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Clinical Molecular Genetics in Hematologic Diseases
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Clinical Molecular Genetics in Hematologic Diseases

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: 25 August 2025 | Viewed by 2401

Special Issue Editors

Dr. Zhenya Tang

E-Mail Website
Guest Editor
Department of Pathology, Microbiology and Immunology, University of Nebraska Medical Center, Omaha, NE 68198, USA
Interests: hematological malignancies; lung cancer; structural chromosomal abnormalities; advanced technologies in molecular diagnostics
Special Issues, Collections and Topics in MDPI journals
Dr. Lei Zhang

E-Mail Website
Guest Editor
Department of Pathology and Laboratory Medicine, Children’s Mercy Hospital, Kansas City, MO 64108, USA
Interests: hematological malignancies; pediatric solid tumors; chromosome abnormalities; advanced technologies in molecular diagnostics

Special Issue Information

Dear Colleagues,

Hematologic diseases comprise a wide spectrum of disorders affecting blood and blood-forming organs, including both cancerous and noncancerous diseases. Many noncancerous hematologic diseases are caused by inherited genetic aberrations. For example, Factor Five Leiden thrombophilia, a blood clotting disorder manifesting as deep vein thrombosis in the legs or pulmonary embolism in adults, is caused by a heterozygous or homozygous c.1601G>A (p.Arg534Gln) variant in the F5 gene, which is inherited from an affected parent in an autosomal dominant manner. Hemophilia A, a type of bleeding disorder manifesting mostly as prolonged bleeding time after injuries and spontaneous bleeding, is caused by various mutations of the F8 gene and inherited in an X-linked manner. Many cancerous hematologic diseases, or hematologic malignancies, have been characterized by recurrent genetic alterations presenting in various forms, e.g., t(9;22)(q34.1;q11.2)/BCR::ABL1 fusion, a variety of 11q23 abnormalities/KMT2A(MLL) rearrangements, and/or KMT2A(MLL) partial tandem duplication (PTD), TP53 deletions/mutations, the NPM1 mutation, and so on. Most of these acquired genetic alterations are widely applied as biomarkers for the diagnosis/classification, targeted therapies, and prognostic stratification in hematologic malignancies. In the past two decades, tremendous progress has been made in the exploration and definition of genetic cause(s) of hematologic diseases, of both noncancerous and cancerous types. The precise detection of these genetic aberrations plays a critical role in the establishment of diagnosis and the optimal clinical management of hematologic diseases.

Dr. Zhenya Tang
Dr. Lei Zhang
Guest Editors

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

  • hematologic diseases
  • genetic aberration
  • hematologic malignancies
  • next generation sequencing (NGS)
  • precision medicine

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Published Papers (2 papers)

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15 pages, 7578 KiB  
Article
Optical Genome Mapping for Detection of BCR::ABL1—Another Tool in Our Toolbox
by Zhenya Tang, Wei Wang, Gokce A. Toruner, Shimin Hu, Hong Fang, Jie Xu, M. James You, L. Jeffrey Medeiros, Joseph D. Khoury and Guilin Tang
Genes 2024, 15(11), 1357; https://doi.org/10.3390/genes15111357 - 22 Oct 2024
Cited by 1 | Viewed by 1112
Abstract
Background: BCR::ABL1 fusion is mostly derived from a reciprocal translocation t(9;22)(q34.1;q11.2) and is rarely caused by insertion. Various methods have been used for the detection of t(9;22)/BCR::ABL1, such as G-banded chromosomal analysis, fluorescence in situ hybridization (FISH), quantitative real-time reverse [...] Read more.
Background: BCR::ABL1 fusion is mostly derived from a reciprocal translocation t(9;22)(q34.1;q11.2) and is rarely caused by insertion. Various methods have been used for the detection of t(9;22)/BCR::ABL1, such as G-banded chromosomal analysis, fluorescence in situ hybridization (FISH), quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR) and optical genome mapping (OGM). Understanding the strengths and limitations of each method is essential for the selection of appropriate method(s) of disease diagnosis and/or during the follow-up. Methods: We compared the results of OGM, chromosomal analysis, FISH, and/or RT-PCR in 12 cases with BCR::ABL1. Results: BCR:ABL1 was detected by FISH and RT-PCR in all 12 cases. One case with ins(22;9)/BCR::ABL1 was cryptic by chromosomal analysis and nearly missed by OGM. Atypical FISH signal patterns were observed in five cases, suggesting additional chromosomal aberrations involving chromosomes 9 and/or 22. RT-PCR identified the transcript isoforms p210 and p190 in seven and five cases, respectively. Chromosomal analysis revealed additional chromosomal aberrations in seven cases. OGM identified extra cytogenomic abnormalities in 10 cases, including chromoanagenesis and IKZF1 deletion, which were only detected by OGM. Conclusions: FISH offers rapid and definitive detection of BCR::ABL1 fusion, while OGM provides a comprehensive cytogenomic analysis. In scenarios where OGM is feasible, chromosomal analysis and RT-PCR may not offer additional diagnostic value. Full article
(This article belongs to the Special Issue Clinical Molecular Genetics in Hematologic Diseases)
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7 pages, 2689 KiB  
Case Report
Cryptic KMT2A::AFDN Fusion Due to AFDN Insertion into KMT2A in a Patient with Acute Monoblastic Leukemia
by Qing Wei, Gokce A. Toruner, Beenu Thakral, Keyur P. Patel, Naveen Pemmaraju, Sa A. Wang, Rashmi Kanagal-Shamanna, Guilin Tang, Ghayas C. Issa, Sanam Loghavi, L Jeffrey Medeiros and Courtney DiNardo
Genes 2025, 16(3), 317; https://doi.org/10.3390/genes16030317 - 7 Mar 2025
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Abstract
Background: KMT2A rearrangements occur in ~10% of acute myeloid leukemia (AML) cases and are critical for classification, risk stratification, and use of targeted therapy. However, insertions involving the KMT2A gene can evade detection using chromosomal analysis and/or fluorescence in situ hybridization (FISH). Methods: [...] Read more.
Background: KMT2A rearrangements occur in ~10% of acute myeloid leukemia (AML) cases and are critical for classification, risk stratification, and use of targeted therapy. However, insertions involving the KMT2A gene can evade detection using chromosomal analysis and/or fluorescence in situ hybridization (FISH). Methods: We present a case of a 22-year-old woman with acute monoblastic leukemia harboring a cryptic KMT2A::AFDN fusion identified by RNA sequencing. Initial FISH showed a 3′ KMT2A deletion, while conventional karyotyping and the automated bioinformatic pipeline for optical genome mapping (OGM) did not identify the canonical translocation. Results: To resolve these discrepancies, metaphase KMT2A FISH (break-apart fusion probe) was performed to assess whether KMT2A was translocated to another chromosome. However, the results did not support this possibility. As the fusion signal remained on the normal chromosome 11, with the 5′ KMT2A signal localized to the derivative chromosome 11. A subsequent manual review of the OGM data revealed a cryptic ~300 kb insertion of AFDN into the 3′ region of KMT2A, reconciling the discrepancies between chromosomal analysis, FISH, and RNA fusion results. Conclusions: This case highlights the importance of integrating multiple testing modalities with expert review when there is a discrepancy. Our findings emphasize the need for a comprehensive approach to genomic assessment to enhance diagnostic accuracy and guide therapeutic decision-making. Full article
(This article belongs to the Special Issue Clinical Molecular Genetics in Hematologic Diseases)
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