Table 2.
Recent studies of ESCC using high-throughput sequencing
| Study | ESCC cases | District | Main Methods | Chromosome change | |
|---|---|---|---|---|---|
|
| |||||
| Amplification | Deletion | ||||
| [11] | 158 | Chaoshan, Guangdong, China | WGS (17), WES (71), array-CGH (123) | Large scale amplification of 3q, 5p, 8q, 12p, 20p and 20q; 43 focal CNAs, like 8q24.3, 11q13.3-13.4, 14q32.33 | Large scale deletion of 3p, 4q, 9p, 13q, 18q, 19p and 21q; 15 focal CNAs, such as 9p21.3, 3q26.1 |
| [12] | 220, (103)1 | North-central China | WES (139), RNA-seq (4), SNP-array (22), array-CGH (59) | 8p11.23, 8q24.21, 7p11.2, 11q13.2-13.3, 12p12.1, 12q15, 3q26, 3q26.32-33, 14q13.3 | Homozygous deletion of 2q22.1-22.2, 9p21.3, 5q12.1, 9p24.1, 3p14.2 |
| [13] | 113 | China | WES (113) | Recurrent CNAs like 11q13.3, 11q13.2, 11q13.4, 11q13.1, 7p11.2, 7q31.1 | Recurrent CNAs like 9p21, Yp11.3, Yq11.222 |
| [14] | 104, (88)2 | North-central China | WGS (14), WES (90), FISH, qPCR | Recurrent CNAs like 3q26.1-q29, 3q29, 3q25.1, 11q13.3-q13.4, 11q13.3, 8p12-p11.23, 7p12.1-p11.2 | Recurrent CNAs like 9p21.3, 19p11, 5p15.33, 21p11.2, 3p11.1, 4p11, Xq11.1 |
| [15] | 388, (70)3 | Guangdong, China | WGS (10), WES (60), IHC (120) | Recurrent CNAs like 3q26.33, 11q13, 20q13.12 | Recurrent CNAs like 2q22.1-22.2, 9p21.3, 13q13.3-q14.11 |
| [16] | 144 | Japan | WES SNP-array | 3q, 8q, 5p, 7p, 20q; recurrent focal CNVs, like 11q13.3, 5p15.33, 7p11.2, 11q22.1, 3q26.33 | 3p, 4p, 9p, 5q; recurrent focal CNVs, like 9p21.3, 2q22.1-22.2, 4q22, 3p14.2 |
| [17] | 90 | 10 counties, such as USA, Korea, Brazil, Germany | WES, SNP-array | CNAs, like 3q26.33, 3q28, 5p15.33, 7p11.2, 8p11.23, 11q13.3, 12p12.1, 12q14.3, 14q13.2 | CNAs, like 13q14.2, 3p25.2, 9p21.3, 2q22.1, 8p23.2, Xp11.3, 10p11.21, 3p14.3, 4p15.2, 4q22.1, 3p14.2 |
| [18] | 94 (704, 94)4 | China | WGS | 3q, 5p, 7p, 8q, 12p, 16p, 20p and 20q; 23 recurrent focal CNVs, like 11q13.3, 3q26.32, 5p15.33, 8q24.21, 7q22.1, 7p11.2, 19p13.3, 14q13.3 | 3p, 4p, 4q, 5q, 9p, 13q, 18q and 21p; 34 focal CNVs, like 9p21.3, 22q11.21, 10p11.22, 5q13.2, 6p24.3, 10q21.1, 12q23.1, 13q31.3 |
WGS: Whole-genome sequencing; WES: Whole-exome sequencing; TS: Targeted sequencing; CGH: Comparative genomic hybridization; RNA-seq: RNA sequence; SNP: Single nucleotide polymorphism; IHC: immunohistochemistry.
2
88 Chaoshan sequencing data from [10].