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Cancer Genomics and Precision Oncology

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Oncology".

Deadline for manuscript submissions: 30 June 2024 | Viewed by 2269

Special Issue Editor


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Guest Editor
Department of Clinical and Experimental Medicine, University of Study of Foggia, 71122 Foggia, Italy
Interests: precision medicine; personalized medicine; cancer genomics; genomics; liquid biopsy; molecular diagnostic; laboratory medicine; clinical molecular biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleague,

Cancer genomics has been a rapidly progressing field in the past few decades and has revolutionized how we diagnose, prognosticate, and treat cancers. As the clinical utility of genomic assays grows, the use of clinical genomics in cancer care has been considered the key to personalized treatment. The new era of precision medicine focuses on the molecular features that each individual patient presents and that distinguish them from other patients. Advances in medicine and technology have led to significant progress in this area. Although the number of clinical, translational, and validation studies is growing, they are often limited by few genetic samples and insights from patients of diverse backgrounds. The lack of cancer genomic data from underrepresented racial and ethnic groups generates a gap and has the potential to hold back the pace of drug discovery and the development of treatments tailored to each patient. Moreover, personalized medicine requires the use of large datasets, which must be processed, analyzed, and integrated before being used for personalized care. Human diversity includes the challenge of studying the complex interplay of genes and the environment, such as diet and education, among different populations. Artificial intelligence (AI) and machine learning (ML) are computational tools that use specific neural networks and algorithms for the analysis of different types of large datasets.

The aim of this Special Issue is to collect and share translational, clinical, and validation studies related, but not limited to, the following topics:

  • Cancer genomic diversity data collection (cancer genomic data from underrepresented racial and ethnic groups);
  • Clinical validation of genomics testing;
  • Application of cancer genomics in cancer diagnostic, prognostic, and therapy selection;
  • The application of AI and ML to genomic data;
  • The application of AI in developing personalized treatments of cancer and cancer prevention.

Dr. Carmela Paolillo
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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 genomics
  • precision medicine
  • cancer biomarker
  • cancer epidemiology
  • cancer prevention
  • cancer screening
  • artificial intelligence
  • machine learning
  • personalized medicine
  • diversity
  • genomics
  • precision oncology

Published Papers (2 papers)

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Research

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18 pages, 3007 KiB  
Article
Distinct Driver Pathway Enrichments and a High Prevalence of TSC2 Mutations in Right Colon Cancer in Chile: A Preliminary Comparative Analysis
by Camilo Tapia-Valladares, Guillermo Valenzuela, Evelin González, Ignacio Maureira, Jessica Toro, Matías Freire, Gonzalo Sepúlveda-Hermosilla, Diego Ampuero, Alejandro Blanco, Iván Gallegos, Fernanda Morales, José I. Erices, Olga Barajas, Mónica Ahumada, Héctor R. Contreras, Jaime González, Ricardo Armisén and Katherine Marcelain
Int. J. Mol. Sci. 2024, 25(9), 4695; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms25094695 - 25 Apr 2024
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Abstract
Colorectal cancer (CRC) is the second leading cause of cancer deaths globally. While ethnic differences in driver gene mutations have been documented, the South American population remains understudied at the genomic level, despite facing a rising burden of CRC. We analyzed tumors of [...] Read more.
Colorectal cancer (CRC) is the second leading cause of cancer deaths globally. While ethnic differences in driver gene mutations have been documented, the South American population remains understudied at the genomic level, despite facing a rising burden of CRC. We analyzed tumors of 40 Chilean CRC patients (Chp) using next-generation sequencing and compared them to data from mainly Caucasian cohorts (TCGA and MSK-IMPACT). We identified 388 mutations in 96 out of 135 genes, with TP53 (45%), KRAS (30%), PIK3CA (22.5%), ATM (20%), and POLE (20%) being the most frequently mutated. TSC2 mutations were associated with right colon cancer (44.44% in RCRC vs. 6.45% in LCRC, p-value = 0.016), and overall frequency was higher compared to TCGA (p-value = 1.847 × 10−5) and MSK-IMPACT cohorts (p-value = 3.062 × 10−2). Limited sample size restricts definitive conclusions, but our data suggest potential differences in driver mutations for Chilean patients, being that the RTK-RAS oncogenic pathway is less affected and the PI3K pathway is more altered in Chp compared to TCGA (45% vs. 25.56%, respectively). The prevalence of actionable pathways and driver mutations can guide therapeutic choices, but can also impact treatment effectiveness. Thus, these findings warrant further investigation in larger Chilean cohorts to confirm these initial observations. Understanding population-specific driver mutations can guide the development of precision medicine programs for CRC patients. Full article
(This article belongs to the Special Issue Cancer Genomics and Precision Oncology)
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Review

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29 pages, 2019 KiB  
Review
Biological Basis of Breast Cancer-Related Disparities in Precision Oncology Era
by Anca-Narcisa Neagu, Pathea Bruno, Kaya R. Johnson, Gabriella Ballestas and Costel C. Darie
Int. J. Mol. Sci. 2024, 25(7), 4113; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms25074113 - 08 Apr 2024
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Abstract
Precision oncology is based on deep knowledge of the molecular profile of tumors, allowing for more accurate and personalized therapy for specific groups of patients who are different in disease susceptibility as well as treatment response. Thus, onco-breastomics is able to discover novel [...] Read more.
Precision oncology is based on deep knowledge of the molecular profile of tumors, allowing for more accurate and personalized therapy for specific groups of patients who are different in disease susceptibility as well as treatment response. Thus, onco-breastomics is able to discover novel biomarkers that have been found to have racial and ethnic differences, among other types of disparities such as chronological or biological age-, sex/gender- or environmental-related ones. Usually, evidence suggests that breast cancer (BC) disparities are due to ethnicity, aging rate, socioeconomic position, environmental or chemical exposures, psycho-social stressors, comorbidities, Western lifestyle, poverty and rurality, or organizational and health care system factors or access. The aim of this review was to deepen the understanding of BC-related disparities, mainly from a biomedical perspective, which includes genomic-based differences, disparities in breast tumor biology and developmental biology, differences in breast tumors’ immune and metabolic landscapes, ecological factors involved in these disparities as well as microbiomics- and metagenomics-based disparities in BC. We can conclude that onco-breastomics, in principle, based on genomics, proteomics, epigenomics, hormonomics, metabolomics and exposomics data, is able to characterize the multiple biological processes and molecular pathways involved in BC disparities, clarifying the differences in incidence, mortality and treatment response for different groups of BC patients. Full article
(This article belongs to the Special Issue Cancer Genomics and Precision Oncology)
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