Page 66 - TD-4-3

Tumor Discovery

ORIGINAL RESEARCH ARTICLE
Highly specific and sensitive gene panels for

cancer screening: First application of only-normal
and only-tumor genes

Gabriel Gil 1 , Claudia Carricarte 2 , Julio C. Drake-Pérez 3 , Yasser Perera 4,5 ,
and Augusto Gonzalez *
1
1 Department of Theoretical Physics, Institute of Cybernetics, Mathematics and Physics, Havana,
Cuba
2 Group of Computation, Faculty of Biology, University of Havana, Cuba
3 Department of General Physics, Faculty of Physics, University of Havana, Cuba
4 Biomedical Research Division, Center for Genetic Engineering and Biotechnology, Havana, Cuba
5 China-Cuba Biotechnology Joint Innovation Center, Yongzhou Zhong Gu Biotechnology Co., Ltd,
Yongzhou, Hunan, China

Abstract
The traditional paradigm of gene expression dysregulation emphasizes log-fold
differential expression, with differentially expressed genes presumed to play
key roles in relevant biological processes. In cancer, where normal tissue and
tumors occupy non-overlapping regions in gene expression space, we propose an
alternative and broader framework based on differentially expressed only-tumor
*Corresponding author:
Augusto Gonzalez genes (T-genes) and non-differentially dysregulated only-normal genes (N-genes).
(agonzale@icimaf.cu) N-genes exhibit expression intervals found exclusively in normal samples, while
Citation: Gil G, Carricarte C, T-genes display intervals exclusive to tumor samples. These N- and T-genes serve
Drake-Pérez JC, Perera Y, as markers that can be combined into small gene panels capable of perfectly
Gonzalez A. Highly specific and discriminating between normal and tumor tissues. In most cases, these panels
sensitive gene panels for cancer
screening: First application of highlight biologically significant properties, such as altered glutamine metabolism
only-normal and only-tumor genes. in tumors. We provide an inventory of perfect gene panels for 12 cancer types, with
Tumor Discov. 2025;4(3):58-69. potential applications in diagnostics and immunotherapy. Significance: Highly
doi: 10.36922/TD025190035
specific and sensitive combinatorial gene panels for the identification of 12 types
Received: May 7, 2025 of solid tumors in humans were derived from RNA sequencing expression profiles
Revised: June 6, 2025 reported by The Cancer Genome Atlas network (https://www.cancer.gov/ccg/
research/genome-sequencing/tcga). The corresponding software is available at the
Accepted: June 20, 2025
GitHub repository https://github.com/gabriel-gil/GenePan. This study revisits the
Published online: July 17, 2025 concept of cancer-related gene expression dysregulation by introducing N-genes
Copyright: © 2025 Author(s). and T-genes as novel dysregulation patterns that can be leveraged in diagnosis,
This is an Open-Access article tumor classification, and therapeutic interventions.
distributed under the terms of the
Creative Commons Attribution
License, permitting distribution, Keywords: Cancer; Combinatorial gene panel; Expression dysregulation; Only-normal
and reproduction in any medium,
provided the original work is genes; Only-tumor genes
properly cited.
Publisher’s Note: AccScience
Publishing remains neutral with 1. Introduction
regard to jurisdictional claims in
published maps and institutional The Human Genome Project of the 1990s opened the door to many large-scale omics
1
affiliations. catalogs. In the following decade, the field advanced further with the advent of
Volume 4 Issue 3 (2025) 58 doi: 10.36922/TD025190035