Special Issue "Optical Genome Mapping in Hematological Malignancies"

A special issue of Cancers (ISSN 2072-6694). This special issue belongs to the section "Cancer Therapy".

Deadline for manuscript submissions: 15 January 2023 | Viewed by 4381

Special Issue Editors

Dr. Adam C. Smith
E-Mail Website
Guest Editor
Cancer Cytogenetics Laboratory, Laboratory Medicine Program, University Health Network and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G 2C4, Canada
Interests: genetics genomics & proteomics; cancer
Dr. Alex Hoischen
E-Mail Website
Guest Editor
Department of Human Genetics & Department of Internal Medicine, Radboud University Medical Center, PO Box 9101, 6500 HB Nijmegen, The Netherland
Interests: genomic technologies; immuno-genomics
Dr. Gordana Raca
E-Mail Website
Guest Editor
Director of Clinical Cytogenomics, Center for Personalized Medicine, Department of Pathology and Lab Medicine, Children's Hospital Los Angeles, Los Angeles, CA 90057, USA
Interests: cancer; tumor biology; pathology and biomarkers epilepsy; neurology genetics; environmental factors hematology; blood and marrow transplantation

Special Issue Information

Dear Colleagues,

For more than 40 years, the clinical evaluation of structural variation in hematological malignancies has primarily been driven by karyotyping.  Karyotyping is a robust tool for evaluating structural and numerical changes in leukemia and other malignancies due to its ability to visualize and catalogue recurrent changes to chromosomes.  As a result, many types of leukemia and lymphoma have a cytogenetic (i.e., karyotyping-based) classification system for diagnosis and prognosis.  However, karyotyping suffers from several challenges, including the need for dividing cells (metaphases) and the relatively “low resolution” of the technique.  Thus, ancillary testing, such as FISH or RT-PCR, is required to identify specific rearrangements between genes.  Optical Genome Mapping is a new technology that can detect structural variation within a sample at a much higher resolution than karyotyping.  As such, it is a promising new technique for the clinical evaluation of chromosomal changes in hematologic malignancies.  

The aim of this Special Issue is stimulate discussion around the use and adoption of Optical Genome Mapping for clinical diagnostics in hematological malignancies. 

  • Carry out the evaluation of optical genome mapping in different types of hematologic malignancies compared to conventional approaches or other novel technologies for structural and molecular classification;
  • Introduce interpretative systems, software tools, or other bioinformatics approaches to improve data analysis and reporting in hematologic malignancies;
  • Provide technical improvements or processes in hematologic malignancies that compare pre-analytical or analytical components in optical genome mapping to improve analysis, diagnostic sensitivity, etc.;
  • Produce novel research findings that may lead to novel diagnostic insights in the future.

In this Special Issue, original research articles and reviews are welcome. Research areas may include (but are not limited to) the following:

  • Myeloid neoplasms;
  • Lymphoid neoplasms;
  • Plasma cell disorders;
  • Technical papers;
  • Economic utility analysis of OGM vs. other technologies;
  • Clinical research discoveries.

We look forward to receiving your contributions.

Dr. Adam C. Smith
Dr. Alex Hoischen
Dr. Gordana Raca
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. Cancers is an international peer-reviewed open access semimonthly 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 2400 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

  • Optical genome mapping
  • Myeloid neoplasia
  • Lymphoid neoplasia
  • Cytogenetics
  • Structural Variation

Published Papers (2 papers)

