Skip to main content

Table 2 Comparison between the genetic alterations and TMB in the present 39 GBMs and in TGCA (PanCancer Atlas cohort) IDH-wt and IDH-mutant GBMs

From: IDH-wild type glioblastomas featuring at least 30% giant cells are characterized by frequent RB1 and NF1 alterations and hypermutation

 

Present GBMs (n = 39)

TGCA IDH-wt GBMs*

P

TGCA IDH-mutant GBMs**

P

Clinical features

Mean age; age range

57.6 years; 15–84 years

60 years; 10–89 years

0.440

38 years; 21–60 years

0.0001

Male:Female

2:1

1.4:1

 

1.5:1

 

TMB ***

median; range; inter-quartile range

9.3 muts/Mb; 5.4–153.8; 8.2–12

1.7 muts/Mb; 0–230; 1.4–2.2

 < 0.0001

1.4 muts/Mb; 0.6–405; 1.1–2

 < 0.0001

MSI****

2

5.1%

3

1.6%

0.210

0

0

0.512

Genetic alterations

n

%

n

%

 

n

%

 

TP53

29

74.4%

100

27.0%

 < 0.0001

25

96.2%

0.022

PTEN

12

30.8%

187

33.9%

0.686

1

4.2%

 < 0.0001

CDKN2A/B hom del

12

30.8%

318

57.7%

0.0011

4

16.7%

0.215

RB1

10

25.6%

52

9.4%

 < 0.0001

1

4.2%

 < 0.0001

NF1

10

25.6%

45

12.1%

0.0003

1

3.8%

0.0227

EGFR ampl

7

17.9%

255

46.3%

0.0006

0

0.0%

0.0001

CDK4 ampl

5

12.8%

76

13.8%

0.864

6

25.0%

0.219

ATRX

5

12.8%

17

4.6%

0.0301

20

76.9%

 < 0.0001

MSH6

4

10.3%

6

1.6%

0.0009

1

3.8%

0.345

PIK3CA

4

10.3%

35

9.4%

0.867

5

19.2%

0.308

PIK3R1

4

10.3%

34

9.2%

0.823

3

11.5%

0.871

PDGFRAampl

4

10.3%

73

13.2%

0.592

2

8.3%

0.802

MSH2

4

10.3%

0

0.0%

 < 0.0001

1

3.8%

0.345

MDM2 ampl

3

7.7%

47

8.5%

0.856

0

0.0%

0.167

MTOR

3

7.7%

5

1.3%

0.0007

1

3.8%

0.530

KIT ampl

3

7.7%

54

9.8%

0.667

2

8.3%

0.927

KDRampl

3

7.7%

35

6.4%

0.742

2

8.3%

0.0927

SETD2

3

7.7%

9

2.4%

0.0638

2

7.7%

1

MLH1

2

5.1%

1

0.3%

0.0007

0

0.0%

0.244

CREBBP

2

5.1%

6

1.6%

0.132

1

3.8%

0.810

DNMT3A

2

5.1%

2

0.5%

0.0056

1

3.8%

0.810

MET ampl

1

2.6%

14

2.5%

0.992

1

4.2%

0.726

ARID1A

1

2.6%

4

1.1%

0.421

1

3.8%

0.771

TSC1

1

2.6%

3

0.8%

0.289

1

3.8%

0.771

TSC2

1

2.6%

1

0.3%

0.0507

0

0.0%

0.414

EGFR mutation

1

2.6%

91

24.5%

0.0018

3

11.5%

0.143

FGFR3

1

2.6%

2

0.5%

0.158

1

3.8%

0.771

FGFR2

1

2.6%

4

1.1%

0.421

0

0.0%

0.414

ARID2

1

2.6%

1

0.3%

0.0507

1

3.8%

0.771

  1. *371 samples were profiled for mutations and 551 for copy number variations (CNV)
  2. **26 samples were profiled for mutations and 24 for CNV
  3. ***Mutation count was available for 368 IDH-wt and 26 IDH-mutant GBMs in TGCA PanCancer Atlas cohort
  4. ****MSI sensor score was available for 184 IDH-wt and 26 IDH-mutant GBMs in TGCA PanCancer Atlas cohort
  5. genetic alterations are arranged by their frequency in the cohort of giant cells enriched GBMs. The statistical difference in the frequency of each genetic alteration between giant cells enriched GBMs and IDH-wt or IDH-mutant GBMs was assessed using Chi-squared test. The statistical difference in TMB was assessed using Mann–Whitney test
Back to article page

Acta Neuropathologica Communications

ISSN: 2051-5960

Contact us