Molecular Cytogenetics最新文献

Introduction: A unique case of mosaic tetrasomy 9p was found using CNV-seq analysis of uncultured amniocytes, which was missed by karyotype analysis of cultured amniocytes.

Case report: The karyotype was determined to be 46, XY, with mosaic duplication of chromosome 9 from p24.3 to p13.1 indicated by CNV sequencing in the initial amniocentesis. Subsequent prenatal testing revealed a normal karyotype, with FISH analysis of cultured amniocytes identifying 2% tetrasomy of chromosome 9p. The karyotype of cord blood revealed mosaic tetrasomy 9p, while CNV-seq on uncultured cord blood indicated nearly complete tetrasomy 9p.

Conclusions: It is recommended to conduct CNV-seq or CMA on uncultured amniocytes in conjunction with karyotype analysis on cultured amniocytes. The presence of mosaic tetrasomy 9p during amniocentesis may result in either a benign condition or an adverse outcome, necessitating informed decision-making for pregnant women facing such circumstances.

The evolution of techniques used to identify structural variants (SVs) and copy number variants (CNVs) in genomes have seen significant development in the last decade. With the growing use of more technologies including chromosomal microarray, genome sequencing and genome mapping in clinical cytogenetics laboratories, reporting the frequency of SVs and CNVs has increased the complexity of genomic results. In conventional testing (e.g. karyotype or FISH) individual cells are analyzed and abnormalities are reported at the single cell level directly as a proportion of the analyzed cells. Whereas for bulk genome assays structural and sequence changes are often reported as variant allele frequencies and fractional copy number states. The International System of Cytogenomic Nomenclature (ISCN) recommends converting these values into a "proportion of the sample", which requires different calculations and underlying assumptions based on the data type. This review illustrates how the different methods of interpreting and reporting data are performed and identifies challenges in the conversion of these values to a proportion of the sample. We stress the need for careful interpretation of data with consideration for factors that may alter how proportions are reported including overlapping SVs and CNVs or regions with acquired homozygosity. We also demonstrate, using validation data of SVs and CNVs tested by multiple techniques how results are largely consistent across methodologies, but can show dramatic differences in rare circumstances. This review focuses on illustrating many of the challenges with aligning reporting using different techniques and their underlying assumptions. As hematologic disease classifications start to incorporate numeric limits (e.g. VAF defining thresholds), it is important for laboratory geneticists, pathologists and clinicians to appreciate the differences in methodologies, potential pitfalls and the nuances when comparing bulk genome analyses to the more conventional single cell techniques.

Automation has been developed and continues to be refined for cytogenetics, including advances in the processing of samples, in analysis of conventional chromosome and fluorescence in situ hybridization (FISH) testing, and with artificial intelligence. Here we provide an overview of the various types of automation available to the cytogenetics laboratory and discuss possible benefits and limitations you may encounter based upon our collective experiences.

Among the human leukemia cell lines described in the literature, only the MDS-L cell line has been definitively established from a patient during the myelodysplastic syndrome (MDS) phase of the disease. However, the limited studies on its genomic complexity have restricted its applicability as an in vitro model for MDS. Here, we aimed to better characterize the chromosomal and genetic alterations of MDS-L. A comprehensive approach was employed combining conventional G banding, multicolor FISH (M-FISH), SNP arrays with the novel Optical Genome Mapping (OGM) technology. In addition, the mutational landscape was defined using targeted next-generation sequencing (NGS). G-banding revealed two karyotypically distinct cell populations, both exhibiting complex karyotypes. Using G-banding and OGM, we identified previously undescribed structural alterations, including der(1)t(1;7)(q11;q11.2), del(1)(q11), der(4)t(4;5)(p16;q11.2), i(5)(p10), der(6)t(6;15)(p21.3;q15), i(8)(q10), der(9)t(9;10)(q34;p11.21), der(19)t(6;19)(p13;p22) and i(22)(q10). Both OGM and SNP microarray analyses detected multiple copy number variants and regions of homozygosity. Chromosome breakpoints were precisely defined by OGM, allowing the identification of gene disruption events. Moreover, M-FISH technique validated the origins of additional chromosomal material observed in the karyotype, identified cryptic rearrangements, and distinguished the two clonal populations within the cell line. Finally, NGS revealed mutations in CEBPA, NRAS, TET2 and TP53 genes associated with MDS pathology. This multi-technique approach has enabled a precise characterization of the MDS-L cell line's genomic complexity, highlighting the unique contributions of each technique in uncovering various genetic alterations and establishing a valuable resource for mechanistic studies and pre-clinical drug development.

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.