Clinical applications of next-generation sequencing in colorectal cancers

Table 2 The list of next-generation sequencing-based studies of colorectal cancer genomes

Ref.	NGS types	Major findings	Alteration types and software used
Bass et al[16]	WGS (9 pairs; tumor-matched normal)	Oncogenic fusion (VTI1A-TCG7L2)	Point mutations (MuTect[83])
			Indels (Indelocator)1
			Rearrangements (dRanger)1
TCGA consortium	WGS (97 pairs; low-pass)	See main text	Point mutations (MuTect)
	RNA-seq (218 tumors)		Recurrent mutations (MutSig)1
	Exome-seq (254 pairs)		DNA copy numbers (BIC-seq[82])
			Rearrangements (BreakDancer[81])
Timmermann et al[84]	Exome-seq (2 pairs, one MSI-H and one MSS)	Comparison of mutation spectrum between MSI-H and MSS CRC genomes	Point mutation and indel (Vendor-provided GS reference mapper, Roche)
Zhou et al[85]	Exome-seq (1 series: normal-adenoma-adenocarcinoma)	Comparison of benign and malignant CRC genomes in the same patient	Point mutation and indel (Samtools[86])
Kloosterman et al[73]	WGS (4 pairs; primary-metastasis-matched normals)Targeted 1300 genes (4 pairs)	Comparison of primary or metastatic CRC genomes	Chromothripsis and mutations (Burrow-Wheeler aligner[87] based in-house tools)
Brannon et al[88] (Proceedings)	Targeted 230 genes (50 pairs: primary-metastasis-matched normals)	Comparison of primary or metastatic CRC genomes	IMPACT (integrated mutation profiling of actionable cancer targets)
Yin et al[89]	RNA-seq (2 pairs)	RNA-seq based mutation study	Point mutations and indels (Samtools)

¹Description of the software is available at https://confluence.broadinstitute.org/display/CGATools/. NGS: Next-generation sequencing; CRC: Colorectal cancer; TCGA: The cancer genome atlas; MSI: Microsatellite instability.