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Cytogenetics and Cytogenomics in Clinical Diagnostics: Innovations and Applications
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Cytogenetics and Cytogenomics in Clinical Diagnostics: Innovations and Applications

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Cytogenomics".

Deadline for manuscript submissions: closed (15 January 2026) | Viewed by 15573

Special Issue Editor

Dr. Jinglan Liu

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Guest Editor
Department of Pathology and Genomic Medicine, Clinical Cytogenomics, Thomas Jefferson University, Philadelphia, PA 19107, USA
Interests: conventional cytogenetics; cytogenomics; epigenetics; epigenomics; laboratory genetics and genomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Chromosomes serve as both structural and regulatory units of the human genome. Clinical cytogenetics and cytogenomics enable the diagnosis of constitutional and oncological chromosomal abnormalities. While conventional karyotyping provides genome-wide analysis at low resolution, the integration of fluorescence in situ hybridization (FISH), microarray analysis, and optical genome mapping (OGM) since the 1990s has significantly enhanced diagnostic precision and sensitivity.

Despite advances in genomic sequencing technologies that detect nucleotide-level variants, our understanding of chromosomal alterations at microscopic and submicroscopic levels in human disease remains incomplete. Genome function and phenotypic manifestation are regulated across multiple layers of resolution and nuclear organization, with topological genome features coordinating higher-order gene activity. Conventional karyotyping, FISH, and emerging cytogenomic approaches remain essential for comprehensive genomic assessment, allowing for the detection of not only numerical, structural, and sub-chromosomal abnormalities but also the multiple regulatory layers that govern the genome. Looking ahead, the incorporation of artificial intelligence (AI) holds promise for overcoming the limitations of traditional cytogenetic analysis and is expected to play a transformative role across all genomic medicine subspecialties, including cytogenomics.

This Special Issue invites submissions on chromosomal abnormalities and submicroscopic genomic variations in developmental disorders, neuropsychiatric diseases, and neoplastic conditions. We welcome research on mechanistic insights, genotype–phenotype correlations, technological innovations, and clinical applications. Studies on three-dimensional chromosome organization in human diseases and AI-driven advancements in cytogenomics are particularly encouraged. As the field continues to evolve, we seek perspectives on emerging challenges, future directions, and the transformative potential of next-generation cytogenomic technologies.

Dr. Jinglan Liu
Guest Editor

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Keywords

  • karyotyping
  • cytogenomics
  • chromosome territory (CT)
  • nuclear architecture
  • clinical oncology
  • germline
  • development
  • neuropsychiatry
  • artificial intelligence (AI)

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Published Papers (9 papers)

