Skip to main content

Table 2 Minimal Common Regions differentiating responders from non-responders to radiation therapy and first-line chemotherapy

From: An ANOCEF genomic and transcriptomic microarray study of the response to radiotherapy or to alkylating first-line chemotherapy in glioblastoma patients

Event

Chr

Treatment

Differentially expressed genes located in the MCR

  

Radiation therapy

 
  

% in NR

% in R

p-value

 

Loss

5p15.3

0

33

0.04

 

Loss

5p15.2-3

0

29

0.01

CMBL (FC = 1.3)

Gain

17q24-25

22

0

0.02

TANC2 (FC = 1.1), DCAF7 (FC = 1.2), LRRC37A (FC = 1.3), PITPNC1 (FC = 1.6)

  

Chemotherapy

 
  

% in NR

% in R

p-value

 

Amp.

7p11.2

0.35

0.81

0.02

 

Del.

9p21.3

0

0.82

< 10-4

MTAP (FC = 2), CDKN2A (FC = 2.6)

Loss

9p24

0.12

0.64

0.01

 

Loss

9p24

0.12

0.64

0.01

KIAA1432 (FC = 1.4), KDM4C (FC = 1.2)

Loss

9p24;p23;p22

0.12

0.64

0.01

ZDHHC21 (FC = 1.6)

Gain

11p15

0.18

0.64

0.02

PGAP2 (FC = 0.8)

Gain

11q13

0.18

0.91

0.0003

C11orf68 (FC = 0.8), B3GNT1 (FC = 0.75), RAB1B (FC = 0.86)

Gain

17p13

0.18

0.64

0.02

CRK (FC = 0.83), INPP5K (FC = 0.88), TSR1 (FC = 0.87), METT10 D (FC = 0.77), SGSM2(FC = 0.75)

Gain

17p13

0.18

0.64

0.02

METT10 D (FC = 0.77)

Gain

19p13.3

0.35

0.91

0.006

PPAP2C (FC = 0.74), SHC2 (FC = 0.8), MOBKL2A (FC = 0.81), SCAMP4 (FC = 0.8), BTBD2 (FC = 0.8), FAM108A1 (0.86), SF3A2 (FC = 0.74), AP3D1 (0.77), GNG7 (0.46), ZNF555 (0.82), DOHH (0.82), C19orf29 (0.8), NFIC (0.75)

Gain

19p13.3;p13.2;p13.1

0.29

0.91

0.002

SLC25A23 (0.6), CLEC4 M (0.85), ZNF846 (0.7), OLFM2 (0.6), S1PR2 (0.8), DHPS (0.85), TNPO2 (0.76), ZNF791 (0.77)

Gain

19p13.1

0.29

0.91

0.002

EPS15L1 (0.83), OCEL1 (0.85), TMEM161A (0.82), NCAN (0.3)

Gain

19p12

0.29

0.91

0.002

 

Gain

19p12;p11

0.29

0.91

0.002

 

Gain

19q11;q12

0.29

0.82

0.002

FXYD3 (0.84)

Gain

19q12;

q13.1

0.35

0.91

0.006

FAM98C (0.77)

Gain

20p13

0.12

0.82

0.0004

ZCCHC3 (0.81), SOX12 (0.84), RBCK1 (0.8), CSNK2A1 (0.81), MAVS (0.8), ATRN (0.76)

Gain

20p12.3;

p11.2

0.18

0.64

0.002

RRBP1 (0.73)

Gain

20p11.2

0.12

0.64

0.003

 

Gain

20p11.2;

p11.1;

q11.1;q11.2

0.24

0.73

0.02

CST8 (0.87)

Gain

20q11.2

0.24

0.82

0.006

PLUNC (0.88), CHMP4B (0.83)

Gain

20q11.2

0.24

0.82

0.006

CHMP4B (0.83), LOC647979 (0.67)

Gain

20q11.2;q12

0.18

0.73

0.006

SNHG11 (0.75)

Gain

20q13.1

0.18

0.73

0.006

SLC13A3 (0.81)

Gain

20q13.1

0.24

0.73

0.02

PREX1 (0.72)

Gain

20q13.3

0.24

0.73

0.02

CDH4 (0.5), OSBPL2 (0.82)

  1. Chr= chromosome, NR= Non-responder, R= Responder, % = Frequency of the event, FC= Fold change in NR versus R, Amp. = Amplification, Del. = Homozygous deletion
  2. Recurrent alterations were defined for the entire population of samples if the identical alteration was present in at least two samples. Computation of recurrent minimal genomic alterations was done in a similar way to a method previously described using original R code [19]. Comparison of the genomic profiles of responders (n = 21) and non-responders (n = 18) demonstrated that three Minimal Common Regions (MCRs) were significantly different between the two groups (Fisher's exact test p-value <0.05). Comparison of the genomic profiles of responders (n = 11) versus non-responders (n = 17) to first-line chemotherapy demonstrated substantial genomic differences, with twenty-four MCRs being significantly (p < 0.05) associated with the chemotherapy response. Differentially expressed genes with a p-value <0.05 and located in the MCR are shown with their corresponding fold changes.