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Genomic Diagnosis of Human Cancer
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Genomic Diagnosis of Human Cancer

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

Deadline for manuscript submissions: closed (20 April 2024) | Viewed by 1976

Special Issue Editor

Dr. Yonggang Zhou

E-Mail Website
Guest Editor
Department of Pathology & Laboratory Medicine, University of California, Los Angeles, CA 90095, USA
Interests: biomarker; cancer; DNA methylation; gene expression; protein; NGS

Special Issue Information

Dear Colleagues,

Genomic diagnosis of human cancer represents a revolutionary approach to understanding the genetic underpinnings of cancer at a molecular level. It involves the comprehensive analysis of an individual’s genetic information, specifically their DNA, to uncover the genetic mutation and alterations that may drive the development and progression of cancer. This diagnostic approach has significantly advanced our understanding of cancer, leading to more precise and personalized treatments, as well as the potential for early detection and prevention.

Key aspects of the genomic diagnosis of human cancer include genetic profiling, identification of driver mutation, personalized treatment strategies, prognostic insights, therapeutic resistance, early detection and prevention, research and drug development, and ethical and privacy considerations.

Overall, genomic diagnosis has revolutionized our approach to cancer by providing a deeper understanding of the molecular mechanisms that drive the disease. It has paved the way for more personalized and effective cancer treatment, giving hope to patient and researchers alike in the ongoing battle against cancer.

Dr. Yonggang Zhou
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

  • biomarker
  • cancer
  • DNA methylation
  • gene expression
  • protein
  • NGS

Published Papers (3 papers)

