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Table 1 Amplification RCNAs detected by 145 WES data and 15 WGS data

From: Copy number alterations detected by whole-exome and whole-genome sequencing of esophageal adenocarcinoma

Cytoband

Peak boundary (Mb)

Width (Mb)

Platform

Residual q value

D

F

P

B

Z

1p36.33

chr1:0.99-3.16

2.174

WES

1.16E−04

     

1q21.3

chr1:149.94-156.69

6.751

WES

2.14E−05

Y

    

3q26.1

chr3:164.71-164.76

0.047

WES and WGS

9.75E−02

     

3q26.2

chr3:169.43-170.59

1.158

WES

4.18E−02

Y

Y

  

Y

6p21.32

chr6:32.56-32.58

0.016

WGS

2.35E−02

     

6p21.1

chr6:42.79-43.97

1.178

WES and WGS

2.00E−13

Y

Y

  

Y

6q23.3

chr6:135.29-135.71

0.421

WES and WGS

4.98E−04

Y

   

Y

7p22.1

chr7:4.29-6.89

2.609

WES

6.42E−02

  

Y

  

7p11.2

chr7:55.00-55.46

0.455

WES

5.48E−14

Y

Y

Y

Y

Y

7q21.2

chr7:91.98-92.76

0.779

WES and WGS

5.07E−12

Y

Y

Y

 

Y

7q22.1

chr7:98.46-100.674

2.217

WES

7.81E−07

Y

 

Y

Y

 

7q31.2

chr7:115.61-117.83

2.211

WES

1.71E−02

Y

    

8p23.1

chr8:6.97-7.16

0.182

WES

5.08E−02

Y

Y

  

Y

8p23.1

chr8:7.37-7.63

0.263

WES

1.79E−03

Y

Y

  

Y

8p23.1

chr8:11.28-11.68

0.402

WES

4.25E−13

Y

Y

  

Y

8q24.21

chr8:126.45-129.02

2.572

WES and WGS

1.79E−10

Y

Y

Y

Y

Y

8q24.3

chr8:141.9-146.36

4.464

WES and WGS

1.19E−03

     

9p13.3

chr9:35.4-35.97

0.571

WES

5.60E−06

Y

   

Y

9q33.3

chr9:124.98-141.21

16.234

WES

6.22E−03

    

Y

10p11.22

chr10:31.61-33.62

2.015

WES

9.75E−02

     

11p11.2

chr11:46.1-47.18

1.076

WES

1.30E−06

    

Y

11q13.3

chr11:68.86-69.63

0.775

WES

5.25E−16

Y

Y

 

Y

Y

11q14.1

chr11:77.73-77.88

0.157

WES

8.70E−05

    

Y

12p13.31

chr12:9.63-9.72

0.082

WES

7.09E−03

     

12p12.1

chr12:25.34-25.67

0.328

WES and WGS

2.63E−32

Y

Y

 

Y

Y

12q13.3

chr12:56.14-57.32

1.181

WES

8.56E−02

     

12q15

chr12:67.07-70.19

3.116

WES

3.88E−02

Y

Y

 

Y

Y

13q13.2

chr13:33.28-35.25

1.972

WES

8.76E−04

Y

    

13q14.11

chr13:39.36-43.16

3.798

WES

1.99E−02

Y

    

13q14.13

chr13:44.73-46.64

1.906

WGS

7.11E−02

     

13q22.1

chr13:72.13-78.67

6.54

WGS

5.39E−02

 

Y

 

Y

Y

15q26.1

chr15:90.03-91.79

1.765

WES

4.45E−03

  

Y

 

Y

16p13.13

chr16:11.37-12.01

0.64

WES

3.88E−02

     

17q12

chr17:37.83-37.9

0.072

WES

1.04E−24

Y

Y

Y

Y

Y

17q21.2

chr17:38.82-39.02

0.2

WES and WGS

4.35E−02

Y

    

17q21.2

chr17:39.85-39.99

0.146

WES and WGS

1.90E−08

Y

    

17q21.33

chr17:48.68-49.12

0.442

WGS

9.71E−02

     

17q25.3

chr17:68.13-81.20

13.067

WES

5.04E−02

     

18p11.21

chr18:12.25-13.44

1.184

WES

9.23E−03

     

18q11.2

chr18:19.75-20.52

0.766

WES

5.94E−11

Y

Y

Y

 

Y

19q12

chr19:30.19-30.48

0.282

WES

6.69E−15

Y

Y

Y

Y

Y

20q13.12

chr20:42.98-43.56

0.584

WES and WGS

8.36E−02

  

Y

  

20q13.2

chr20:47.90-52.77

4.877

WES

1.00E−02

 

Y

Y

  

20q13.33

chr20:58.42-58.51

0.099

WES

1.75E−03

  

Y

  

22q11.23

chr22:24.39-24.41

0.016

WGS

7.11E−02

     

Xp11.1

chrX:58.52-58.53

0.014

WGS

8.53E−02

 

Y

   

Xq28

chrX:152.11-153.91

1.793

WES

5.53E−04

    

Y

  1. A region may span multiple cytobands, in which case the longest one was listed. The regions were verified by checking if they were identified in any of the five previous microarray-based studies
  2. D Dulak et al. 2012 [14], F Frankel et al. 2014 [16], P Paulson et al. 2009 [13], B Beroukhim et al. 2010 [3], Z Zack et al. 2013 [4], Y indicates a region was identified in a study