. Author manuscript; available in PMC: 2016 Nov 15.

Published in final edited form as: J Healthc Eng. 2016;2016:10.1155/2016/3617572. doi: 10.1155/2016/3617572

Table 1.

Sequencing assays

Characteristic	DNA sequencing			RNA-seq
Characteristic	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 – 1000 ×^†	80 – 100 ×^†	30 – 50 ×^†	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 is needed to detect rare transcripts.