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Biomedicines
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Advances in Molecular Cytogenetics Volume II
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Advances in Molecular Cytogenetics Volume II

A special issue of Biomedicines (ISSN 2227-9059). This special issue belongs to the section "Gene and Cell Therapy".

Deadline for manuscript submissions: closed (31 January 2024) | Viewed by 1867

Special Issue Editor

Dr. Igor Lebedev

E-Mail Website
Guest Editor
Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
Interests: cytogenetics; chromosomal mosaicism; chromosomal diseases; microdeletion and microduplication syndromes; epigenetics; genomic imprinting; induced pluripotent stem cells; spontaneous abortions; pregnancy loss; preimplantation genetic testing
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Since its origin many decades ago, classical cytogenetics has been a crucial tool in the life sciences. During this time, technical advancements have been made and applied in both research and diagnostics. In medicine, the obtained results are universally well-known and appreciated.

Cellular biology improved our knowledge on the nucleus, nucleolus, chromosomes, and chromatin, and the advent of molecular cytogenetics confirmed the necessity of continuing these efforts to deepen our knowledge of the molecular bases of genetic diseases. 

The aim of this Special Issue is to describe the state of the art of cytogenetics and cytogenomics, as well as identify their future evolutions.

The main topics that will be covered are:

  • The role of conventional cytogenetics in the cytogenomic era;
  • Metaphase and/or interphase FISH in the cytogenomic era;
  • The role of chromosomal microarrays in prenatal and postnatal diagnoses of structural abnormalities;
  • Detection and clinical interpretation of copy number variants;
  • PGT-A and PGT-SR strategies in reproductive medicine;
  • Non-invasive prenatal testing of chromosomal disorders;
  • Next-generation sequencing in cytogenetics;
  • Optical genome mapping in cytogenetics;
  • Three-dimensional genomics and chromosomal disorders;
  • Diagnostic odysseys in cytogenetics and applications of advanced cytogenetic techniques in peculiar cases.

Dr. Igor Lebedev
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. Biomedicines 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

  • 3D genomics
  • chromosomal microarray
  • conventional cytogenetics
  • copy number variations
  • FISH
  • karyotype
  • next-generation sequencing
  • non-invasive prenatal testing
  • optical genome mapping
  • PGT-A
  • PGT-SR

Related Special Issue

Published Papers (1 paper)

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Research

15 pages, 6968 KiB  
Article
Analytic Validation of Optical Genome Mapping in Hematological Malignancies
by Andy W. C. Pang, Karena Kosco, Nikhil S. Sahajpal, Arthi Sridhar, Jen Hauenstein, Benjamin Clifford, Joey Estabrook, Alex D. Chitsazan, Trilochan Sahoo, Anwar Iqbal, Ravindra Kolhe, Gordana Raca, Alex R. Hastie and Alka Chaubey
Biomedicines 2023, 11(12), 3263; https://doi.org/10.3390/biomedicines11123263 - 9 Dec 2023
Cited by 1 | Viewed by 1673
Abstract
Structural variations (SVs) play a key role in the pathogenicity of hematological malignancies. Standard-of-care (SOC) methods such as karyotyping and fluorescence in situ hybridization (FISH), which have been employed globally for the past three decades, have significant limitations in terms of resolution and [...] Read more.
Structural variations (SVs) play a key role in the pathogenicity of hematological malignancies. Standard-of-care (SOC) methods such as karyotyping and fluorescence in situ hybridization (FISH), which have been employed globally for the past three decades, have significant limitations in terms of resolution and the number of recurrent aberrations that can be simultaneously assessed, respectively. Next-generation sequencing (NGS)-based technologies are now widely used to detect clinically significant sequence variants but are limited in their ability to accurately detect SVs. Optical genome mapping (OGM) is an emerging technology enabling the genome-wide detection of all classes of SVs at a significantly higher resolution than karyotyping and FISH. OGM requires neither cultured cells nor amplification of DNA, addressing the limitations of culture and amplification biases. This study reports the clinical validation of OGM as a laboratory-developed test (LDT) according to stringent regulatory (CAP/CLIA) guidelines for genome-wide SV detection in different hematological malignancies. In total, 60 cases with hematological malignancies (of various subtypes), 18 controls, and 2 cancer cell lines were used for this study. Ultra-high-molecular-weight DNA was extracted from the samples, fluorescently labeled, and run on the Bionano Saphyr system. A total of 215 datasets, Inc.luding replicates, were generated, and analyzed successfully. Sample data were then analyzed using either disease-specific or pan-cancer-specific BED files to prioritize calls that are known to be diagnostically or prognostically relevant. Sensitivity, specificity, and reproducibility were 100%, 100%, and 96%, respectively. Following the validation, 14 cases and 10 controls were run and analyzed using OGM at three outside laboratories showing reproducibility of 96.4%. OGM found more clinically relevant SVs compared to SOC testing due to its ability to detect all classes of SVs at higher resolution. The results of this validation study demonstrate the superiority of OGM over traditional SOC methods for the detection of SVs for the accurate diagnosis of various hematological malignancies. Full article
(This article belongs to the Special Issue Advances in Molecular Cytogenetics Volume II)
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