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Volume 16
Issue 7
10.3390/genes16070780
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This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Review

Cytogenetics and Cytogenomics in Clinical Diagnostics: Genome Architecture, Structural Variants, and Translational Applications

by
Concetta Federico
1,
Desiree Brancato
1,
Francesca Bruno
2,
Elvira Coniglio
1,
Valentina Sturiale
1 and
Salvatore Saccone
1,*
1
Department of Biological, Geological and Environmental Sciences, University of Catania, 95124 Catania, Italy
2
Department of Medicine and Surgery, Kore University of Enna, 94100 Enna, Italy
*
Author to whom correspondence should be addressed.
Genes 2025, 16(7), 780; https://doi.org/10.3390/genes16070780
Submission received: 10 June 2025 / Revised: 29 June 2025 / Accepted: 30 June 2025 / Published: 30 June 2025
(This article belongs to the Special Issue Cytogenetics and Cytogenomics in Clinical Diagnostics: Innovations and Applications)
Versions Notes

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 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.
Keywords: nuclear genome architecture; chromosomal rearrangements; 3D genome organization; cytogenomic diagnostics; replication timing; structural variants; cancer genomics; high-resolution genomic technologies nuclear genome architecture; chromosomal rearrangements; 3D genome organization; cytogenomic diagnostics; replication timing; structural variants; cancer genomics; high-resolution genomic technologies

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MDPI and ACS Style

Federico, C.; Brancato, D.; Bruno, F.; Coniglio, E.; Sturiale, V.; Saccone, S. Cytogenetics and Cytogenomics in Clinical Diagnostics: Genome Architecture, Structural Variants, and Translational Applications. Genes 2025, 16, 780. https://doi.org/10.3390/genes16070780

AMA Style

Federico C, Brancato D, Bruno F, Coniglio E, Sturiale V, Saccone S. Cytogenetics and Cytogenomics in Clinical Diagnostics: Genome Architecture, Structural Variants, and Translational Applications. Genes. 2025; 16(7):780. https://doi.org/10.3390/genes16070780

Chicago/Turabian Style

Federico, Concetta, Desiree Brancato, Francesca Bruno, Elvira Coniglio, Valentina Sturiale, and Salvatore Saccone. 2025. "Cytogenetics and Cytogenomics in Clinical Diagnostics: Genome Architecture, Structural Variants, and Translational Applications" Genes 16, no. 7: 780. https://doi.org/10.3390/genes16070780

APA Style

Federico, C., Brancato, D., Bruno, F., Coniglio, E., Sturiale, V., & Saccone, S. (2025). Cytogenetics and Cytogenomics in Clinical Diagnostics: Genome Architecture, Structural Variants, and Translational Applications. Genes, 16(7), 780. https://doi.org/10.3390/genes16070780

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