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Research

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15 pages, 237 KB  
Article
Prenatal Microarray Analysis of Pregnancies Without Ultrasound Anomalies: Establishment of Copy Number and Homozygosity Frequencies in Low-Risk Population
by Stuart Schwartz and Robert G. Best
Genes 2026, 17(2), 127; https://doi.org/10.3390/genes17020127 - 25 Jan 2026
Viewed by 473
Abstract
Objectives: The overall objective of this study is to examine prenatal patients ascertained without an abnormal ultrasound (US) or an abnormal cell-free DNA (cfDNA) finding to provide a unique understanding of pathogenic copy number variants, identity by descent (IBD) and variants of uncertain [...] Read more.
Objectives: The overall objective of this study is to examine prenatal patients ascertained without an abnormal ultrasound (US) or an abnormal cell-free DNA (cfDNA) finding to provide a unique understanding of pathogenic copy number variants, identity by descent (IBD) and variants of uncertain significance (VUSs) in a normal population. Methods: This study retrospectively provides an analysis of over 28,362 prenatal specimens ascertained without an abnormal US or abnormal cfDNA finding utilizing an SNP microarray. These specimens include at least 10 different ascertainment groups, including advanced maternal age (AMA), anxiety, abnormal maternal serum screen (MSS) with/without AMA, and a previous or familial child/pregnancy with a chromosome abnormality or a genetic disorder. Results: This study provides a basic understanding of pathogenic copy number variants (CNVs), homozygosity and VUSs in an essentially normal population. This low-risk population has a frequency of pathogenic CNVs of ~1.26%; however, ~52% were associated with neurodevelopmental microdeletions/microduplications and ~13% were associated with incidental findings. Overall, ~1.32% of these patients showed an increase in homozygosity, the majority due to consanguinity. Lastly, VUSs were seen in 1.41% of this group, of which ~90% were familial. Conclusions: Overall, these findings provide a better estimate of the baseline frequencies and types of pathogenic CNVs and homozygosity in a low-risk population. It provides insight into the distribution of stretches of homozygosity associated with identity by descent in this population and gives a better understanding of the extent of variants of uncertain significance in phenotypically unaffected individuals. Full article
(This article belongs to the Special Issue Cytogenetics and Cytogenomics in Clinical Diagnostics: Innovations and Applications)
17 pages, 1796 KB  
Article
Optical Genome Mapping Enhances Structural Variant Detection and Refines Risk Stratification in Chronic Lymphocytic Leukemia
by Soma Roy Chakraborty, Michelle A. Bickford, Narcisa A. Smuliac, Kyle A. Tonseth, Jing Bao, Farzana Murad, Irma G. Domínguez Vigil, Heather B. Steinmetz, Lauren M. Wainman, Parth Shah, Elizabeth M. Bengtson, Swaroopa PonnamReddy, Gabriella A. Harmon, Liam L. Donnelly, Laura J. Tafe, Jeremiah X. Karrs, Prabhjot Kaur and Wahab A. Khan
Genes 2026, 17(1), 106; https://doi.org/10.3390/genes17010106 - 19 Jan 2026
Viewed by 832
Abstract
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 [...] Read more.
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
(This article belongs to the Special Issue Cytogenetics and Cytogenomics in Clinical Diagnostics: Innovations and Applications)
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16 pages, 8433 KB  
Article
Hi-C Technology Reveals Actionable Gene Fusions and Rearrangements in Diffuse Large B-Cell Lymphoma Unidentified by Conventional FISH
by Sichen Liang, Candice Ament, Melanie Klausner, Victoria Stinnett, Laura Morsberger, Jen Ghabrial, William Middlezong, Anthony D. Schmitt, Alex R. Hastie and Ying S. Zou
Genes 2025, 16(9), 1093; https://doi.org/10.3390/genes16091093 - 16 Sep 2025
Viewed by 1467
Abstract
Background/Objectives: Fluorescence in situ hybridization (FISH) is a standard diagnostic tool for detecting gene fusions and rearrangements in lymphomas but is limited by incomplete genomic coverage, dependence on predefined probes, and difficulty identifying atypical or noncanonical fusion partners. These constraints often result in [...] Read more.
Background/Objectives: Fluorescence in situ hybridization (FISH) is a standard diagnostic tool for detecting gene fusions and rearrangements in lymphomas but is limited by incomplete genomic coverage, dependence on predefined probes, and difficulty identifying atypical or noncanonical fusion partners. These constraints often result in inconclusive diagnoses in complex lymphoma cases. This study evaluates a novel Hi-C-based sequencing assay from formalin-fixed paraffin-embedded (FFPE) samples to detect clinically significant gene fusions and rearrangements in cases where conventional FISH was inconclusive or expected biomarkers were not detected. Methods: Five diffuse large B-cell lymphoma cases with previously atypical gene fusions or rearrangements by FISH were analyzed using both standard FISH and a Hi-C-based lymphoma assay. Standard FISH was performed using break-apart probes targeting MYC, BCL2, and BCL6, and dual-fusion probes targeting IGH::MYC and IGH::BCL2. The Hi-C assay utilized high-resolution sequencing of FFPE tissue to map chromatin interactions and identify structural variations across the genome and assessment of their clinical relevance. Results: In this series of five lymphoma cases, Hi-C detected additional structural variants beyond those identified by FISH. It identified typical and atypical translocation partners of key oncogenes (MYC, BCL2, BCL6), cryptic breakpoints, and novel genomic events, including TP53 loss, KMT2A amplification, and complex rearrangements, which were undetectable by FISH. The Hi-C assay’s whole-genome coverage enabled comprehensive profiling. Conclusions: The Hi-C-based lymphoma assay offers a transformative diagnostic tool, overcoming FISH limitations by providing unbiased, high-resolution detection of structural variations. This approach enhances diagnostic accuracy and supports personalized therapeutic strategies in lymphoma management, warranting further validation for clinical adoption. Full article
