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Special Issues
Clinical Cytogenetics: Current Advances and Future Perspectives
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Clinical Cytogenetics: Current Advances and Future Perspectives

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

Deadline for manuscript submissions: closed (25 April 2025) | Viewed by 3898

Special Issue Editor

Dr. Rachel D Burnside

E-Mail Website
Guest Editor
Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, USA
Interests: molecular cytogenetics; microarray; karyotyping; chromosomes; medical genetics

Special Issue Information

Dear Colleagues,

Clinical cytogenetics has undergone remarkable transformations since the early days of G-banded chromosome analysis. High-resolution molecular techniques including fluorescence in situ hybridization (FISH), chromosomal microarray, and genome mapping technologies continue to revolutionize our ability to detect and understand chromosomal abnormalities at an unprecedented level of detail.

These advancements have significantly impacted clinical practice and improved patient outcomes. However, chronic staffing shortages and an aging workforce continue to challenge cytogenetics laboratories and were exacerbated by the COVID-19 pandemic. These challenges have been compounded by the increasing complexity of genetic data and a move towards more molecular-based technologies, requiring a different skill set than what has been historically in the cytogenetic technologists’ repertoire. Automation and the introduction of AI algorithms in cytogenetics labs for sample processing, image analysis, and data interpretation have helped to alleviate some of the burdens on laboratory staff. These technologies not only improve efficiencies but also enhance the accuracy and reproducibility of cytogenetic analyses. Currently, AI algorithms are limited to digital karyotyping and FISH applications, but the future of AI in the cytogenetics lab will certainly continue to drive efficiencies in other areas of data analysis.

Despite the exciting technological advancements, we must continue to adapt to the evolving landscape of genetic/genomic testing and advocate for our profession to attract and retain new talent among technical staff. As we look to the future, it is essential to explore innovative solutions and collaborative efforts to overcome the current challenges and harness the full potential of cytogenetics and cytogenomics.

This Special Issue, dedicated to the current advances and future perspectives in the field of clinical cytogenetics/cytogenomics, will address these topics. As such, experts in the field are invited to submit their original research or review papers.

This call for papers was generated with the assistance of Microsoft Copilot.

Dr. Rachel D Burnside
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • molecular cytogenetics
  • cytogenomics
  • staffing shortages
  • microarray
  • optical genome mapping
  • chromosome analysis
  • digital karyotyping
  • oncology
  • medical genetics
  • laboratory genetics

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Published Papers (5 papers)

