Precision Oncology: Artificial Intelligence and DNA Methylation Analysis of Circulating Cell-Free DNA for Lung Cancer Detection.
Frontiers in Oncology
Background: Lung cancer (LC) is a leading cause of cancer-deaths globally. Its lethality is due in large part to the paucity of accurate screening markers. Precision Medicine includes the use of omics technology and novel analytic approaches for biomarker development. We combined Artificial Intelligence (AI) and DNA methylation analysis of circulating cell-free tumor DNA (ctDNA), to identify putative biomarkers for and to elucidate the pathogenesis of LC.
Methods: Illumina Infinium MethylationEPIC BeadChip array analysis was used to measure cytosine (CpG) methylation changes across the genome in LC. Six different AI platforms including support vector machine (SVM) and Deep Learning (DL) were used to identify CpG biomarkers and for LC detection. Training set and validation sets were generated, and 10-fold cross validation performed. Gene enrichment analysis using g:profiler and GREAT enrichment was used to elucidate the LC pathogenesis.
Results: Using a stringent GWAS significance threshold, p-value
Conclusion: Using AI and DNA methylation analysis of ctDNA, high LC detection rates were achieved. Further, many of the genes that were epigenetically altered are known to be involved in the biology of neoplasms in general and lung cancer in particular.
Bahado-Singh RO, Vlachos KT, Aydas B, Gordevicius J, Radhakrishna U, Vishweswaraiah S. Precision oncology: artificial intelligence and DNA methylation analysis of circulating cell-free DNA for lung cancer detection. Front Oncol. 2022 May 4;12:790645. doi: 10.3389/fonc.2022.790645. PMID: 35600397.