Table 4.
Mutational Status of CT and CMK-T Specimens in Exons 2–11 of TP53
| Tumor specimen | TP53 exon | Variant (nt) | Protein change | Result | MPLX + HRM- conv. PCR | MPLX + HRM-COLD-PCR | Chromatogram conv. PCR | Chromatogram COLD-PCR | Matched normal conv./COLD-PCR | Chromatogram genomic DNA conv. PCR | Chromatogram genomic DNA COLD-PCR |
|---|---|---|---|---|---|---|---|---|---|---|---|
| CMK-T7 | 2 | c.40del2 | p.L14del2 | Frameshift (novel) | Y | Y | Y | Y | |||
| CT12 | 4 | c.108G>A | p.P36P | SNP- synonymous | Y | Y | Y | Y | Y | ||
| CMK-T3 | 4 | c.108G>A | p.P36P | SNP- synonymous | Y | Y | Y | Y | |||
| CMK-T12 | 4 | c.108G>A | p.P36P | SNP- synonymous | Y | Y | Y | Y | |||
| CMK-T13 | 4 | c.108G>A | p.P36P | SNP- synonymous | Y | Y | Y | Y | |||
| CMK-T14 | 4 | c.108G>A | p.P36P | SNP- synonymous | Y | Y | Y | Y | |||
| CMK-T1 | 5 | c.403del3 | p.C135del3 | Frameshift (novel) | Y | Y | Y | Y | |||
| CT6 | 5 | c.476C>T | p.A159V | Missense | Y | Y | Y | ||||
| CT2 | 5 | c.523C>A | p.R175S | Missense | Undetectable | Y | Undetectable | Y | WT/WT | Undetectable | Y |
| CT10 | 5 | c.524G>T | p.R175K | Missense | Y | Y | Y | ||||
| CT17 | 5 | c.524G>A | p.R175H | Missense | Y | Y | Y | ||||
| CT20 | 5 | c.527G>T | p.C176F | Missense | Y | Y | Y | Y | WT/MUTANT | Y | Y |
| CMK-T3 | 6 | c.568C>T | p.P190L | Missense | Y | Y | Y | ||||
| CMK-T5 | 6 | c.610del3 | p.E204del3 | Frameshift | Y | Y | Y | ||||
| CMK-T12 | 6 | c.639A>G | p.R213R | SNP- synonymous | Y | Y | Y | ||||
| CMK-T16 | 7 | c.712T>G | p.C238W | Missense | Y | Y | Y | ||||
| CT2 | 7 | c.739A>T | p.N247I | Missense | Y | Y | Y | ||||
| CT11 | 7-intronic | c.782 + 1G>T | Splice | Undetectable | Y | Undetectable | Y | WT/WT | Undetectable | Y | |
| CT10 | 8 | c.817C>T | p.R273C | Missense | Y | Y | Y | ||||
| CMK-T7 | 8 | c.817C>T | p.R273C | Missense | Y | Y | Y | ||||
| CT20 | 8 | c.818G>A | p.R273H | Missense | Undetectable | Y | Undetectable | Y | WT/WT | Undetectable | Y |
| CT5 | 8 | c.853G>A | p.E285K | Missense | Y | Y | Y | ||||
| CMK-T16 | 8 | c.916C>T | p.R306X | Nonsense | Y | Y | Y | ||||
| CT20 | 9 | c.925C>T | p.P309S | Missense | Undetectable | Y | Undetectable | Y | WT/WT | Undetectable | Y |
| CT12 | 9-intronic | c.993 + 12T>C | Intronic | Y | Y | Y | Y | ||||
| CMK-T3 | 9-intronic | c.993 + 12T>C | Intronic | Y | Y | Y | Y | ||||
| CMK-T12 | 9-intronic | c.993 + 12T>C | Intronic | Y | Y | Y | Y | ||||
| CMK-T13 | 9-intronic | c.993 + 12T>C | Intronic | Y | Y | Y | Y | ||||
| CMK-T14 | 9-intronic | c.993 + 12T>C | Intronic | Y | Y | Y | Y | ||||
| CT4 | 9-intronic | c.994-1G>C | Splice | Y | Y | Y |
Mid- to high-abundance mutants and SNPs could be detected in HRM analysis of both conventional (conv.) and COLD-PCR amplicons (denoted “Y”) amplified from the multiplex-PCR product; however, four low-abundance mutations (in bold) were not detected by HRM analysis of conventional PCR (denoted “undetectable”), though could be detected in COLD-PCR amplicons (denoted “Y”). Sanger sequence analysis was used to identify the mutations in the product amplified from the multiplex-PCR. Furthermore, low-abundance mutations, and additional mutations of interest, were secondarily sequenced from amplified genomic DNA.
CT, colorectal tumor; CMK-T, glioblastoma tumor.