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Table 1.

Details ot DNA copy number alterations in MPNST samples

SI. NoSampleGradeDeleted genesAmplified genes
1 M-1 Intermediate FABP7, HMMR, HSPCA, MMP13, NF1,p16-INK4a,* BIRC5, CCNE2, CMA1, CCND1, EGFR, FLT4, HGF, ITGB4, MET, MMP9, PDGFRA, SPP1, TERT, TP73, TSC2 
2 M-2 High HMMR, NF1, p16-INK4a* CCNE2, HGF, ITGB4, MET, MMP9, PDGFRA, SPP1, TERT, TP73 
3 M-3 Unknown HMMR, L1CAM2 CCND1, RASSF2 
4 M-4 Intermediate FABP7, HMMR, L1CAM2, MMP13, NF1, p16-INK4a BIRC5, CCNE2, CMA1, EGFR, HGF, ITGB4, MET, PDGFRA, SPP1, TERT, TP73 
5 M-5 Intermediate HGF, HMMR, MET, NF1,OSF2, p16-INK4a, RASSF2, RB1, TNFRSF10A TP53 EGFR  
6 M-6 Unknown FABP7, L1CAM2, MKi-67, mTOR, NF1, p16-INK4a*, PTCH2, PTEN, RASSF2, TIMP4 BIRC5 
7 M-7 High HGF, HMMR HSPCA, L1CAM2, MET, NF1, OSF2, p16-INK4a, RASSF2, RB1 EGFR, ITGB4, MMP9 
8 M-8 High HMMR, L1CAM2, MMP13, NF1, PTEN, RB1, TP53 CCNE2, CCND1, EGFR, ERBB3, IL8, PDGFRA, SOX10 
9 M-9 High L1CAM2, NF1, p16-INK4a BIRC5, CCNE2, CCND1, EGFR, FLT4, FOS, FOXA2, HGF, ITGB4, MET, PDGFRA, SOX10, TERT, TGFB1, TP73, TSC1 
10 M-10 High L1CAM2, MMP13, mTOR, NF1, OSF2, p16-INK4a, PTCH2, RASSF2, RB1 MDM4, MPZ 
11 M-11 Low NF1,† OSF2, RB1, TOP2A CDKN1A, CCND1, FLT4, FOXA2, Gl1, ITGB4, SOX10, TERT, TGFB1, TP73, TSC2 
12 M-12 Low — — 
13 M-13 High (Triton) HMMR, MMP13, mTOR, NF1, OSF2, p16-INK4a, PTCH2, RB1, TP53 CCNE2, SOX10, TOP2A 
14 M-14 Unknown FABP7, HMMR, HSPCA, Mki-67, MMP13, NF1,‡ p16-INK4a, PTEN, TP53 BIRC5, CCND1, EGFR, ITGB4, TERT, TOP2A 
15 M-15 Low — mTOR 
16 M-16 High MMP13, NF1 BIRC5, ITGB4, MPZ, RASSF2, TSC2 
17 M-17 Low NF1,† TOP2A FOXA2 
18 M-18 High — BIRC5, CCNE2, HGF, MET, PDGFRA 
19 M-19 High NF1 CCND1, ITGB4, MMP9, PTCH2, SOX10, TERT, TP73, TSC2 
20 M-20 High EPHA7, FN1, HMMR, Mki-67, MMP13, NF1, P16-INK4a, RB1 BIRC5, ITGB4, TERT 
21 M-21 High Mki-67, mTOR, NF1, PTEN, SPP1 HGF, MDM4, MET, MPZ, PDGFRA 
22 M-22 High FABP7, EPHA7, MKi-67, MMP13, RASSF2 TOP2A 
23 M-23 High HMMR, MMP13, NF1, RASSF2, TP53 — 
24 M-24 High — — 
25 M-25 High HMMR, HSPCA, Mki-67, MMP13, NF1, SPP1 — 
26 M-26 High HMMR, HSPCA, L1CAM2, MMP13, NF1, RASSF2 mTOR 
27 M-27 High L1CAM2,† RASSF2, RB — 
28 M-28 High — — 
29 M-29 Unknown — — 
30 M-30 Unknown MMP13, NF1, RASSF2, TP53 BIRC5, CCNE2, CCND1, EGFR, FLT4, FOXA2, HGF, HSPCA, ITGB4, MDM4, MET, MTOR, PDGFRA, S100B, TERT, TOP2A, TP73 
31 M-31 Unknown FABP7, HMMR, MMP13, NF1, OSF2, p16-INK4a, RB1 CDKN1B/p27, FLT4, FOXM1, RASSF2 
32 M-32 Unknown FN1, NF1, p16-INK4a, TOP2A BIRC5, CCND1, ITGB4 
33 M-33 Unknown HMMR, L1CAM2, SPP1 ITGB4 
34 M-34 Unknown FABP7, EPHA7, MMP13, p16-INK4a, RB1, TNFRSF10A, TNFRSF10B FLT4, L1CAM2, SOX10 
35 M-35 Unknown CCNE2, HMMR, HSPCA† OSF2 
