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Table 2 I-FISH, MLPA and SNP array findings for two lesions of case no. 2

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

  MLPA MS-MLPA I-FISH SNP array Treatment
Gene Location Result Gene Result
First resection - anaplastic astrocytoma IDH1 2q33.3 R132H MSH2 normal deletion of CDKN2A deletion of subtelomeric 16q (X)x1, (2)x2hmz, 3p26.3p11.1(66,894-90,089,238)x2hmz, 4q12q13.1(52,728,324-66,300,425)x1, (5)x1,6p25.3p21.33(204,909-31,335,647)x1, 6q22.33q27(128,989,302-170,898,549)x1, 7p22.3p22.1(46,239-5,016,400) x1, 7q22.1q36.3(98,451,358-159,119,486)x3, 9p24.3p13.1(46,587-38,771,460)x1, 10q21.2q26(61,465,713-135,430,043)x1, 11p15.5p11.2(203,788-47,430,599)x2hmz, 11p11.2 (47,801,101-51,274,692)x1, 12q12q24.33(38,416,139-133,429,634) x2hmz, 13q12.11q14.2(19,888,741-50,144,613)x2hmz, 13q14.2q21.33(50,283,115-69,338,113)cth, 14q11.2q22.2(20,213,937-54,316,607)x2hmz, 14q23.2q32,12(62,420,606-93,152,220)x1, 15q21.1q24.1(46,805,269-74,506,930)x1, (16)x2hmz, 17p13.3p11.2(18,901-20,219,226) x2hmz, 17q25.3(79,894,097-81,047,565)x1, 18q23(76,324,504-78,014,582)x1, 19p13.3 (267,039-1,569,839)x3, (21)x2hmz, (22)x2hmz Chemotherapy
CRBN 3p26.3 normal
CRELD1 3p25.3 normal
VHL 3p25.3 normal MSH6 normal
PPARG 3p25.1 normal
RAF1 3p25.1 normal
HESX1 3p14.3 normal MLH1 normal
LFNG 7p22.2 del
FKBP9 7p14.3 normal
GLI3 7p14.1 normal MSH3 normal
ADAM22 7q21.12 normal
TFR2 7q22.1 normal
KIAA1549 7q34 amp PMS2 normal
HIPK2 7q34 amp
MKRN1 7q34 amp
BRAF 7q34 amp MGMT methylated (19 %)
DPP6 7q36.2 amp
MIR31 9p21.3 del
CDKN2A 9p21.3 del MLH3 normal
CDKN2B 9p21.3 del
IDH2 15q26.1 normal
Second resection - anaplastic astrocytoma IDH1 2q33.3 R132H MSH2 normal deletion of CDKN2A deletion of PTEN (X)x1, 1q41q43(216,318,021-241,388,129) x2hmz, 2q14.2q22.3(120,617,488-144,598,432) x2hmz, 4q12q13.1 (52,728,324-66,300,425)x1, (5)x1,6p25.3p21.33 (204,909-31,335,647)x1, 6q22.33q27(128,989,302-170,898,549)x1, 7p22.3p22.1 (46,239-5,016,400)x1, 7q22.1q36.3(98,451,358-159,119,486)x3, 9p24.3p13.1 (46,587-38,771,460)x1, 10q21.2q26(61,465,713-135,430,043)x1, 11p15.5p11.2 (203,788-47,430,599)x2hmz, 11p11.2(47,801,101-51,274,692)x1, 13q14.2q21.33 (50,283,115-69,338,113)cth, 14q23.2q32,12 (62,420,606-93,152,220)x1, (16)x2hmz, 17p13.3p11.2(18,901-20,219,226)x2hmz, 17q25.3(79,894,097-81,047,565)x1, 18q23(76,324,504-78,014,582)x1, 19p13.3(267,039-1,569,839)x3, (22)x2hmz Chemotherapy
CRBN 3p26.3 normal
CRELD1 3p25.3 normal
VHL 3p25.3 normal MSH6 normal
PPARG 3p25.1 normal
RAF1 3p25.1 normal
HESX1 3p14.3 normal MLH1 normal
LFNG 7p22.2 del
FKBP9 7p14.3 normal
GLI3 7p14.1 normal MSH3 normal
ADAM22 7q21.12 normal
TFR2 7q22.1 normal
KIAA1549 7q34 amp PMS2 normal
HIPK2 7q34 amp
MKRN1 7q34 amp
BRAF 7q34 amp MGMT methylated (25 %)
DPP6 7q36.2 amp
MIR31 9p21.3 del
CDKN2A 9p21.3 del MLH3 methylated
CDKN2B 9p21.3 del
IDH2 15q26.1 normal
  1. The pathogenetic findings for MLPA, MS-MLPA and I-FISH are marked with bold type. Abbreviation del means deleted, amp is amplificated. 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]. Aberrations unique to each resection are marked with bold text