Review
Copyright ©The Author(s) 2016.
World J Gastroenterol. Feb 21, 2016; 22(7): 2284-2293
Published online Feb 21, 2016. doi: 10.3748/wjg.v22.i7.2284
Table 1 Commercial next-generation sequencing platforms for human genome sequencing
454 GS FLXGAIIxMiSeqHiSeq 2500SOLiD 5500Ion PGMIon ProtonPacBio RS
(318 chip)
Reads per run1 M150 M50 M6 G1.4 G5.5 M60 M50 K
Read length (bp)7002 × 1502 × 1502 × 1002 × 50400200250-10000
Output per run700 Mb90 Gb15 Gb600 Gb120 Gb2 Gb12 Gb200 Mb
Run time24 h14 d55 h10 d7 d5 h3 h2 h
Cost/Mb1$10.00$0.15$0.50$0.05$0.10$1.00$0.08$2.00
AdvantageLong read lengthWidly usedWidly usedHigh-throughput, widly usedHigh-throughput, accuracyFast, flexible chipHigh-throughput, fastLong read length, fast
DisadvantageLong hand-on time, low outputLong run timeLong run timeLong run timeLong run time, short read lengthHigh error rate (homopolymer)High error rate (homopolymer)High error rate
Table 2 Next-generation sequencing studies of esophageal squamous cell carcinoma to date
StudyMethodSample numberNumber of non-silent mutations/tumorAdditional analysesPlatform
Agrawal et al[31]WES12 WES83-GA IIx
Song et al[34]WGS and WES17 WGS, 71 WES61123 CGHHiSeq 2000
Lin et al[33]WES and TS20 WES, 119 TS594 RNA-seq, 59 CGH,HiSeq 2000
125 SNP-array
Gao et al[32]WES113 WES82-HiSeq 2000
Zhang et al[35]WGS and WES14 WGS, 90 WES104-HiSeq 2000
Table 3 Frequently altered genes in esophageal squamous cell carcinoma
Gene symbolTP53NOTCH1PIK3CACDKN2ACCND1FAT1
Chromosomal location17p13.19q34.33q26.39p21.311q134q35.2
Alteration frequency (%)
Agrawal et all[31]92 (M)33 (M)0 (M)8 (M)NA8 (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)