Challenges of Identifying Clinically Actionable Genetic Variants for Precision Medicine

Table 1

Sequencing assays.

Characteristic	DNA sequencing			RNA-seq
	Targeted genomic regions	Whole exome	Whole genome	Targeted	Transcriptome profiling
Capture method	Amplicon-based targeting; hybrid capture; in-solution capture	Hybrid capture; in-solution capture	None	Hybridization only; hybridization and extension; multiplexed PCR	None
Amount of genome/transcriptome sequenced	~150 bp–62 Mb (≤2% of genome)	~30–60 Mb (1-2% of genome)	~3 Gb (≥95% of genome)	Variable: transcripts of ~10–1000 genes	Entire transcriptome
Amplification	Yes	Yes	Not required	Yes	Required for low-quantity RNA samples
Sequencing depth	100–1000x	80–100x	30–50x	0.3–25 million reads^‡	15–200 million reads^‡
Amount of sequence data generated per sample	~0.3–5 Gb	~4-5 Gb	~90 Gb	~0.5–3 Gb	~5-6 Gb

bp, base pairs; Mb, megabases; Gb, gigabases; PCR, polymerase chain reaction.
Method used to select genomic regions for sequencing.
Number of times a single base is read during a sequencing run.
^‡A greater number of reads are needed to detect rare transcripts.