Assay | Platform | Main advantages and disadvantages | Standard bioinformatics pipelines | |
Genomics | Identify nucleotide variants (SNPs) in the whole genome associated with clinical traits (GWAS) | Genotyping arrays, whole-exome sequencing | SNP variability is stable during life; provides limited information in complex diseases due to several loci implicated | GWAS protocol review [10] |
Transcriptomics | Quantify expression levels of cellular transcripts (e.g. mRNA) | Expression arrays, RNA sequencing | Widely used due to its high information content on cell status; differences in mRNA expression do not imply differences in proteins; does not take into account post-transcriptional modifications | RNA sequencing pipelines review [11] |
Proteomics | Characterise protein expression levels of cells/samples | MS-based approaches | Expected to be closer to the phenotype; not widely used, expensive and more cumbersome analysis | Next-generation proteomics review [12] |
Metabolomics | Characterise abundance profile of metabolites and their relative ratios | MS-based approaches | Representative of the cellular status; applicable to many biological fluids (i.e. breath, blood, urine, etc.); not widely used | Review of analytical methods for metabolomics [13] |
Epigenomics | Determine modifications in DNA and small RNA that interfere with gene expression | DNA methylation analysis with arrays (Infinium MethylationEPIC 850K; Illumina, San Diego, CA, USA), next-generation sequencing, small RNA sequencing, arrays, etc. | Provides additional information to transcriptomics; related to exposures; more expensive than transcriptomics; sequencing-based approaches have computational tools in active development | Bioinformatics aspect of DNA methylation studies [14] |
Microbiomics | Characterise bacterial (and viral) composition of a sample | Targeted sequencing of 16S rRNA gene, shotgun metagenomics sequencing | Provides information of external factors likely to be associated with disease; 16S sequencing does not differentiate between the presence of live/dead bacteria | Bioinformatics analysis for the characterisation of the human microbiome [15] |
SNP: single nucleotide polymorphism; GWAS: genome-wide association study; MS: mass spectrometry.