Table 1A, PDX Tumors: Patient Demographics and Molecular Characterization.
A panel of 15 PDX melanoma tumors is arranged by distinct genetic phenotypes based on the mutation status. For each PDX, the patient demographics are shown including Clark’s Level tumor stage and prior treatments. Prior treatments are list in the order they were received. The gene mutation status was determined by NGS of the primary tumor sample or PDX P2 passage (PDX1577, 1668, 2316 and 2552, indicated by a *) using a Human Comprehensive Cancer Panel (QIAGEN Sciences, Frederick, MD), and the results for 10 melanoma driver mutations are shown. The metastatic tumor was used to generate the PDX. Abbreviations for therapies patients received are as follows: D,dabrafenib (Tafinlar), V600B-Raf mutant Inhibitor; G, GM-CSF (Oncovax); I,interferon; Ipi,ipilimumab (Yervoy), monoclonal Ab CTLA-4; N,nivolumab (Opdivo), monoclonal Ab PD-1; Pem,pembrolizumab (Keytruda), IgG4 isotype antibody PD-1; S,sunitinib (Sutent), multi-targeted receptor tyrosine kinase (RTK) inhibitor; S+T, sorafenib (Nexavar) + tivantinib, tyrosine-protein kinase inhibitor, MET inhibitor; T, trametinib (Mekinist), MEK1/2 inhibitor; V, vemurafenib (Zelboraf), B-Raf inhibitor. Table 1B, TP53 Mutation Status.The specific TP53 mutations detected by tumor NGS are shown for each PDX. NON_SYN, indicates a non-synonomous mutation, STOP, indicates a nonsense mutation resulting in a stop codon and SPL_SITE indicates a mutation (deletion) involving a splice site. The identification of the mutations, the small nucleotide polymorphism (SNP) effect and impact, and the designation of germline or somatic mutation was determined by using QIAGEN NGS Data Web Analysis Web Portal based on sequence analysis of the tumor and patient blood when available. SnpEff is an open-source tool that annotates variants and predicts their effects on genes by using an interval forest approach (48). The variant frequency is also listed for each non-synonymous mutation (NSM). The determination of somatic versus germline was based upon analysis of the patient’s blood, when available. The patient tumor (P0) was used to determine TP53 mutation status, except for PDX1577, 1668, 2316, and 2552. For these four PDX, the second PDX passage (P2) was sequenced.
| Patient Information | Gene Mutation Status | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PDX | Sex | Age | Clark Stage | Prior Treatment | BRAF | NRAS | TP53 | NF1 | CDKN2A | PTEN | MTOR | MAP2K1 | KIT | CDK4 |
| 1351 | F | 61 | V | Pem, V | V600E Stop Lost | N | N | A1226T | N | Stop Lost | H1366Y | E203K | Stop Lost | N |
| 2552* | M | 40 | IIIB | Pem | V600E | N | N | N | Stop Lost | T398S | G580A N382S | N | G265S | I51V G45A G44A |
| 1577* | F | 38 | IV | D+T | V600E | N | N | N | N | T398S | T1837S G580A N382S | N | N | I51V G45A G44A |
| 2195 | M | 45 | V | None | V600E | N | N | V530I | N | N | N | N | N | N |
| 1839 | F | 38 | IV | I | V600E | N | N | N | N | Stop Lost | N | N | N | N |
