Microarrays and NGS for Drug Discovery

Abstract

Novel technologies and state of the art platforms developed and launched over the last two decades such as microarrays, next-generation sequencing, and droplet PCR have provided the medical field many opportunities to generate and analyze big data from the human genome, particularly of genomes altered by different diseases like cancer, cardiovascular, diabetes and obesity. This knowledge further serves for either new drug discovery or drug repositioning. Designing drugs for specific mutations and genotypes will dramatically modify a patient’s response to treatment. Among other altered mechanisms, drug resistance is of concern, particularly when there is no response to cancer therapy. Once these new platforms for omics data are in place, available information will be used to pursue precision medicine and to establish new therapeutic guidelines. Target identification for new drugs is necessary, and it is of great benefit for critical cases where no alternatives are available. While mutational status is of highest importance as some mutations can be pathogenic, screening of known compounds in different preclinical models offer new and quick strategies to find alternative frameworks for treating more diseases with limited therapeutic options.

Genome‑wide expression and methylation analyses reveal aberrant cell adhesion signaling in tyrosine kinase inhibitor‑resistant CML cells

“…In the present study, gene expression profiles of treatment-naïve and TKI resistant cell lines were obtained using microarrays. These arrays are a well-established system to analyze gene expression, biomarker identification or genotyping ( 25 , 26 ). Although next generation sequencing has several benefits, such as being a flexible, open, but also cost-intensive system for a high coverage, microarrays still provide a useful tool for expression analyses of low expressed genes, thereby being a closed system with only a limited straightforward bioinformatic pipeline ( 26 ).…”

“…These arrays are a well-established system to analyze gene expression, biomarker identification or genotyping ( 25 , 26 ). Although next generation sequencing has several benefits, such as being a flexible, open, but also cost-intensive system for a high coverage, microarrays still provide a useful tool for expression analyses of low expressed genes, thereby being a closed system with only a limited straightforward bioinformatic pipeline ( 26 ). The HuGene 2.0 ST arrays (as well as their successor Clariom D) from Affymetrix/Thermo Fisher Scientific, Inc. are well known to have a high reproducibility of >0.9 ( 27 – 29 ).…”

Miniaturized surface engineered technologies for multiplex biosensing devices

“…Microarray chips have rapidly been an industry-oriented platform for drug discovery [75] and biomarker identification [76] due to their characteristics to analyze nucleic acid and protein profiles in parallel pipeline. One of the first strategies for detecting biomarkers was the use of the ELISA technique.…”

Data-driven analysis and druggability assessment methods to accelerate the identification of novel cancer targets

“…One of the standard methods to identify novel drug targets is the microarray technology. Microarrays enable gene expression profiling and the analysis of disease versus healthy can highlight target genes of interest [12] . Having identified and validated the function of a target gene in the context of disease, another requirement is to assess the druggability of the target.…”