From Omics to Multi-Omics: A Review of Advantages and Tradeoffs

Abstract

Bioinformatics is a rapidly evolving field charged with cataloging, disseminating, and analyzing biological data. Bioinformatics started with genomics, but while genomics focuses more narrowly on the genes comprising a genome, bioinformatics now encompasses a much broader range of omics technologies. Overcoming barriers of scale and effort that plagued earlier sequencing methods, bioinformatics adopted an ambitious strategy involving high-throughput and highly automated assays. However, as the list of omics technologies continues to grow, the field of bioinformatics has changed in two fundamental ways. Despite enormous success in expanding our understanding of the biological world, the failure of bulk methods to account for biologically important variability among cells of the same or different type has led to a major shift toward single-cell and spatially resolved omics methods, which attempt to disentangle the conflicting signals contained in heterogeneous samples by examining individual cells or cell clusters. The second major shift has been the attempt to integrate two or more different classes of omics data in a single multimodal analysis to identify patterns that bridge biological layers. For example, unraveling the cause of disease may reveal a metabolite deficiency caused by the failure of an enzyme to be phosphorylated because a gene is not expressed due to aberrant methylation as a result of a rare germline variant. Conclusions: There is a fine line between superficial understanding and analysis paralysis, but like a detective novel, multi-omics increasingly provides the clues we need, if only we are able to see them.

Keywords: bioinformatics; epigenomics; glycoinformatics; lipidomics; metabolomics; proteomics; single-cell RNA sequencing; spatially resolved transcriptomics; transcriptomics.

Figure 1

There are numerous omics methods, but each provides insight into a distinct aspect of the biological state of a sample. Genomics and epigenomics focus on the sequence and accessibility of the genetic material, whereas transcriptomics, proteomics, metabolomics, and glycoinformatics examine the expression levels, post-translational modifications, and biochemical activity of proteins and other biomolecules under different conditions.

Figure 2

Multi-omics concepts. Each distinct omics method provides information about a different but incomplete aspect of the internal state of the cell. Joint analysis of two or more omics methods provides more comprehensive insight into key factors that can be used for classification or prediction and or serve as potential biomarkers or drug targets. Created in part using BioRender.com (accessed on 25 November 2024).