Evaluation of DNA Microarray in Biomarker Detection in Cell-free DNA from Colorectal Cancer Cell Lines: A Proof-of-Concept Study

Abstract

Objective: DNA microarray is a powerful method to identify genomic anomalies including small insertions, duplications and/or deletions. This method is widely used in routine genetic screening for explaining the genetic background of certain phenotypes, for example, cancer. Cell-free DNA (cfDNA), which is an approach that may give information about the somatic tissues in peripheral blood, is another popular method used in routine genetic screening to understand the background of particular phenotypes, one of which is cancer. There is limited available research that investigates the involvement of these two approaches to decipher novel cancer biomarkers in the literature. However, detection of cancer biomarkers, especially non-invasive types, has been of great interest to research groups. Materials and Methods: In the present study, we used colorectal cancer as a model tumor to figure out whether we could determine definite biomarkers from cfDNA using DNA microarray methodology. We isolated cfDNA from the cell-free mediums of the cultures of colorectal cancer cell lines in the presence of the control group which was the healthy epithelial colon cell line. Results: Our results underlined significant alterations that were deletions and/or duplications in some of the genomic regions in a cell line-specific manner. Conclusion: We propose that DNA microarray be used to assess the sub-types of certain cancers in a non-invasive manner using cfDNA approaches.

Keywords

• cfDNA
• carcinogenesis
• colorectal cancer
• DNA microarray
• biomarker

References

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