Table 3.

Comparison of pros and cons of whole-genome sequencing, exome-sequencing, and RNA-sequencing.

Characteristics	Whole-genome sequencing	Exome-sequencing	Transcriptome-sequencing
Cost	$5000–$15,000 per sample	$1000–$2000 per sample	The cheapest method: $300–$500 per sample
Starting material	1 μg of genomic DNA	3 μg of genomic DNA	0.1–4 μg of RNA
Detectable variants	All possible variants	Restricted to exonic regions, hard to identify structural variants, and copy number variations	Detection of variants present in the transcriptome and fusion genes
Pros	Detection of all the possible variants present in a genome	Lower cost, greater depth of coverage, and corresponding improvement in data quality essential to detect mutations at lower frequency	Identification of tumor-specific fusion transcripts, mRNA-splice variants, and information on gene expression levels
Cons	Very expensive, so typically designed with low coverage	Hard to identify structural variants and copy number alterations	Hard to identify the corresponding normal samples. Hard to identify SNVs and indels in transcripts at low expression or for which mutations may induce mRNA degradation. Errors due to reverse transcriptase and the phenomenon of RNA editing can make these data difficult to interpret