Table 1.
“Omics” technologies used in preclinical and clinical studies
| Omics Approach | Omics Technology | Source Material | Readout | Application | |
|---|---|---|---|---|---|
| Preclinical | Clinical | ||||
| WGS, WES | Genomics | Genomic DNA (Germline) | WGS: Sequence of entire chromosomal and
mitochondrial DNA WES: Sequence of all exomes in genome |
Discover new mechanisms of drug resistance, biomarker discovery | Patient risk stratification, predict response to therapy, guide therapeutic decisions |
| Cancer genome sequencing | Genomic DNA (Tumour) | Mutational profile of cancer | |||
| SNP array, CNV microarray | Genomic DNA (Germline or Tumour) |
Unbiased association of genotype and phenotype | Identification of genetic variation associated with response and/or adverse events to treatment | ||
| RNA Seq, RNA microarray | Transcriptomics | mRNA (cDNA) | Gene expression profile, disease associated genes, chemoresistance- associated genes | Monitor changes in mutational landscape of cancer, predict response to therapy, guide therapeutic decisions | |
| Protein analysis by LC-MS/MS, SILAC-MS, ITRAQ-MS | Proteomics | Proteins | Protein maps and predicted networks, disease-associated proteins, chemoresistance-associated proteins | Predict treatment response, guide therapeutic decisions, monitor treatment response and relapse | |
| Metabolome analysis by LC-MS/MS, NMR, ion-mobility spectrometry, Raman spectroscopy | Metabolomics | Metabolites | Metabolite profiles in cancer, tissues, and body fluids | ||
| Genome-wide DNA methylation assays, miRNA array, Histone modification assays | Epigenomics | DNA, proteins | DNA methylation, miRNAs, histone modifications | ||
| High-throughput screen
(knockdown/knockout shRNA/CRISPR-Cas9 screens, overexpression screens, drug screens) |
Genomics, Multi-omics |
Cells, proteins, embryo | Phenotype (i.e. survival, proliferation, chemoresistance), biochemical, etc… | NA | |
WGS: whole genome sequencing; WES: whole exome sequencing; SNP: single nucleotide polymorphism; CNV: copy number variant; LC-MS/MS: liquid chromatography-tandem mass spectrometry; miRNA: microRNA; NMR: nuclear magnetic resonance; shRNA: short hairpin RNA; CRISPR: clustered regularly interspaced short palindromic repeats