Table 2.

Comparison of targeted gene sequencing, WES, and WGS.

Region sequenced	Targeted sequencing	WES	WGS
	Selected genes/gene sections	Entire exome	Entire genome
Cost per sample (USD) as of 2020	$21	$50	$1000–1600
Variants detected	Depends upon panel size	∼20,000	∼4,000,000
Sequencing depth	$300\to 1000\times$	$100\to 200\times$	$30\to 60\times$
Methodology	Targeted enrichment using hybridization-based protocol; PCR-based amplicon sequencing	Exome enrichment	PCR-free library preparation
Pros	Low cost, short duration, high coverage for rare variants, customizable	Low cost, identifies majority of mutations in protein coding regions	Identifies novel mutations in both coding and non-coding regions; detects structural and copy number variants, uniform sequencing depth
Cons	Limited to selected genes, requires database to be regularly updated as new genes are discovered, unable to detect CNVs and SNPs	Unable to detect variants in intronic regions and SVs	High cost, large data storage and its processing required, complex data analysis

Note: Comparison of NGS techniques (i) targeted gene sequencing, (ii) WES, and (iii) WGS.

CNV: copy number variant; SNP: single nucleotide polymorphism; SV: structural variants.