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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