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Table 2 Significant cancer germline copy number variable regions

From: Identification of rare germline copy number variations over-represented in five human cancer types

Cancer

Chr

Start

Size

Freq (control)

Freq (case)

Type

OR

P-value a

P-value (PCA) b

Gene(s) c

BRCA

11

51185363

8472

0%

1.49%

Loss

-

1.08E-05

9.66E-01

 

BRCA

3

62936471

30079

0.07%

1.79%

Loss

26.85

2.54E-05

1.05E-04

 

BRCA

3

26586501

3489

0.17%

2.08%

Loss

12.56

5.47E-05

3.44E-06

 

COAD

3

107601890

16832

0.03%

2.34%

Loss

70.78

1.02E-07

4.90E-05

 

COAD

10

101261779

22068

0%

1.46%

Loss

-

1.20E-06

9.63E-01

NKX2-3

COAD

4

156797864

71044

0.24%

2.34%

Loss

10.09

4.13E-05

9.20E-06

GUCY1A3

COAD

7

29635116

120414

0.03%

1.46%

Gain

43.84

6.41E-05

6.13E-04

DPY19L2P3, LOC100271874, LOC646762

GBM

14

21685305

117313

0.30%

5.41%

Loss

18.74

5.54E-13

6.54E-12

TRA@, TRD

GBM

5

57361784

7507

16.50%

33.00%

Loss

2.5

1.54E-12

2.52E-20

 

GBM

22

47288391

152640

0.07%

2.85%

Loss

43.31

8.76E-09

6.97E-06

FAM19A5

GBM

7

38257218

88038

0.84%

5.41%

Loss

6.71

2.25E-08

1.24E-09

TARP

GBM

5

10927644

15240

0%

1.99%

Loss

-

1.44E-07

9.60E-01

 

GBM

14

21804698

2132

0.10%

2.28%

Loss

22.96

1.85E-06

1.42E-05

TRA@, TRD

GBM

14

21681152

2379

0.20%

2.56%

Loss

12.94

4.34E-06

6.42E-06

TRA@, TRD

GBM

10

42882051

56351

0.30%

2.56%

Loss

8.62

3.15E-05

3.75E-06

RET

GBM

7

61793773

26492

1.56%

5.13%

Loss

3.42

6.89E-05

5.00E-07

 

KIRC

14

21681152

2379

0.20%

5.41%

Loss

28.1

6.44E-15

3.49E-12

TRA@, TRD

KIRC

10

96855083

4614

0.07%

3.24%

Loss

49.51

2.26E-10

1.23E-07

 

KIRC

3

89250592

142689

0%

1.62%

Gain

-

1.83E-06

9.63E-01

EPHA3

KIRC

2

97429511

99111

2.17%

7.03%

Loss

3.42

2.33E-06

1.26E-08

ANKRD36B

KIRC

6

118470482

5095

0.24%

2.43%

Loss

10.5

1.33E-05

3.52E-06

SLC35F1

KIRC

17

34990311

173216

0.64%

3.51%

Gain

5.63

1.56E-05

1.54E-05

C17orf37, ERBB2, GRB7, NEUROD2, PGAP3, PNMT, PPP1R1B, STARD3, TCAP

KIRC

4

103363913

68353

0.10%

1.89%

Loss

18.99

1.78E-05

4.83E-05

SLC39A8

KIRC

2

91049141

1293

0.58%

3.24%

Loss

5.79

2.68E-05

3.67E-06

 

KIRC

4

2281

109282

3.45%

8.38%

Gain

2.56

5.16E-05

2.94E-06

ZNF595, ZNF718

KIRC

7

19542080

79082

0.04%

1.35%

Loss

40.48

9.06E-05

6.47E-04

 

KIRC

12

130123182

31743

0.04%

1.35%

Loss

40.48

9.06E-05

1.11E-03

GPR133

OV

13

54589383

6308

0.07%

2.37%

Loss

35.83

1.32E-07

1.13E-05

 

OV

4

36584413

19612

0.03%

2.11%

Loss

63.55

2.15E-07

1.52E-04

 

OV

1

244904225

32016

0%

1.84%

Gain

-

2.37E-07

9.60E-01

 

OV

10

66977929

15004

4.57%

11.60%

Gain

2.74

3.29E-07

3.64E-11

 

OV

2

192993

16566

0%

1.58%

Gain

-

2.11E-06

9.63E-01

SH3YL1

OV

1

229982231

47730

0%

1.58%

Gain

-

2.11E-06

9.63E-01

DISC1, DISC2, TSNAX-DISC1

OV

2

7529134

41988

0%

1.58%

Gain

-

2.11E-06

9.63E-01

 

OV

10

495985

75956

0%

1.32%

Gain

-

1.87E-05

9.47E-01

DIP2C

OV

5

174076632

49822

0%

1.32%

Gain

-

1.87E-05

9.47E-01

MSX2

OV

18

48381779

37120

0%

1.32%

Gain

-

1.87E-05

9.48E-01

DCC

OV

18

45329306

46009

0%

1.32%

Gain

-

1.87E-05

9.47E-01

LIPG

OV

4

172611459

3050

4.63%

10.00%

Loss

2.29

6.75E-05

1.95E-09

 
  1. aThe P-value is based on two-tailed Fisher’s exact test comparing gain and loss frequency in cases versus controls using a threshold of 10−4. bThe significance estimated in a regression analysis using the first component of principal component analysis as covariates. cOverlapping genes with CNVRs (in either case or control) were determined using Refseq as the annotation source.
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Molecular Cancer

ISSN: 1476-4598