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Clinical Diagnosis and Analysis of Cancers
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Clinical Diagnosis and Analysis of Cancers

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

Deadline for manuscript submissions: closed (25 August 2025) | Viewed by 4636

Special Issue Editor

Dr. Elisa De Paolis

E-Mail Website
Guest Editor
1. Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Gemelli IRCCS, 00168 Rome, Italy
2. Genomics Core Facility, G-STeP, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
Interests: genomics; lung cancer; liquid biopsy; tissue biopsy; molecular biology; cancer genomics; precision medicine; next-generation sequencing; proteogenomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Technological advances in the evaluation and diagnosis of cancer over the most recent decade have made it possible to improve the treatment of patients with oncological diseases. By exploring molecular and epigenetic alterations, proteomic features and signatures, and functional pathways, we seek to enhance our understanding of cancer pathophysiology.

Most recently, the availability of computational approaches, machine learning, and artificial intelligence has revolutionized our understanding of complex molecular system, allowing the identification of novel biomarkers and therapeutic approaches.

This Special Issue, titled “Clinical Diagnosis and Analysis of Cancers”, aims to collect high-quality articles on advances in oncological research with a focus on molecular, omics, and technological approaches.

The topics of interest include, but are not limited to, the following:

  • Molecular and cellular genetics of cancer;
  • Proteogenomic and bioinformatic approaches to understanding cancer;
  • New genetic editing techniques and their clinical applications in cancer research;
  • New pre-clinical and clinical approaches to cancer diagnosis and evaluation
  • Machine learning and artificial intelligence analyses;
  • Understanding of genetics and molecular biomarkers of rare cancers.

Dr. Elisa De Paolis
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 250 words) can be sent to the Editorial Office for assessment.

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

  • cancer genetics
  • cancer proteomics
  • cancer diagnosis
  • cancer treatments
  • next-generation sequencing
  • genetic editing 
  • machine learning 
  • artificial intelligence

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (2 papers)

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Research

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12 pages, 1269 KB  
Article
Familial NSD1 Exon 3 Deletion Associated with Phenotypic and Epigenetic Variability
by Sunwoo Liv Lee, Alison Foster, Dalit May, Ciara Batterton, Eguzkine Ochoa, Bryndis Yngvadottir, Ruth Armstrong, Meena Balasubramanian, Mary O’Driscoll, Marc Tischkowitz, France Docquier, Fay Rodger, Ezequiel Martin, Ana Toribio and Eamonn R. Maher
Genes 2025, 16(10), 1190; https://doi.org/10.3390/genes16101190 - 13 Oct 2025
Viewed by 1030
Abstract
Background: Germline pathogenic variants in NSD1 cause Sotos syndrome, a developmental disorder characterised by overgrowth, intellectual disability, macrocephaly, developmental anomalies, and, in some cases, tumour development. Familial cases of Sotos syndrome are rare and genotype–phenotype correlations are not well described. NSD1, a lysine-specific [...] Read more.
Background: Germline pathogenic variants in NSD1 cause Sotos syndrome, a developmental disorder characterised by overgrowth, intellectual disability, macrocephaly, developmental anomalies, and, in some cases, tumour development. Familial cases of Sotos syndrome are rare and genotype–phenotype correlations are not well described. NSD1, a lysine-specific histone methyltransferase, is an important epigenetic regulator and pathogenic variants in NSD1 are associated with a distinctive blood DNA methylation pattern (episignature). We described a family with an NSD1 exon 3 deletion and an atypical clinical phenotype. Methods: DNA episignature profiling was undertaken with a next generation sequencing-based approach. Results: Within the family, the three affected individuals showed clinical variability with the proband being most severely affected, although none showed unequivocal macrocephaly or the characteristic facial features of Sotos syndrome. DNA methylation profiling was performed in the three affected family members, eight individuals with Sotos syndrome, and compared to control samples. The eight individuals with Sotos syndrome displayed genome-wide hypomethylation as previously described. DNA hypomethylation was also apparent in the three family members with the NSD1 exon 3 deletion with the proband being most similar to the episignature observed in confirmed Sotos syndrome patients. The two more mildly affected relatives had less pronounced DNA hypomethylation. Conclusions: A familial germline exon 3 NSD1 deletion was associated with mild Sotos syndrome phenotype with variable expressivity and a DNA methylation episignature that was less marked in milder cases than in individuals with classical Sotos syndrome. These findings support the use of methylation episignature analysis to explore intrafamilial variability in chromatin disorders. Full article
(This article belongs to the Special Issue Clinical Diagnosis and Analysis of Cancers)
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Review

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16 pages, 901 KB  
Review
Genomics in Lung Cancer: A Scoping Review of the Role of ctDNA in Non-Advanced Non-Small-Cell Lung Cancer in the Prediction of Prognosis After Multimodality Therapeutic Approaches
by Carolina Sassorossi, Jessica Evangelista, Alessio Stefani, Marco Chiappetta, Antonella Martino, Annalisa Campanella, Elisa De Paolis, Dania Nachira, Marzia Del Re, Francesco Guerrera, Luca Boldrini, Andrea Urbani, Stefano Margaritora, Angelo Minucci, Emilio Bria and Filippo Lococo
Genes 2025, 16(8), 962; https://doi.org/10.3390/genes16080962 - 15 Aug 2025
Cited by 2 | Viewed by 3195
Abstract
Background: Circulating tumor DNA (ctDNA), shed into bodily fluids by cancer cells through apoptosis, necrosis, or active secretion, is currently used in the field of genomic investigation in clinical settings, primarily for advanced stages of non-small-cell lung cancer (NSCLC). However, its potential [...] Read more.
Background: Circulating tumor DNA (ctDNA), shed into bodily fluids by cancer cells through apoptosis, necrosis, or active secretion, is currently used in the field of genomic investigation in clinical settings, primarily for advanced stages of non-small-cell lung cancer (NSCLC). However, its potential role in guiding the multi-omic approach to early-stage NSCLC is emerging as a promising area of investigation. Efforts are being made to integrate the genomics not only in surgery, but also in the definition of long-term prognosis after surgical or radiotherapy and for the prediction of recurrence. Methods: An extensive literature search was conducted on PubMed, covering publications from 2000 to 2024. Using the advanced search tool, titles and abstracts were filtered based on the following keywords: ctDNA, early stage, NSCLC. From this search, 20 studies that fulfilled all inclusion criteria were selected for analysis in this review. Results: This review highlights the growing body of evidence supporting the potential clinical use of ctDNA as a genomic biomarker in managing early-stage NSCLC. Baseline ctDNA levels offer valuable information about tumor molecular biology and histological characteristics. Beyond its prognostic value before treatment, liquid biopsy has proven useful for tracking minimal residual disease and forecasting recurrence following curative interventions such as surgery or radiotherapy. Future adjuvant treatment decisions may increasingly rely on predictive models that incorporate liquid biopsy findings alongside other clinical factors. Conclusions: The potential use of this analyte introduces new opportunities for the integration of genomic data in treatment, as well as relapse monitoring with more accurate and innovative than traditional methods, particularly in patients with early-stage NSCLC Full article
(This article belongs to the Special Issue Clinical Diagnosis and Analysis of Cancers)
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