Table 6. Targeted DNA sequencing of additional MGMT-methylated and unmethylated GBMs.
| Gene | hg19 Coord | Base Change (Context)* | Amino Acid Change | Variant Allele Frequency (Gene Copy Number) | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| GBM4 P22 | GBM4 P21 TMZ | GBM5 P6 | GBM5 P6 IR/TMZ | GBM6 P3 | GBM6 P6 TMZ | GBM7 P8 | GBM7 P8 TMZ | ||||
| CDKN2A | (0) | (0) | (0) | (0) | (0) | (0) | |||||
| MDM4 | (26) | (20) | |||||||||
| MYCN | (112) | (74) | |||||||||
| PDGFRA | (5.8) | (4.6) | |||||||||
| MSH2 | 2:47709922 | G>A (ACC-) | G880D | 0.06 (2) | |||||||
| CTNNB1 | 3:41266078 | G>A (GCC-) | W25ter | 0.13 (2) | |||||||
| BAP1 | 3:52436821 | C>T (TCC-) | E653K | 0.13 (2) | |||||||
| BAP1 | 3:52436887 | C>T (TCC-) | E631K | 0.13 (2) | |||||||
| KDR | 4:55946320 | G>A (GCC+) | P1287S | 0.08 (3) | |||||||
| PIK3R1 | 5:67591097 | A>G (TTC-) | N564D | 0.44 (2) | 0.48 (2) | ||||||
| APC | 5:112162897 | G>A (GCA-) | A501T | 0.11 (1) | |||||||
| APC | 5:112178024 | C>T (TCC+) | P2245S | 0.08 (2) | |||||||
| EGFR | 7:55220274 | C>T (GCG+) | R222C | 0.20 (12) | 0.03 (3.4) | ||||||
| EGFR | 7:55221710 | C>T (CCG+) | R252C | 0.05 (12) | |||||||
| EGFR | 7:55221822 | C>T (GCC+) | A289V | 0.07 (12) | |||||||
| TSC1 | 9:135779106 | G>A (CCT+) | L714F | 0.09 (1) | |||||||
| PTEN | 10:89653807 | G>C (CCA-) | M35I | 1.00 (1) | 1.00 (1) | (0) | (0) | ||||
| PTPN11 | 12:112888189 | G>A (TCC-) | E69K | 0.05 (2) | 0.06 (2) | ||||||
| PTPN11 | 12:112926900 | C>A (ACA+) | T511K | 0.43 (2) | 0.43 (2) | ||||||
| TP53 | 17:7577524 | GTGAGGATGG>G | P250del | 0.48 (2) | 0.47 (2) | ||||||
| TP53 | 17:7578236 | A>C (GTA+) | Y205D | 0.02 (2) | |||||||
| NF1 | 17:29556257 | G>A (ACC-) | G875D | 0.15 (2) | |||||||
| NF1 | 17:29667616 | G>T (TCA-) | E2339ter | 0.05 (2) | 0.08 (2) | ||||||
| NF1 | 17:29679366 | C>T (CCG+) | R2517ter | 0.05 (2) | 0.07 (2) | ||||||
| BRCA1 | 17:41223252 | C>T (TCC-) | G1560E | 0.12 (1.6) | |||||||
Putative TMZ-induced variants are denoted in bold.
*As per convention, context is denoted in reference to the substituted pyrimidine. + denotes that the pyrimidine substitution occurs on the transcribed strand.