SI. NoSampleGradeDeleted genesAmplified genes
1 M-1 Intermediate FABP7, HMMR, HSPCA, MMP13, NF1,p16-INK4a,* BIRC5, CCNE2, CMA1, CCND1, EGFR, FLT4, HGF, ITGB4, MET, MMP9, PDGFRA, SPP1, TERT, TP73, TSC2 
2 M-2 High HMMR, NF1, p16-INK4a* CCNE2, HGF, ITGB4, MET, MMP9, PDGFRA, SPP1, TERT, TP73 
3 M-3 Unknown HMMR, L1CAM2 CCND1, RASSF2 
4 M-4 Intermediate FABP7, HMMR, L1CAM2, MMP13, NF1, p16-INK4a BIRC5, CCNE2, CMA1, EGFR, HGF, ITGB4, MET, PDGFRA, SPP1, TERT, TP73 
5 M-5 Intermediate HGF, HMMR, MET, NF1,OSF2, p16-INK4a, RASSF2, RB1, TNFRSF10A TP53 EGFR  
6 M-6 Unknown FABP7, L1CAM2, MKi-67, mTOR, NF1, p16-INK4a*, PTCH2, PTEN, RASSF2, TIMP4 BIRC5 
7 M-7 High HGF, HMMR HSPCA, L1CAM2, MET, NF1, OSF2, p16-INK4a, RASSF2, RB1 EGFR, ITGB4, MMP9 
8 M-8 High HMMR, L1CAM2, MMP13, NF1, PTEN, RB1, TP53 CCNE2, CCND1, EGFR, ERBB3, IL8, PDGFRA, SOX10 
9 M-9 High L1CAM2, NF1, p16-INK4a BIRC5, CCNE2, CCND1, EGFR, FLT4, FOS, FOXA2, HGF, ITGB4, MET, PDGFRA, SOX10, TERT, TGFB1, TP73, TSC1 
10 M-10 High L1CAM2, MMP13, mTOR, NF1, OSF2, p16-INK4a, PTCH2, RASSF2, RB1 MDM4, MPZ 
11 M-11 Low NF1,† OSF2, RB1, TOP2A CDKN1A, CCND1, FLT4, FOXA2, Gl1, ITGB4, SOX10, TERT, TGFB1, TP73, TSC2 
12 M-12 Low — — 
13 M-13 High (Triton) HMMR, MMP13, mTOR, NF1, OSF2, p16-INK4a, PTCH2, RB1, TP53 CCNE2, SOX10, TOP2A 
14 M-14 Unknown FABP7, HMMR, HSPCA, Mki-67, MMP13, NF1,‡ p16-INK4a, PTEN, TP53 BIRC5, CCND1, EGFR, ITGB4, TERT, TOP2A 
15 M-15 Low — mTOR 
16 M-16 High MMP13, NF1 BIRC5, ITGB4, MPZ, RASSF2, TSC2 
17 M-17 Low NF1,† TOP2A FOXA2 
18 M-18 High — BIRC5, CCNE2, HGF, MET, PDGFRA 
19 M-19 High NF1 CCND1, ITGB4, MMP9, PTCH2, SOX10, TERT, TP73, TSC2 
20 M-20 High EPHA7, FN1, HMMR, Mki-67, MMP13, NF1, P16-INK4a, RB1 BIRC5, ITGB4, TERT 
21 M-21 High Mki-67, mTOR, NF1, PTEN, SPP1 HGF, MDM4, MET, MPZ, PDGFRA 
22 M-22 High FABP7, EPHA7, MKi-67, MMP13, RASSF2 TOP2A 
23 M-23 High HMMR, MMP13, NF1, RASSF2, TP53 — 
24 M-24 High — — 
25 M-25 High HMMR, HSPCA, Mki-67, MMP13, NF1, SPP1 — 
26 M-26 High HMMR, HSPCA, L1CAM2, MMP13, NF1, RASSF2 mTOR 
27 M-27 High L1CAM2,† RASSF2, RB — 
28 M-28 High — — 
29 M-29 Unknown — — 
30 M-30 Unknown MMP13, NF1, RASSF2, TP53 BIRC5, CCNE2, CCND1, EGFR, FLT4, FOXA2, HGF, HSPCA, ITGB4, MDM4, MET, MTOR, PDGFRA, S100B, TERT, TOP2A, TP73 
31 M-31 Unknown FABP7, HMMR, MMP13, NF1, OSF2, p16-INK4a, RB1 CDKN1B/p27, FLT4, FOXM1, RASSF2 
32 M-32 Unknown FN1, NF1, p16-INK4a, TOP2A BIRC5, CCND1, ITGB4 
33 M-33 Unknown HMMR, L1CAM2, SPP1 ITGB4 
34 M-34 Unknown FABP7, EPHA7, MMP13, p16-INK4a, RB1, TNFRSF10A, TNFRSF10B FLT4, L1CAM2, SOX10 
35 M-35 Unknown CCNE2, HMMR, HSPCA† OSF2 
*

Homozygous deletion.

†

Partial deletion of the gene.

‡

Partial homozygous deletion.

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