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Table 1 I-FISH, MLPA and SNP array findings for three lesions of case no. 1

From: Primary and recurrent diffuse astrocytomas: genomic profile comparison reveals acquisition of biologically relevant aberrations

 

MLPA

MS-MLPA

I-FISH result

SNP array result

Treatment

Gene

Location

Result

Gene

Result

   

First resection - geminocystal astrocytoma

IDH1

2q33.3

R132H

MSH2

normal

deletion of 19q

amplification of 13q

3p26.3p11.1(4,367,515-90,526,515)x1,

3q28q29(195,706,944-195,724,476)x1,

7p22.3p14.1(141,332-43,215,151)x2hmz,

12q12qq22(40,031,350-93,333,050)x1,

12q23.1q23.2(109,796,312-111,857,062)x1,

13q14.3(51,016,936-54,208,554)x1,

13q21.33q34(68,955,942-115,106,996)x3,

19q13.2q13.43(41,004,075-58,610,254)x1

NO

CRBN

3p26.3

del

CRELD1

3p25.3

del

VHL

3p25.3

del

MSH6

normal

PPARG

3p25.1

del

RAF1

3p25.1

del

HESX1

3p14.3

del

MLH1

normal

LFNG

7p22.2

normal

FKBP9

7p14.3

normal

GLI3

7p14.1

normal

MSH3

normal

ADAM22

7q21.12

normal

TFR2

7q22.1

normal

KIAA1549

7q34

normal

PMS2

normal

HIPK2

7q34

normal

MKRN1

7q34

normal

BRAF

7q34

normal

MGMT

normal

DPP6

7q36.2

normal

MIR31

9p21.3

normal

CDKN2A

9p21.3

normal

MLH3

normal

CDKN2B

9p21.3

normal

IDH2

15q26.1

normal

Second resection - diffuse astrocytoma

IDH1

2q33.3

R132H

MSH2

normal

deletion of 19q amplification of 13q

3p26.3p11.1(4,367,515-90,526,515)x1,

3q28q29(195,706,944-195,724,476)x1,

7p22.3p14.1(141,332-43,215,151) x2hmz,

9q34.11q34.3(131,306,847-138,275,572)x3,

10p15.3(135,708-1,639,362)x3,

12q12qq22(40,031,350-93,333,050)x1,

12q23.1q23.2(109,796,312-111,857,062)x1,

13q14.3(51,016,936-54,208,554)x1,

13q21.2q21.3 (61,757,866-62,558,596)x3,

13q21.31(62,603,583-62,702,893)x1,

13q21.31q21.33 (63,341,681-70,114,200)x1,

13q21.33q34 (68,955,942-115,106,996)x3,

19q13.2q13.43(41,004,075-58,610,254)x1

NO

CRBN

3p26.3

del

CRELD1

3p25.3

del

VHL

3p25.3

del

MSH6

normal

PPARG

3p25.1

del

RAF1

3p25.1

del

HESX1

3p14.3

del

MLH1

normal

LFNG

7p22.2

normal

FKBP9

7p14.3

normal

GLI3

7p14.1

normal

MSH3

normal

ADAM22

7q21.12

normal

TFR2

7q22.1

normal

KIAA1549

7q34

normal

PMS2

normal

HIPK2

7q34

normal

MKRN1

7q34

normal

BRAF

7q34

normal

MGMT

methylated (51 %)

DPP6

7q36.2

normal

MIR31

9p21.3

normal

CDKN2A

9p21.3

normal

MLH3

normal

CDKN2B

9p21.3

normal

IDH2

15q26.1

normal

Third resection - anaplastic astrocytoma

IDH1

2q33.3

R132H

MSH2

normal

deletion of 19q

amplification of 13q

trisomy 7

3p26.3p11.1(4,367,515-90,526,515)x1,

3q28q29(195,706,944-195,724,476)x1,

7p22.3p14.1(141,332-43,215,151) x2hmz,

8q11.1q22.3 (48,043,253-106,052,343)x1,

9q34.11q34.3(131,306,847-138,275,572)x3,

10p15.3 (135,708-1,639,362)x3,

10q22.3q23.1(81,643,451-84,775,286)x1,

12q12qq22 (40,031,350-93,333,050)x1,

12q23.1q23.2(109,796,312-111,857,062)x1,

13q14.3 (51,016,936-54,208,554)x1,

13q21.2q21.3 (61,757,866-62,558,596)x3,

13q21.31 (62,603,583-62,702,893)x1,

13q21.31q21.33(63,341,681-70,114,200)x1,

13q21.33q34(68,955,942-115,106,996)x3,

19q13.2q13.43(41,004,075-58,610,254)x1

Chemotherapy

CRBN

3p26.3

del

CRELD1

3p25.3

del

VHL

3p25.3

del

MSH6

normal

PPARG

3p25.1

del

RAF1

3p25.1

del

HESX1

3p14.3

del

MLH1

normal

LFNG

7p22.2

normal

FKBP9

7p14.3

normal

GLI3

7p14.1

normal

MSH3

normal

ADAM22

7q21.12

normal

TFR2

7q22.1

normal

KIAA1549

7q34

normal

PMS2

normal

HIPK2

7q34

normal

MKRN1

7q34

normal

BRAF

7q34

normal

MGMT

methylated (51 %)

DPP6

7q36.2

normal

MIR31

9p21.3

normal

CDKN2A

9p21.3

normal

MLH3

normal

CDKN2B

9p21.3

normal

IDH2

15q26.1

normal

  1. The pathogenetic findings for MLPA, MS-MLPA are marked with bold type. Abbreviation del means deleted. The SNP array results for each resection are notated according to the latest version of the International System of Human Cytogenetic Nomenclature (ISCN 2013) [17]. Findings described for first resection were found in all following samples therefore additional changes detected only in subsequent lesions are marked with bold type