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11 pages, 780 KiB  
Article
Conventional Cytogenetic Analysis of Solid Tumor Abnormalities: A 25-Year Review of Proficiency Test Results from the College of American Pathologists/American College of Medical Genetics and Genomics Cytogenetics Committee
by Rachel K. Vanderschelden, William R. Sukov, Juli-Anne Gardner, Catherine W. Rehder, Brynn Levy, Gopalrao V. Velagaleti, Reha M. Toydemir, Guilin Tang, Brittany Boles, Yang Cao, Christopher Mixon, Ying S. Zou, Caroline Astbury, Karen D. Tsuchiya and Jess F. Peterson
Genes 2024, 15(12), 1612; https://doi.org/10.3390/genes15121612 - 17 Dec 2024
Viewed by 1096
Abstract
Background: The joint College of American Pathologists/American College of Medical Genetics and Genomics Cytogenetics Committee works to ensure the competency and proficiency of clinical cytogenetic testing laboratories through proficiency testing (PT) programs for various clinical tests offered by such laboratories, including the evaluation [...] Read more.
Background: The joint College of American Pathologists/American College of Medical Genetics and Genomics Cytogenetics Committee works to ensure the competency and proficiency of clinical cytogenetic testing laboratories through proficiency testing (PT) programs for various clinical tests offered by such laboratories, including the evaluation of cytogenetic abnormalities in solid tumors. Methods: Review and analyze 25 years (1999–2023) of solid tumor chromosome analysis PT results, utilizing G-banded karyograms. A retrospective review of results from 1999 to 2023 was performed, identifying the challenges addressing solid tumors. The chromosomal abnormalities and overall performance were evaluated. Results: A total of 21 solid tumor challenges were administered during the period 1999–2018. No solid tumor challenges were administered during the period 2019–2023. Challenges consisted of metaphase images and accompanying clinical history for the evaluation of numerical and/or structural abnormalities. All 21 cases reached 80% grading consensus for abnormality recognition. However, five cases (24%) failed to reach consensus for nomenclature reporting by participating laboratories. These cases illustrate errors in reporting chromosomal abnormalities, including whole-arm translocations and those involving sex chromosomes. In addition, they highlight the challenges with differentiation of terminal and interstitial deletions, difficulties in identifying correct breakpoints, and omission of brackets in neoplastic cases. Conclusions: This comprehensive 25-year review demonstrates the exceptional proficiency of cytogenetic laboratories in accurately identifying chromosome abnormalities in solid tumors, while also highlighting the challenges of reporting specific types of chromosomal abnormalities. Full article
(This article belongs to the Special Issue Clinical Cytogenetics: Current Advances and Future Perspectives)
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8 pages, 1023 KiB  
Case Report
Phase Determination and Demonstration of Parental Mosaicism of Intragenic PRKN Deletions Initially Identified by Chromosomal Microarray Analysis
by Lauren A. Choate, Francis Hoffman, Jessica H. Newman, Cassandra Runke, Matthew Webley, Nicole L. Hoppman and Erik C. Thorland
Genes 2025, 16(6), 630; https://doi.org/10.3390/genes16060630 (registering DOI) - 24 May 2025
Abstract
Background: Autosomal recessive juvenile Parkinson disease (ARJP) is an early-onset neurodegenerative disorder characterized by Parkinsonian motor symptoms with slow progression and preserved cognition. Biallelic pathogenic variants within the PRKN gene are associated with ARJP. Among PRKN pathogenic variants, deletions are a frequent occurrence [...] Read more.
Background: Autosomal recessive juvenile Parkinson disease (ARJP) is an early-onset neurodegenerative disorder characterized by Parkinsonian motor symptoms with slow progression and preserved cognition. Biallelic pathogenic variants within the PRKN gene are associated with ARJP. Among PRKN pathogenic variants, deletions are a frequent occurrence and may be identified through chromosomal microarray testing. Methods: Here we present a case with two intragenic PRKN deletions initially identified as a secondary finding using chromosomal microarray. One deletion was paternally inherited and the second initially appeared to be de novo. In addition to microarray which initially identified the two deletions, long-range GAP-PCR and Sanger sequencing were used to further characterize the de novo deletion and phase of the deletions. Results: Molecular characterization of the apparently de novo deletion demonstrated low-level maternal mosaicism of this deletion, thus proving that these deletions are in trans in the proband, yielding a diagnosis of autosomal recessive juvenile Parkinson disease. Conclusions: This case highlights the utility of a diagnostic approach combining microarray, long-range PCR, and Sanger sequencing to establish the phase and confirm biallelic PRKN deletions in a patient with ARJP. Furthermore, these findings highlight the importance of investigating the possibility of parental mosaicism to determine the phase of autosomal recessive variants and establish accurate recurrence risks. Full article
(This article belongs to the Special Issue Clinical Cytogenetics: Current Advances and Future Perspectives)
8 pages, 202 KiB  
Perspective
The Need for a Concert of Cytogenomic Methods in Chromosomic Research and Diagnostics
by Yiping Wang and Thomas Liehr
Genes 2025, 16(5), 533; https://doi.org/10.3390/genes16050533 - 29 Apr 2025
Viewed by 297
Abstract