| 1946 | F | 32 | IV | D+ T,Ipi | V600E | N | N | N | N | G129E | N | N | N | N |
| 9164 | M | n/a | n/a | Pem | V600E | N | Stop Lost | N | N | N | N | N | N | N |
| 2252 | M | 34 | IV | None | V600M V600E | N | Stop Lost | N | Stop Lost | Stop Lost | N | N | N | N |
| 0807 | F | 29 | IV | D, D+T | P192Q | N | A138ADG T140S | N | N | N | LR282L | D67N P124S | N | N |
| 1668* | M | 61 | IV | None | S147N N140T | N | N | Stop Lost | Stop Lost | T398S | T1837S G580A N382S | N | M541L | I51V G45A G44A |
| 1129 | F | 69 | V | Ipi | D549N K483T | N | N | N | N | N | N | N | N | N |
| 1767 | F | 49 | n/a: spindle | Ipi | N | N | N | N | N | N | N | N | N | N |
| 2316* | F | 71 | IIIB | None | N | N | N | Stop Lost | Stop Lost | Y | T1837S G580A | N | M541L K642E | N |
| 1595 | M | 33 | IV | S, G | P334S | Q61R | N | N | N | N | T1837S G580A N382S | N | N | I51V G45A G44A |
| 1179 | M | 77 | likely V | S+T, Pem | N | Q61H | N | N | N | N | K1981E | N | N | N |
| PDX | Gene Name | Germline/Somatic | Ref | Variant | Codon Change | AA Change | Variant Frequency | snpEff Effect | snpEff Impact |
|---|---|---|---|---|---|---|---|---|---|
| 0807 | TP53 | G | CCGATCT | p.A138ADG | 0.265 | NON_SYN | MOD | ||
| 0807 | TP53 | G | C | c.419C>G | p.T140S | 0.269 | NON_SYN | MOD | |
| 0807 | TP53 | G | C | c.215C>G | p.P72R | 0.458 | NON_SYN | MOD | |
| 1129 | TP53 | G | C | c.215C>G | p.P72R | 1 | NON_SYN | MOD | |
| 1179 | TP53 | G | C | c.215C>G | p.P72R | 1 | NON_SYN | MOD | |
| 1351 | TP53 | germline | G | C | c.215C>G | p.P72R | 0.58 | NON_SYN | MOD |
| 1577 | TP53 | germline | G | C | c.215C>G | p.P72R | 1 | NON_SYN | MOD |
| 1595 | TP53 | G | C | c.215C>G | p.P72R | 0.486 | NON_SYN | MOD | |
| 1668 | TP53 | somatic | C | <DEL> | SPL_SITE | HIGH | |||
| 1668 | TP53 | germline | G | C | c.215C>G | p.P72R | 0.986 | NON_SYN | MOD |
| 1767 | TP53 | G | C | c.215C>G | p.P72R | 0.556 | NON_SYN | MOD | |
| 1839 | TP53 | somatic | G | A | c.916C>T | p.R306* | 0.484 | STOP | HIGH |
| 1839 | TP53 | somatic | G | A | c.483C>T | p.A161 | 0.468 | NON_SYN | LOW |
| 1839 | TP53 | somatic | A | G | c.706T>C | p.Y236H | 0.235 | NON_SYN | MOD |
| 1839 | TP53 | germline | G | C | c.215C>G | p.P72R | 0.359 | NON_SYN | MOD |
| 1946 | TP53 | somatic | C | <DEL> | SPL_SITE | HIGH | |||
| 1946 | TP53 | germline | G | C | c.215C>G | p.P72R | 1 | NON_SYN | MOD |
| 2195 | TP53 | G | C | c.215C>G | p.P72R | 1 | NON_SYN | MOD | |
| 2252 | TP53 | somatic | C | <DEL> | SPL_SITE | HIGH | |||
| 2252 | TP53 | germline | GG | AA | p.IR0I* | 0.607 | STOP | HIGH | |
| 2252 | TP53 | somatic | G | A | c.586C>T | p.R196* | 0.607 | STOP | HIGH |
| 2252 | TP53 | germline | G | C | c.215C>G | p.P72R | 1 | NON_SYN | MOD |
| 2316 | TP53 | germline | G | C | c.215C>G | p.P72R | 1 | NON_SYN | MOD |
| 2552 | TP53 | germline | G | C | c.215C>G | p.P72R | 0.605 | NON_SYN | MOD |
| 9164 | TP53 | G | A | c.574C>T | p.Q192* | 1 | STOP | HIGH | |
| 9164 | TP53 | C | T | c.108G>A | p.P36 | 0.939 | NON_SYN | LOW | |
| 9164 | TP53 | A | G | 1 | INTRON | MODIFIER |