Genomic characterization of esophageal squamous cell carcinoma: Insights from next-generation sequencing

Table 1 Commercial next-generation sequencing platforms for human genome sequencing

	454 GS FLX	GAIIx	MiSeq	HiSeq 2500	SOLiD 5500	Ion PGM	Ion Proton	PacBio RS
						(318 chip)
Reads per run	1 M	150 M	50 M	6 G	1.4 G	5.5 M	60 M	50 K
Read length (bp)	700	2 × 150	2 × 150	2 × 100	2 × 50	400	200	250-10000
Output per run	700 Mb	90 Gb	15 Gb	600 Gb	120 Gb	2 Gb	12 Gb	200 Mb
Run time	24 h	14 d	55 h	10 d	7 d	5 h	3 h	2 h
Cost/Mb1	$10.00	$0.15	$0.50	$0.05	$0.10	$1.00	$0.08	$2.00
Advantage	Long read length	Widly used	Widly used	High-throughput, widly used	High-throughput, accuracy	Fast, flexible chip	High-throughput, fast	Long read length, fast
Disadvantage	Long hand-on time, low output	Long run time	Long run time	Long run time	Long run time, short read length	High error rate (homopolymer)	High error rate (homopolymer)	High error rate

¹Cost calculations are based on list price quotations obtained from the manufacturer. Mb: Megabase; Gb: Gigabase.

Table 2 Next-generation sequencing studies of esophageal squamous cell carcinoma to date

Study	Method	Sample number	Number of non-silent mutations/tumor	Additional analyses	Platform
Agrawal et al[31]	WES	12 WES	83	-	GA IIx
Song et al[34]	WGS and WES	17 WGS, 71 WES	61	123 CGH	HiSeq 2000
Lin et al[33]	WES and TS	20 WES, 119 TS	59	4 RNA-seq, 59 CGH,	HiSeq 2000
				125 SNP-array
Gao et al[32]	WES	113 WES	82	-	HiSeq 2000
Zhang et al[35]	WGS and WES	14 WGS, 90 WES	104	-	HiSeq 2000

WGS: Whole-genome sequencing; WES: Whole-exome sequencing; TS: Targeted sequencing; CGH: Comparative genomic hybridization; RNA-seq: RNA sequence; SNP: Single nucleotide polymorphism.

Table 3 Frequently altered genes in esophageal squamous cell carcinoma

Gene symbol	TP53	NOTCH1	PIK3CA	CDKN2A	CCND1	FAT1
Chromosomal location	17p13.1	9q34.3	3q26.3	9p21.3	11q13	4q35.2
Alteration frequency (%)
Agrawal et all[31]	92 (M)	33 (M)	0 (M)	8 (M)	NA	8 (M)
Song et al[34]	83 (M)	9 (M)	5 (M)	5 (M)	46 (G)	5 (M)
	1 (L)		41 (G)	44 (L)
Lin et al[33]	60 (M)	8 (M)	7 (M)	3 (M)	46 (G)	12 (M)
			10 (G)	33 (L)
Gao et al[32]	93 (M)	14 (M)	9 (M)	8 (M)	33 (G)	11 (M)
			2 (G)	12 (L)
Zhang et al[35]	88 (M)	21 (M)	17 (M)	8 (M)	64 (G)	15 (M)
				64 (L)

M: Nonsynonymous mutation; L: Copy number loss; G: Copy number gain; NA: Not applicable.