(This article belongs to the Special Issue Cytogenetics and Cytogenomics in Clinical Diagnostics: Innovations and Applications)
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9 pages, 645 KB  
Article
Results of Chromosomal Microarray Need to Always Be Checked by (Molecular) Cytogenetics—Even If They Seem to Be Simple Deletions
by Thomas Liehr, Sylke Singer, Ulrike Mau-Holzmann, Stefanie Kankel, Niklas Padutsch, Luisa Person, Eva Daumiller and Uwe Kornak
Genes 2025, 16(6), 714; https://doi.org/10.3390/genes16060714 - 17 Jun 2025
Viewed by 2196
Abstract
Background/Objectives: Chromosome microarrays (CMAs) tend to be used as the first line test or as a test that does not require confirmation or verification by a second test. However, to understand the implications of a duplication or deletion for a family seeking genetic [...] Read more.
Background/Objectives: Chromosome microarrays (CMAs) tend to be used as the first line test or as a test that does not require confirmation or verification by a second test. However, to understand the implications of a duplication or deletion for a family seeking genetic counseling, it is crucial to know the nature of the underlying chromosomal rearrangement. Here, we present seven cases with apparent isolated copy number loss, five of which showed unexpected complexity. Methods: Seven cases were investigated by CMA due to intellectual disability and/or dysmorphic features. Isolated deletions ranging in size from ~0.6 to ~21 Mb were found and referred for further characterization of the underlying chromosomal rearrangement. To elucidate the cases, fluorescence in situ hybridization was performed using locus-specific, whole and partial chromosome painting and/or multicolor banding. Results: Among the seven selected cases, there were five with unexpected complexity. Isolated deletions were actually evidence of chromoanasynthesis, ring chromosome formation, unbalanced translocation, or unbalanced insertion. Conclusions: These results clearly underscore that it seems reasonable to examine every case with a copy number variant—even if it appears to be “only” a simple partial deletion—using banding and/or molecular cytogenetic testing in order to make a qualified assessment of the situation and, on this basis, ensure sound genetic counseling. Full article
(This article belongs to the Special Issue Cytogenetics and Cytogenomics in Clinical Diagnostics: Innovations and Applications)
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12 pages, 1158 KB  
Article
ChromoCheck: Predicting Postnatal Chromosomal Trisomy Cases Using a Support Vector Machine Learning Model
by Nabras Al-Mahrami, Nuha Al Jabri, Amal A. W. Sallam, Najwa Al Jahdhami and Fahad Zadjali
Genes 2025, 16(6), 695; https://doi.org/10.3390/genes16060695 - 8 Jun 2025
Cited by 2 | Viewed by 1373
Abstract
Introduction: Chromosomal study via karyotype is one of the historical gold-standard procedures used to provide a clearer view of chromosomal trisomy abnormalities. It has been used to correlate several phenotypic manifestations that require immediate medical intervention. However, the laboratory procedure persisted with various [...] Read more.
Introduction: Chromosomal study via karyotype is one of the historical gold-standard procedures used to provide a clearer view of chromosomal trisomy abnormalities. It has been used to correlate several phenotypic manifestations that require immediate medical intervention. However, the laboratory procedure persisted with various drawbacks. The recent machine learning model shed light on prediction capabilities in the medical field. In this study, we aimed to use a support vector machine model for predicting postnatal chromosomal trisomy cases. Methods: A dataset of 946 neonatal records from the Royal Hospital, Muscat, Oman, covering the period from 2013 to 2023, has been used in this model. The model is based on features such as thyroxine hormone levels and thyroid-stimulating hormone levels. With different R packages, we used a support vector machine model with leave-one-out cross-validation and ten iterations to test three kernel functions: linear, radial, and polynomial. Results: Among the obtained kernel performances, the linear kernel has optimal classification performance. The training accuracy was 81%, and the testing accuracy was 82%. Sensitivity ranged from 97 to 98%, and specificity ranged from 79 to 80%. The area under the curve in relation to the training dataset came to 0.89, and it came to 0.90 for the test dataset. We deployed the trained models in a website tool called ChromoCheck. Conclusions: Our study is an example of how machine learning can be instrumental in augmenting conventional methods of cytogenetics diagnosis and decision-making in a clinical setup. Full article
(This article belongs to the Special Issue Cytogenetics and Cytogenomics in Clinical Diagnostics: Innovations and Applications)
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Review