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Research

Article
Optical Genome Mapping: A Promising New Tool to Assess Genomic Complexity in Chronic Lymphocytic Leukemia (CLL)
Cancers 2022, 14(14), 3376; https://doi.org/10.3390/cancers14143376 - 11 Jul 2022
Cited by 2 | Viewed by 1261
Abstract
Novel treatments in chronic lymphocytic leukemia (CLL) have generated interest regarding the clinical impact of genomic complexity, currently assessed by chromosome banding analysis (CBA) and chromosomal microarray analysis (CMA). Optical genome mapping (OGM), a novel technique based on imaging of long DNA molecules [...] Read more.
Novel treatments in chronic lymphocytic leukemia (CLL) have generated interest regarding the clinical impact of genomic complexity, currently assessed by chromosome banding analysis (CBA) and chromosomal microarray analysis (CMA). Optical genome mapping (OGM), a novel technique based on imaging of long DNA molecules labeled at specific sites, allows the identification of multiple cytogenetic abnormalities in a single test. We aimed to determine whether OGM is a suitable alternative to cytogenomic assessment in CLL, especially focused on genomic complexity. Cytogenomic OGM aberrations from 42 patients were compared with CBA, FISH, and CMA information. Clinical–biological characteristics and time to first treatment (TTFT) were analyzed according to the complexity detected by OGM. Globally, OGM identified 90.3% of the known alterations (279/309). Discordances were mainly found in (peri-)centromeric or telomeric regions or subclonal aberrations (<15–20%). OGM underscored additional abnormalities, providing novel structural information on known aberrations in 55% of patients. Regarding genomic complexity, the number of OGM abnormalities had better accuracy in predicting TTFT than current methods (C-index: 0.696, 0.602, 0.661 by OGM, CBA, and CMA, respectively). A cut-off of ≥10 alterations defined a complex OGM group (C-OGM, n = 12), which included 11/14 patients with ≥5 abnormalities by CBA/CMA and one patient with chromothripsis (Kappa index = 0.778; p < 0.001). Moreover, C-OGM displayed enrichment of TP53 abnormalities (58.3% vs. 3.3%, p < 0.001) and a significantly shorter TTFT (median: 2 vs. 43 months, p = 0.014). OGM is a robust technology for implementation in the routine management of CLL patients, although further studies are required to define standard genomic complexity criteria. Full article
(This article belongs to the Special Issue Optical Genome Mapping in Hematological Malignancies)
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Article
Optical Genome Mapping as a Diagnostic Tool in Pediatric Acute Myeloid Leukemia
Cancers 2022, 14(9), 2058; https://doi.org/10.3390/cancers14092058 - 19 Apr 2022
Cited by 1 | Viewed by 1746
Abstract
Pediatric AML is characterized by numerous genetic aberrations (chromosomal translocations, deletions, insertions) impacting its classification for risk of treatment failure. Aberrations are described by classical cytogenetic procedures (karyotyping, FISH), which harbor limitations (low resolution, need for cell cultivation, cost-intensiveness, experienced staff required). Optical [...] Read more.
Pediatric AML is characterized by numerous genetic aberrations (chromosomal translocations, deletions, insertions) impacting its classification for risk of treatment failure. Aberrations are described by classical cytogenetic procedures (karyotyping, FISH), which harbor limitations (low resolution, need for cell cultivation, cost-intensiveness, experienced staff required). Optical Genome Mapping (OGM) is an emerging chip-based DNA technique combining high resolution (~500 bp) with a relatively short turnaround time. Twenty-four pediatric patients with AML, bi-lineage leukemia, and mixed-phenotype acute leukemia were analyzed by OGM, and the results were compared with cytogenetics. Results were discrepant in 17/24 (70%) cases, including 32 previously unknown alterations called by OGM only. One newly detected deletion and two translocations were validated by primer walking, breakpoint-spanning PCR, and DNA sequencing. As an added benefit, in two cases, OGM identified a new minimal residual disease (MRD) marker. Comparing impact on risk stratification in de novo AML, 19/20 (95%) cases had concordant results while only OGM unraveled another high-risk aberration. Thus, OGM considerably expands the methodological spectrum to optimize the diagnosis of pediatric AML via the identification of new aberrations. Results will contribute to a better understanding of leukemogenesis in pediatric AML. In addition, aberrations identified by OGM may provide markers for MRD monitoring. Full article
(This article belongs to the Special Issue Optical Genome Mapping in Hematological Malignancies)
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