Table 3. Overview of TP53 aberrations and MDM2 amplification identified in the 25 osteosarcoma tumors.
| Gene/Sample | Type of aberration | Position | Consequence | Aberr. allele frequency | WT allele frequency |
|---|---|---|---|---|---|
| TP53 | |||||
| PD7507a | Del (7.5 Mb) | Intron 9 | TSS-exon i9 deleted | 40% | 20% |
| Trans | Intron 9 | Loss of exon i9-3′UTR | 40% | ||
| PD7513a | Trans | Intron 1 | Loss of exon2-3′UTR | 40% | 25% |
| Trans | Intron 1 | Loss of TSS and exon1 | 35% | ||
| PD7194a | Inv (50.3 Mb) | Intron 1 | Loss of exon2-3′UTR | 40% | 30% |
| Trans | 1.8 Mb upstream TP53 TSS | Gene loss (unbalanced translocation) | 30% | ||
| PD7197a | Small del (10 bp) | Exon5/intron5 | Splice site disruption | 55% | 45% |
| PD13491a | Del (416kb) | 364 kb upstream - 31 kb downstream TP53 3′ UTR | Gene loss | 70% | 30% |
| PD13492a | Trans | Intron 1 | Loss of exon2-3′UTR | 55% | 15% |
| Trans | Intron 1 | Loss of TSS and exon1 | 30% | ||
| PD13493a | Del (72 kb) | 50 kb upstream - 3 kb downstream TP53 | Gene loss | 60% | 40% |
| PD13496a | Trans | 76 kb downstream TP53 | Gene loss | 50% | 30% |
| Trans | 2 kb upstream TP53 | Gene loss | 20% | ||
| PD7193 | Del (93 kb) | Intron 1 | Loss of exon2-3′UTR | 40% | 30% |
| Trans | Intron 1 | Loss of exon2-3′UTR | 30% | ||
| PD13485a | Del (9 kb) | Intron 9 | Loss of exon i9-3′UTR | 20% | 80% |
| PD13486a | Trans | Intron 1 | Loss of exon2-3′UTR | 75% | 25% |
| PD13484a | SNV | c.843C>A | p.D281E | 32% | 68% |
| PD13487a | SNV | c.713G>T | p.C238F | 82% | 18% |
| PD13488a | SNV | c.764T>C | p.I255T | 62% | 38% |
| PD7196a | SNV | c.818G>T | p.R273L | 47% | 53% |
| PD13490a | SNV | c.824G>A | p.C275Y | 72% | 28% |
| MDM2 | |||||
| PD7508a | High level Ampl | chr12 q15 | Total CN of 20 | - | 10 fold increased |
| PD7510a | High level Ampl | chr12 q15 | Total CN of 60 | - | 30 fold increased |
(WT= wild-type, Aberr= aberrant, Ampl= amplification, Del= deletion, Trans= translocation, Inv= inversion, SNV= single nucleotide variation, CN= copy number)