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16 pages, 871 KB  
Review
Uncovering the PML::RARA Fusion in Cytogenetically Cryptic and FISH-Negative Acute Promyelocytic Leukemia—A Case Report and Comprehensive Literature Review
by Busra N. Delikkaya, Jaime Eberle-Singh, Arianna B. Morton, Jerald Z. Gong and Jinglan Liu
Genes 2025, 16(10), 1159; https://doi.org/10.3390/genes16101159 - 29 Sep 2025
Cited by 1 | Viewed by 1565
Abstract
The PML::RARA fusion resulting from t(15;17) is the genetic hallmark of acute promyelocytic leukemia (APL), typically detected by cytogenetics and/or fluorescence in situ hybridization (FISH) studies. Rarely, APL patients present with normal cytogenetics and FISH findings, complicating diagnosis and delaying life-saving therapy. We [...] Read more.
The PML::RARA fusion resulting from t(15;17) is the genetic hallmark of acute promyelocytic leukemia (APL), typically detected by cytogenetics and/or fluorescence in situ hybridization (FISH) studies. Rarely, APL patients present with normal cytogenetics and FISH findings, complicating diagnosis and delaying life-saving therapy. We report a 23-year-old male with clinical, morphologic and immunophenotypic features consistent with APL but negative for FISH studies. Despite prompt initiation of all-trans retinoic acid (ATRA) based on clinical suspicion, the patient succumbed to intracranial hemorrhage. Quantitative reverse transcriptase PCR (qRT-PCR) confirmed a long isoform PML::RARA fusion. A review of 34 published cytogenetics- and FISH-negative cases since 1995 demonstrates that RT-PCR-based methods reliably detect cryptic fusions. While advanced genomic approaches may identify these fusions at higher resolution, their accessibility, complexity, cost, and turnaround time often limit diagnostic utility in the urgent setting of APL. Given the extreme rarity of this subset, cytogenetics and FISH remain the standard frontline tests; however, these cases underscore the critical need to incorporate molecular testing into routine workflows. Early recognition and timely therapy are essential to reducing mortality in cryptic APL, and these cases also provide insight into mechanisms of atypical leukemia biology. Full article
(This article belongs to the Special Issue Cytogenetics and Cytogenomics in Clinical Diagnostics: Innovations and Applications)
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30 pages, 2229 KB  
Review
Cytogenetics and Cytogenomics in Clinical Diagnostics: Genome Architecture, Structural Variants, and Translational Applications
by Concetta Federico, Desiree Brancato, Francesca Bruno, Elvira Coniglio, Valentina Sturiale and Salvatore Saccone
Genes 2025, 16(7), 780; https://doi.org/10.3390/genes16070780 - 30 Jun 2025
Cited by 5 | Viewed by 4294
Abstract
The spatial organization of the genome within the nucleus is a fundamental regulator of gene expression, genome stability, and cell identity. This review addresses the central question of how nuclear genome architecture contributes to disease mechanisms and diagnostics, and how technological advances enable [...] Read more.
The spatial organization of the genome within the nucleus is a fundamental regulator of gene expression, genome stability, and cell identity. This review addresses the central question of how nuclear genome architecture contributes to disease mechanisms and diagnostics, and how technological advances enable its clinical exploration. We first outline the principles of nuclear genome architecture, including chromosome territories, replication timing, and 3D domains, and their role in gene regulation and disease. We then explore the mechanisms and consequences of chromosomal rearrangements, and how replication dynamics intersect with epigenetic regulation and genome stability. Diagnostic tools are presented in chronological progression, from conventional cytogenetics to high-resolution genomic and single-cell techniques. A dedicated section focuses on cancer cytogenomics and its clinical implications. We further highlight emerging technologies for 3D genome and epigenome profiling and their integration into diagnostic workflows. Finally, we discuss current challenges, such as standardization and cost, and the transformative potential of multi-omics and artificial intelligence for future precision diagnostics. Overall, we provide a comprehensive overview of how cytogenetics and cytogenomics contribute to the understanding and clinical diagnosis of genetic and neoplastic diseases. Full article
(This article belongs to the Special Issue Cytogenetics and Cytogenomics in Clinical Diagnostics: Innovations and Applications)
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Other

