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Table 2 Common sequencing-based tests used in cancer genomics: their targeted regions, primary use cases, and limitations

From: Technological considerations for genome-guided diagnosis and management of cancer

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