Clinical applications of next-generation sequencing in colorectal cancers

Table 1 The next-generation sequencing platforms for cancer genome analysis

NGS types	Whole genome sequencing	Exome sequencing	Epigenome sequencing1	RNA-seq
Source	Genomic DNA	Genomic DNA (targeted)	Genomic DNA (targeted)	RNA
Alteration types	Point mutations and indels, rearrangements2, DNA copy number changes	Point mutations and indels	DNA methylation and posttranscriptional histone modifications	Gene fusions3, alternative splicing events, point mutations and indels

¹Epigenome sequencing can be classified into chromatin immunoprecipitation (ChIP)-based methods to detect genomic domains with epigenetic modifications[80] and more direct DNA methylation sequencing such as bisulfite-sequencing[59,60];

²From whole genome sequencing data, the genomic rearrangements and DNA copy number changes are generally detected by paired-end mapping[81] and read-depth based methods[82], respectively;

³Gene fusions can also be identified by paired-end, high-coverage whole genome sequencing, but the transcription-related events such as exon skipping or other alternative splicing events can only be identified by RNA-seq. NGS: Next-generation sequencing.