This review focuses on the experimental methods and technologies of cytogenomics and how they can be combined in the process of chromosomic diagnostics and research. It is stressed that no cytogenomic methods can be comprehensive on their own. The strengths and weaknesses of [...] Read more.
This review focuses on the experimental methods and technologies of cytogenomics and how they can be combined in the process of chromosomic diagnostics and research. It is stressed that no cytogenomic methods can be comprehensive on their own. The strengths and weaknesses of each method have to be considered. This is especially important in a time where the main stream of human genetics diagnostics is actively proclaiming that high throughput methods are able to replace all other established tests. Full article
(This article belongs to the Special Issue Clinical Cytogenetics: Current Advances and Future Perspectives)
8 pages, 4084 KiB  
Case Report
Systemic EBV+ T-Cell Lymphoma of Childhood with Hemophagocytic Lymphohistiocytosis in a Patient with a Highly Complex Karyotype
by Patrick Maher, Emilia Guzman, Joanna Chaffin, Reema Kashif and Rachel D. Burnside
Genes 2025, 16(4), 382; https://doi.org/10.3390/genes16040382 - 27 Mar 2025
Viewed by 358
Abstract
Background/Objective: Epstein-Barr Virus (EBV) infection can be associated with lymphocytic hematological malignancies, including systemic Epstein-Barr virus-positive T-cell lymphoma of childhood (SEBVTCL). A common complication of EBV infection, hemophagocytic lymphohistiocytosis (HLH), is a life-threatening condition of immune activation present in virtually all cases of [...] Read more.
Background/Objective: Epstein-Barr Virus (EBV) infection can be associated with lymphocytic hematological malignancies, including systemic Epstein-Barr virus-positive T-cell lymphoma of childhood (SEBVTCL). A common complication of EBV infection, hemophagocytic lymphohistiocytosis (HLH), is a life-threatening condition of immune activation present in virtually all cases of SEBVTCL that requires urgent treatment, as this malignancy can be rapidly fatal. Abnormal karyotypes have been strongly associated with SEBVTCL as a distinguishing feature from HLH in the literature. Here, we discuss the diagnostic challenges and social complications in the case of an unaccompanied minor immigrant patient with a highly complex karyotype diagnosed with SEBVTCL with associated HLH. Methods: Laboratory testing confirmed the presence of EBV+ HLH and cytogenetic analysis was performed to investigate a neoplastic process in this patient, confirming SEBVTCL. Chromosomal microarray (CMA) was performed to try to clarify the complex findings by chromosome analysis but demonstrated normal results. Results: Chromosome analysis demonstrated a highly complex hypertriploid clone that confirmed the diagnosis of SEBVTCL. After declining treatment, the patient was discharged to his guardian against medical advice and succumbed to his disease shortly after. Conclusions: SEBVTCL can be challenging to diagnose due to the similarity in clinical and pathological presentations. In virtually all cases reported in the literature, an abnormal karyotype has been reported to be the most important prognostic factor. We propose that in cases with diagnostic ambiguity, an abnormal karyotype can help favor SEBVTCL over EBV+ HLH. Full article
(This article belongs to the Special Issue Clinical Cytogenetics: Current Advances and Future Perspectives)
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15 pages, 1033 KiB  
Case Report
Utilization of RT-PCR and Optical Genome Mapping in Acute Promyelocytic Leukemia with Cryptic PML::RARA Rearrangement: A Case Discussion and Systemic Literature Review
by Giby V. George, Murad Elsadawi, Andrew G. Evans, Sarmad Ali, Bin Zhang and M. Anwar Iqbal
Genes 2025, 16(1), 7; https://doi.org/10.3390/genes16010007 - 25 Dec 2024
Cited by 1 | Viewed by 1047
Abstract
Background: Acute promyelocytic leukemia (APL) is characterized by abnormal promyelocytes and t(15;17)(q24;q21) PML::RARA. Rarely, patients may have cryptic or variant rearrangements. All-trans retinoic acid (ATRA)/arsenic trioxide (ATO) is largely curative provided that the diagnosis is established early. Methods: We present the case [...] Read more.
Background: Acute promyelocytic leukemia (APL) is characterized by abnormal promyelocytes and t(15;17)(q24;q21) PML::RARA. Rarely, patients may have cryptic or variant rearrangements. All-trans retinoic acid (ATRA)/arsenic trioxide (ATO) is largely curative provided that the diagnosis is established early. Methods: We present the case of a 36-year-old male who presented with features concerning for disseminated intravascular coagulation. Although the initial diagnostic work-up, including pathology and flow cytometry evaluation, suggested a diagnosis of APL, karyotype and fluorescence in situ hybridization (FISH), using the PML/RARA dual fusion and RARA breakapart probes, were negative. We performed real-time polymerase chain reaction (RT-PCR) and optical genome mapping (OGM) to further confirm the clinicopathological findings. Results: RT-PCR revealed a cryptic PML::RARA fusion transcript. OGM further confirmed the nature and orientation of a cryptic rearrangement with an insertion of RARA into PML at intron 3 (bcr3). In light of these findings, we performed a systematic literature review to understand the prevalence, diagnosis, and prognosis of APL with cryptic PML::RARA rearrangements. Conclusions: This case, in conjunction with the results of our systematic literature review, highlights the importance of performing confirmatory testing in FISH-negative cases of suspected APL to enable prompt diagnosis and appropriate treatment. Full article
(This article belongs to the Special Issue Clinical Cytogenetics: Current Advances and Future Perspectives)
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