the utility of IW-prepared chromosome spreads for cytogenetic studies.

Conclusions: We strongly recommend ice water pretreatment as a suitable and effective method for obtaining many metaphase spreads of high-quality in C. sativus and related species, particularly for applications involving a detailed cytogenetic analysis.