Towards Improving Skin Cancer Diagnosis by Integrating Microarray and RNA-Seq Datasets.

TitleTowards Improving Skin Cancer Diagnosis by Integrating Microarray and RNA-Seq Datasets.
Publication TypeJournal Article
Year of Publication2020
AuthorsGalvez, JM, Castillo-Secilla, D, Herrera, LJ, Valenzuela, O, Caba, O, Prados, JC, Ortuno, FM, Rojas, I
JournalIEEE J Biomed Health Inform
Date Published2020 07
KeywordsBiomarkers, Tumor; Computational Biology; Diagnosis, Computer-Assisted; Gene Expression Profiling; Humans; Machine Learning; RNA-seq; Skin Neoplasms

Many clinical studies have revealed the high biological similarities existing among different skin pathological states. These similarities create difficulties in the efficient diagnosis of skin cancer, and encourage to study and design new intelligent clinical decision support systems. In this sense, gene expression analysis can help find differentially expressed genes (DEGs) simultaneously discerning multiple skin pathological states in a single test. The integration of multiple heterogeneous transcriptomic datasets requires different pipeline stages to be properly designed: from suitable batch merging and efficient biomarker selection to automated classification assessment. This article presents a novel approach addressing all these technical issues, with the intention of providing new sights about skin cancer diagnosis. Although new future efforts will have to be made in the search for better biomarkers recognizing specific skin pathological states, our study found a panel of 8 highly relevant multiclass DEGs for discerning up to 10 skin pathological states: 2 healthy skin conditions a priori, 2 cataloged precancerous skin diseases and 6 cancerous skin states. Their power of diagnosis over new samples was widely tested by previously well-trained classification models. Robust performance metrics such as overall and mean multiclass F1-score outperformed recognition rates of 94% and 80%, respectively. Clinicians should give special attention to highlighted multiclass DEGs that have high gene expression changes present among them, and understand their biological relationship to different skin pathological states.

Alternate JournalIEEE J Biomed Health Inform
PubMed ID31871000