Table 2.

Array comparative genomic hybridization analysis of primary MPNSTs

Reference	# MPNSTs (NF1, non-NF1)	Findings
22	31 (9,22)	Two NF1 high-grade tumors had no SCNAs; others: average 11 SCNAs/tumor. Gains more common than losses, and most frequent gains were 8q23-q24.1 (12 cases), 5p14 (11 cases), 6p22-pter, 7p15-p21, 7q32-q35, 8q21.1-q22, 8q24.2-qter, and 17q22-qter (10 cases each). Eight samples (two NF1) had amplifications: 8q24-ter (three cases), and two cases each at 5p14, 7p14-pter, 8q21.1-q23, and 13q32-q33. Most common losses were 14q24.3-qter (five cases), and 1p22-p36.1, 13q21-q31, and 14q21-q24.2 (four cases each). One MPNST recurrence had a novel gain of 1p21-22. Gain of 7p15-p21 or 17q22-qter correlated with poorer survival rate. Chromosome 7 over-represented among abnormalities.
94	19 (6,13)	One MPNST (non-NF1) had no SCNAs; others: average 13 SCNAs/tumor. Gains more common than losses. The only amplifications were in non-NF1 (sporadic) tumors, with 5p and 12q coamplified, and other amplifications unique. Gain of 7p11-p13 and 17q24-q25 in 52% of cases. Gain of 5p15 in 47% cases. About 42% of cases had gain of 8q22-q24 or 12q21-q24. One sporadic had only 17q25 gain. One sporadic only had gain of 9q34 and 14q31q32. One sporadic only had gains 4p15p16, 5p15, 9q31q33, 12q14q22, 12q24.3, 14q31q32, and 21q22. Gains of 1q31-q32, 7q11-q31, and 9q32-q33 were each in 37% of tumors.
95	12 (8,4)	All had at least some SCNAs. Losses included 3p21-pter (2), 9p23-pter (4), chrom.10 (4), 11q23-qter (6), chromosome 16 or16q24 (4), chromosome 17 (2), and chromosome 22 or 22q (10). Gains included chromosome 7 or 7q (3) and chromosome 8 or 8q (2). No obvious differences between NF1 and non-NF1.
96	8 (5,3)	All had at least some SCNAs. No clear differences between NF1 and non-NF1. Most had amplifications, and had more gains than losses. Average 17 SCNAs/tumor. No losses common to more than two tumors except 16q12-22 in three. Gains: 4q26 and 6q (7 each), 4q12-q26, 11q14, 15q21, 21q21 (6 each), and 5p14, 5q21, 11q14-q22, 12q21, 14q21 (5 each). One had loss of chromosome 22. Specific gains found at genes EGFR, MSH2, CDK6, DDX15; specific losses were at genes CDH1, EGR1, CTSB, GATA3.
21	7 (4,3)	One case had no SCNAs except gain of 8q. Most frequent minimal recurrent gains: 1q24.1-q24.2, 1q24.3-q25.1, 8p23.1-p12, 9q34.11-q34.13, and 17q23.2-q25.3, in 5/7 cases (those five patients had a poor outcome, but not the other two (NF1)). Gains in <4 cases: 2q11.2-q13, 3p26.2-p25.1, 5q34-q35.3, 7q11.23-q21.11, 9q21.32-q22.33, 12q13.3-q15, 13q22.1-q22.2, 16p13.3-p13.2,16p13.12-p13.11, and 19p13.3-p13.2. Losses: four tumors showed loss of 11p13; 11q22.3-q23.1 and 11q23.2-q23.3 were lost in three tumors. Loss of 9p22.3-p21.2 and 14q21.3-q23.3 were observed in three cases (two homozygous and one heterozygous, all with poor survival). Loss of 11q23.2-11q23.3 was seen only in the three sporadic tumors. A few high-level amplifications were seen, predominantly on 1q and 12q.