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21 pages, 446 KB  
Perspective
Conversation with Future Clinical Cytogeneticists: The New Frontiers
by Jing Christine Ye, Rishi Chowdhury and Henry H. Heng
Genes 2026, 17(2), 232; https://doi.org/10.3390/genes17020232 - 12 Feb 2026
Viewed by 757
Abstract
The post-genomic era has transformed medical genetics, raising renewed debate over the role of medical cytogenetics in clinical practice. High-throughput sequencing and chromosomal microarray technologies now dominate cancer diagnostics, prenatal testing, and rare disease evaluation by enabling rapid detection of gene-level variation, often [...] Read more.
The post-genomic era has transformed medical genetics, raising renewed debate over the role of medical cytogenetics in clinical practice. High-throughput sequencing and chromosomal microarray technologies now dominate cancer diagnostics, prenatal testing, and rare disease evaluation by enabling rapid detection of gene-level variation, often leading to the perception that cytogenetics is obsolete. However, this view overlooks the unique and complementary strengths of cytogenetic analysis. Although the relationship between cytogenetics and current NGS technologies can be compared to that between forests and trees versus leaves—both of which are necessary for clinical diagnosis—cytogenetic methods uniquely enable direct in situ visualization of chromosomes, allowing detection of large-scale structural and numerical genome alterations at the level of individual cells and cell populations. These system-level features that are frequently invisible or difficult to interpret using sequencing-based approaches alone yet are critical in disease contexts where genome architecture itself carries biological and clinical significance beyond individual genes. This article, therefore, advances a new perspective based on Genome Architecture Theory: that karyotype-level information organizes gene-level function and that many previous gene-centric genetic concepts require reexamination within a unified framework of clinical genomics. Rather than being replaced, cytogenetics is increasingly integrated with sequencing within a unified framework of clinical genomics that combines high-resolution molecular detail with system-level insight into genome organization. Reassessing the role of cytogenetics, therefore, has important implications for medical education, diagnostic strategy, and healthcare policy, as cytogenetics provides the appropriate platform for understanding system-level inheritance through karyotype coding and for advancing molecular medicine from a genome systems perspective. Full article
(This article belongs to the Special Issue Cytogenetics and Cytogenomics in Clinical Diagnostics: Innovations and Applications)
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9 pages, 760 KB  
Case Report
CBFB::MYH11 Fusion Located on a Supernumerary Ring Chromosome 16 in Pediatric Acute Myeloid Leukemia: Diagnostic Challenges and Prognostic Implications
by Changqing Xia, Melissa Acquazzino, Pamela A. Althof, Marilu Nelson, Rachel A. Harris, Joanna R. Spaulding, Joseph D. Khoury and Zhenya Tang
Genes 2025, 16(11), 1283; https://doi.org/10.3390/genes16111283 - 29 Oct 2025
Viewed by 1328
Abstract
We report a unique pediatric acute myeloid leukemia (AML) case characterized by a CBFB::MYH11 fusion located on a supernumerary ring chromosome 16. Following diagnosis through comprehensive blood and bone marrow assays, the patient was enrolled in the Children’s Oncology Group (COG) study AAML1831 [...] Read more.
We report a unique pediatric acute myeloid leukemia (AML) case characterized by a CBFB::MYH11 fusion located on a supernumerary ring chromosome 16. Following diagnosis through comprehensive blood and bone marrow assays, the patient was enrolled in the Children’s Oncology Group (COG) study AAML1831 and randomized to the experimental treatment arm (Arm B). She received induction chemotherapy with CPX-351 (liposomal daunorubicin and cytarabine), gemtuzumab and ozogamicin (GO), and the cardioprotectant dexrazoxane and achieved complete remission (CR). The patient completed the treatment with sustained CR for 18 months. This case represents a rare cytogenetic phenomenon that is not well-documented in the current literature. Through a review of relevant publications, we contextualize this case within the spectrum of core binding factor AML (CBF-AML), highlighting diagnostic approaches, treatment strategies, and prognostic implications, particularly in cases involving atypical CBFB::MYH11 fusions. The durable remission observed in this patient, despite the unusual cytogenetic presentation, provides valuable insights into therapeutic management. This report underscores the cytogenetic and molecular heterogeneity of CBFB::MYH11 AML and emphasizes the importance of comprehensive genetic profiling using advanced techniques such as chromosomal microarray and next-generation sequencing. Full article
(This article belongs to the Special Issue Cytogenetics and Cytogenomics in Clinical Diagnostics: Innovations and Applications)
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