Table 2.

Common sequencing-based tests used in cancer genomics: their targeted regions, primary use cases, and limitations

Sequencing assay	Targeted regions	Primary use	Limitations
Whole genome sequencing	All genes, all exons, all non-coding regions	Discovery	Cost; depth; limited sensitivity for low allele fraction
Whole exome sequencing	All genes, all exons	Clinical research; panel-negative diagnostic testing; neo-epitope prediction	Cost; depth; moderate sensitivity for low allele fraction
Large gene panel	300–600 genes	Diagnostics; clinical trials; clinical research	Breadth; neo-epitope prediction
Small gene panel	<100 genes	Diagnostics; disease progression monitoring	Breadth; neo-epitope prediction
Hotspot panel	Portions of 50–80 genes, specific exons, variants	Diagnostics	Breadth; neo-epitope prediction
Transcriptome	mRNA	Variant validation; neo-epitope expression; fusion calling	Cost
Targeted RNA panel	Fusion genes	Fusion calling	Breadth; variant validation capability limited to targeted territory