19	51 (16,35)	Loss of 9p21.3 (containing CDKN2A/B genes) was seen in 33 cases. EGFR amplification (7q11) was seen in 19 (FISH validated). At least one EGF pathway gene was altered in 84% of samples: EGFR amplification (19), GRB2 amplification (16, at 17q25), HRAS deletion (17, at 11p15), MAPK1 deletion (21, at 22q11), AKT1 deletion (16, at 14q32), JAK2 deletion (24, at 9p24). No correlations with survival.
97	2 (0,2)	Gain regions common to both: 4q28-qter, 8q12-q21.1. One had multiple other gains but no losses; the other also had gain of 17q22-qter and loss of 4p14-pter.
32	48 (28,20)	Chromosomal and array CGH were used. Four tumors had no SCNAs; the others had median of 18 SCNAs/tumor (median 18 in NF1 tumors, 12 in sporadic tumors). Most frequent gains: 8q (in 30 cases), 17q (29), and 7p (23). Most frequent losses: 9p (30), 11q (21), and 17p (19). Most tumors had similar number of gains and losses, regardless of NF1 status. NF1 tumors more likely to have gains at 6q, 7p, 17q and losses at 4q, 11q, 13q, 18p. Most frequent amplification was 17q24.2-25.3 (in 45%). Six had homozygous deletion at 9p21.3. Worse survival was associated with tumors having gain of 16p, or loss of 10q or loss of Xq.
98	24 (24,0)	Gains more common than losses. Average of 12.8 SCNAs/sample. Gains seen in 15 or more tumors: 7p14, 5q14.1, 7q36.1. Most frequent loss: 9p21.3 in 8 cases. Gains in >9 tumors: 7p14.1-p13, 5q14.1, 7q36.1, 5q32.2, 6p22.3, 1q25.3, 3q13.11, 5q21.3, 5q33.2, 5q11.2, 5q33.3, 5p15.31, 6p21.1, 7q21.3, 5q31.2, 6p21.1, 7q21.3, 5q31.2, 5q32, 6q24.2, 7p22.3-p22.2. Losses common to seven tumors: 1p35.1, 1p33, 10q35.2, 11p11.2, 11q22.1, 11q23.1-q23.2, 20p12.2, 20p12.1
96	5 (3,2)	Average SCNAs was 17.3, samples had more gains than losses. Gains in four to five cases: 2ptel, 2p22.1-p22.3, 4p15.3, 5p13, 7p12.1-p12.3, 7q21-22, 18q11.2. Losses in four to five cases: 5q31.1, 8p22, 10.15, 16q22.1, 16qtel, 17ptel, 19q13.32. No clear differences NF1 vs. non-NF1.
99	5 (3,1,1*)	Gains seen in 2 or 3 MPNSTs: 1p36.11-1p34.2, 2q35-q37.2, 2q37, 12p11.2, 17q24-q25.3, 19p13.2-p13.3, 19p13.12-q12, 20q11.2-q12. Losses seen in two or three MPNSTs: 9p23-24, 13q12.3-q14.3, 16q12.1, 21q21.
100	38 (23,15)	Utilized SNP array to identify SCNAs, and characterized SCNAs were listed by gene names and corresponding cytogenetic bands. Gains in at least 21% of tumors: 8q22.1, 7p11.2, 17q25, 7q21.1, 7q31, 5p15.33, 4q11-q13, 2p25.3, 7p21.1, 8q24.21, 19q12, 12p12.1, 12p13.33, 12q14.1. Losses in at least 18% of tumors: 9p21.3, 17q11.2, 11q22.3, 13q14.2, 3p26.1, 20p12.1-pter, 5q33.2-qter, 9p22.3, 17p13.1, 9p23-24.1, 10q23.31, 22q12.2, 18q21.1. TP53 deletion (in half of cases) was not associated with survival.

*Thought to be a radiation-induced MPNST in person without NF1.