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 |