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Table 2 LOH by copy number in ESCC cases by chromosomal arm (N = 30 cases)

From: Genome wide analysis of DNA copy number neutral loss of heterozygosity (CNNLOH) and its relation to gene expression in esophageal squamous cell carcinoma

Chromosomal arm

Total no. informative SNPs with LOH

No. informative SNPs with LOH and CN = 1 (fraction)

No. informative SNPs with LOH and CN = 2 (fraction)

No. informative SNPs with LOH and CN = 3 or 4 (fraction)

1p

10,576

2,930 (0.28)

6,522 (0.62)

1,124 (0.11)

1q

8,366

459 (0.05)

7,674 (0.92)

233 (0.03)

2p

11,321

371 (0.03)

10,770 (0.95)

180 (0.02)

2q

23,115

3,015 (0.13)

18,939 (0.82)

1,161 (0.05)

3p

27,593

15,335 (0.56)

12,064 (0.44)

194 (0.01)

3q

7,256

41 (0.01)

4,168 (0.57)

3,047 (0.42)

4p

12,223

4,771 (0.39)

7,452 (0.61)

0 (0)

4q

28,105

9,142 (0.33)

17,905 (0.64)

1,958 (0.04)

5p

1,315

0 (0)

1,259 (0.96)

56 (0.04)

5q

16,537

7,744 (0.47)

8,777 (0.53)

16 (0)

6p

5,622

342 (0.06)

4,870 (0.87)

410 (0.07)

6q

3,365

165 (0.05)

2,773 (0.82)

427 (0.13)

7p

7,389

9 (0)

5,491 (0.74)

1,889 (0.26)

7q

8,001

151 (0.02)

6,452 (0.74)

1,398 (0.17)

8p

8,803

1,580 (0.18)

6,234 (0.71)

989 (0.11)

8q

17,321

47 (0)

4,633 (0.27)

12,641 (0.74)

9p

18,292

2,772 (0.15)

13,333 (0.73)

2,187 (0.12)

9q

31,400

1,965 (0.06)

27,212 (0.87)

2,223 (0.07)

10p

2,739

472 (0.17)

2,063 (0.75)

204 (0.07)

10q

14,651

1,728 (0.12)

12,075 (0.82)

848 (0.06)

11p

9,391

2,367 (0.25)

6,902 (0.73)

122 (0.01)

11q

17,377

5,116 (0.29)

10,422 (0.60)

1,839 (0.11)

12p

5,229

156 (0.03)

3,251 (0.62)

1,822 (0.34)

12q

6,794

67 (0.01)

5,980 (0.88)

747 (0.11)

13q

35,648

5,897 (0.17)

25,964 (0.73)

3,787 (0.11)

14q

10,931

1,484 (0.14)

7,446 (0.68)

2,001 (0.18)

15q

10,194

685 (0.07)

8,313 (0.82)

1,196 (0.12)

16p

1,395

111 (0.08)

1,284 (0.92)

0 (0)

16q

3,127

1 (0)

2,832 (0.91)

294 (0.09)

17p

7,719

324 (0.04)

6,939 (0.90)

456 (0.06)

17q

16,328

38 (0)

14,754 (0.90)

1,536 (0.09)

18p

2,596

488 (0.19)

1,147 (0.44)

961 (0.37)

18q

9,978

3,108 (0.31)

6,838 (0.69)

32 (0)

19p

1,069

1 (0)

1,065 (1.00)

3 (0)

19q

3,505

932 (0.27)

2,482 (0.71)

91 (0.03)

20p

1,278

0 (0)

229 (0.18)

1,049 (0.82)

20q

1,773

60 (0.03)

1,677 (0.95)

36 (0.02)

21q

9,444

3,825 (0.41)

5,599 (0.59)

20 (0)

22q

4,177

621 (0.15)

3,274 (0.80)

222 (0.05)

Range (fraction SNPs with LOH)

0-0.56

0.18-1.00

0-0.82

Median (fraction SNPs with LOH)

0.05

0.71

0.05

Global average (fraction SNPs with LOH)

0.19

0.70

0.11