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Research

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10 pages, 570 KiB  
Article
Distribution of BCR::ABL1 Transcripts in the Different Clinical Phases of Chronic Myeloid Leukemia: Effect on Hematological Parameters and Patient Survival
by Pablo Romero-Morelos, Ana Lilia González-Yebra, Anaid Herrerías-García, Francisco Arath Ruíz-Velázquez, Luis Jonathan Bueno-Rosario and Beatríz González-Yebra
Genes 2024, 15(5), 567; https://0-doi-org.brum.beds.ac.uk/10.3390/genes15050567 (registering DOI) - 28 Apr 2024
Viewed by 295
Abstract
Chronic myeloid leukemia (CML) is a hematopoietic stem cell disorder characterized by the presence of the Philadelphia chromosome, a product of the reciprocal translocation t(9;22)(q34;q11), in the BCR and ABL genes. These rearrangements in both genes lead to the formation of various fusion [...] Read more.
Chronic myeloid leukemia (CML) is a hematopoietic stem cell disorder characterized by the presence of the Philadelphia chromosome, a product of the reciprocal translocation t(9;22)(q34;q11), in the BCR and ABL genes. These rearrangements in both genes lead to the formation of various fusion mRNA products, with preferential expression of b2a2, b3a2, and other BCR::ABL1 mRNA variants, combined with additional chromosomal abnormalities. Notably, the distribution and frequency of different mRNA variants vary in different populations. However, studies concerning this in Mexico are limited, and the results have been inconclusive. This study therefore aimed to determine the distribution of BCR::ABL1 mRNA variants in different clinical phases of CML and their effect on hematological parameters and patient survival. This study included 33 patients, whose demographic, clinical, and molecular data on BCR::ABL1 mRNA variants and hematological parameters were collected to identify potential associations. A total of 84.8% (n = 28) of patients had BCR::ABL1 translocation and increased platelet and basophil counts. The most frequent mRNA variant was b3a2 (64.3%), followed by b2a2 (28.6%) and e1a2 (3.6%). Concerning the clinical phases of CML, 75.8% (n = 25), 21.2% (n = 7), and 3% (n = 1) of patients were in the chronic, blast, and accelerated phases, respectively. Moreover, the b3a2 mRNA variant was more commonly identified in patients in the chronic phase. No correlation was observed between mRNA variant expression and patient survival. However, b2a2 was indicative of patients with longer survival as well as those treated with imatinib or nilotinib. Additionally, platelet count could be a marker of BCR::ABL1 translocation. Full article
(This article belongs to the Special Issue Genomic Diagnosis of Human Cancer)
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13 pages, 963 KiB  
Article
Frequencies of BCR::ABL1 Transcripts in Patients with Chronic Myeloid Leukemia: A Meta-Analysis
by Pablo Romero-Morelos, Ana Lilia González-Yebra, Daniela Muñoz-López, Elia Lara-Lona and Beatriz González-Yebra
Genes 2024, 15(2), 232; https://0-doi-org.brum.beds.ac.uk/10.3390/genes15020232 - 12 Feb 2024
Viewed by 1162
Abstract
Chronic myeloid leukemia (CML) is associated with the Philadelphia chromosome and distinct BCR::ABL1 gene transcripts. We assessed the frequencies of these transcripts in Mexico, Latin America, and worldwide. We determined the prevalence of BCR::ABL1 transcripts in CML patients and intercontinental or regional variations [...] Read more.
Chronic myeloid leukemia (CML) is associated with the Philadelphia chromosome and distinct BCR::ABL1 gene transcripts. We assessed the frequencies of these transcripts in Mexico, Latin America, and worldwide. We determined the prevalence of BCR::ABL1 transcripts in CML patients and intercontinental or regional variations using specialized databases and keywords. We analyzed 34 studies from 20 countries, encompassing 5795 patients. Keyword-based searches in specialized databases guided data collection. ANOVA was employed for transcript distribution analysis. The b3a2 transcript was most prevalent globally, followed by b2a2, with e1a2 being the least frequent. Interestingly, Mexico City exhibited a higher incidence of b2a2, while b3a2 predominated in the remaining country. Overall, no significant intercontinental or regional variations were observed. b3a2 was the most common BCR::ABL1 transcript worldwide, with b2a2 following closely; e1a2 was infrequent. Notably, this trend remained consistent in Mexico. Evaluating transcript frequencies holds clinical relevance for CML management. Understanding the frequency of transcript informs personalized CML treatments. Full article
(This article belongs to the Special Issue Genomic Diagnosis of Human Cancer)
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8 pages, 547 KiB  
Brief Report
Preservation of 5-Hydroxymethylcytosine Levels in LRIG1 across Genomic DNA and Cell-Free DNA in Glioma Patients
by Daša Jevšinek Skok, Luka Bolha and Nina Hauptman
Genes 2024, 15(5), 535; https://0-doi-org.brum.beds.ac.uk/10.3390/genes15050535 - 24 Apr 2024
Viewed by 267
Abstract
Cell-free DNA (cfDNA) has recently emerged as a promising minimally invasive diagnostic biomarker for various cancers. In this study, our aim was to identify cfDNA biomarkers by investigating genes that displayed significant differences between glioma patients and their corresponding controls. To accomplish this, [...] Read more.
Cell-free DNA (cfDNA) has recently emerged as a promising minimally invasive diagnostic biomarker for various cancers. In this study, our aim was to identify cfDNA biomarkers by investigating genes that displayed significant differences between glioma patients and their corresponding controls. To accomplish this, we utilized publicly available data from the Gene Expression Omnibus, focusing on 5-hydroxymethylcytosine (5hmC) profiles in both cfDNA and genomic DNA (gDNA) from glioma patients and healthy individuals. The intersection of gene lists derived from these comparative analyses unveiled LRIG1 and ZNF703 as the two genes with elevated 5hmC levels in both the cfDNA of glioma patients and gDNA of glioma tissue compared to their respective controls. The gene expression data revealed both genes were upregulated in glioma tissue compared to normal brain tissue. Integration of 5hmC data revealed a strong positive correlation in the glioma tissue group between 5hmC and the gene expression of the LRIG1 gene. Furthermore, exploration using the AmiCa web tool indicated that LRIG1 gene expression was elevated compared to 17 other cancers included in the database, emphasizing its potential as a distinctive biomarker across multiple cancer types. Full article
(This article belongs to the Special Issue Genomic Diagnosis of Human Cancer)
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