TABLE II.

Comparison of next-generation sequencing assays^a

Assay	Advantages	Disadvantages
Targeted panels	▪ High depth of coverage ▪ Can be modified to suit needs ▪ Rapid analysis ▪ More easily interpreted ▪ Low costs ▪ Efficient use of sample (for example, few “quantity not sufficient” errors)	▪ Limited to region of interest analyzed ▪ Limited identification of novel variants
Whole-exome sequencing	▪ Greater detection of unknown variants ▪ Feasible with bioinformatics support	▪ Can miss some noncoding variants and fusion genes ▪ Lower copy-number variant resolution ▪ Exon capture and enrichment necessary ▪ High specimen requirement ▪ Need for bioinformatics support ▪ Difficult clinical interpretation ▪ Time consuming
Whole-genome sequencing	▪ Fully comprehensive ▪ Highest resolution of genomic alterations ▪ Does not require exon capture or enrichment methods	▪ Most expensive and time-consuming ▪ Lowest depth of coverage ▪ Least sensitive ▪ High specimen requirement ▪ Even more difficult clinical interpretation
RNA sequencing	▪ Can be used for gene expression profiling and fusion gene detection ▪ Adds to information from DNA sequencing ▪ Enhances detection of variants in low-purity samples	▪ Affected by quantity of cancer cells, tumour heterogeneity, inadequate references of baseline expression

^aAdapted from Horak et al., 2016⁴¹.