Table 3.

SWOT analysis of omics-based malaria diagnostic methodologies.

	Genomics/Epigenetics	Proteomics	Metabolomics	Phenomics
Strength	Has SNP level information and indicates the effect of environmental factors on gene expression. The most stable as compared to other omics. With advancements in NGS, the cost has declined for gene-based diagnostics.	Has different outcome variations, modulating unit of phenome.	Modulating biomolecules are highly dynamic; ideal for indicating prognosis.	Leads to easier detection, morphology-centric.
Weakness	Gene deletion or mutations due to various factors may change the identification status of a gene; it does not correlate with the amount of protein produced.	The final product of gene expression may lack information on SNPs or copy numbers of a gene. Does not correlate with all the SNPs and gene transcript levels. The method is low-cost effective.	Highly dynamic biomolecules may get converted to byproducts if not handled with care; byproducts may not be disease drivers. The method is low-cost effective.	Artifacts and morphological changes don’t represent changes due to pathogen confidently; any intracellular parasite may deform the RBCs.
Opportunity	Facilitates understanding of SNPs-based antimalarial resistance such as k13 polymorphs and provides haplotyping and mapping of parasite strain origin mapping. SNP-based severity is a possibility, such as G6PD deficiency for Primaquine-based treatment. Helps the preparation of a customized/predicted proteome database for new proteins. Low-cost, efficient, and accurate diagnostics may soon be delivered to low economic regions of endemic states.	Provides insight into the immune response against pathogens for vaccine purposes, i.e. pathways affected and effector proteins for drug targets. The receptor-based study suggests the potential interacting pathways for establishing pathogenesis.	Highly dynamic, representative of slightest stimulus making it best prognostic biomarker candidate. No traces of post-infection clearance.	Quick diagnosis; basic staining, and microscopy may be used to check the deformities.
Threat	Gene deletion in parasites may lead to false-negative results such as pfHRPII based RDTs. Genetic mutants do not translate to proteins, hence proteomics of mutants is essential to understand.	Antibody traces remain long before the infection is cleared, resulting in false positives. Post-translation modifications may help in understanding cascade regulation for pathobiology.	Highly dynamic, resulting in a quick byproduct formation under in vitro situations that might not be related to pathobiology. Samples are high maintenance and require freezing of biomolecules as soon as samples are procured.	Artifacts may lead to false results and require an expert to differentiate the different characteristic features for reliable results.