Table 1. Summary of next-generation sequencing of 50 cancer genes from the initial F0 and late F4 passages of FNA-PDX #008 (FNA) and patient-matched metastatic-PDX (M1/M2) models.
Alleles that were detected but eliminated from NGS data due to read quality were subsequently validated with a SNaPshot genotyping approach. Italicized variants were detected at an allelic frequency < 10%.
| Sample | Gene | Nucleotide Change | AA Change | COSMIC ID | NGS? | SNaPshot? |
|---|---|---|---|---|---|---|
| FNA F0 | KRAS | c.34G>C | G12R | COSM518 | Yes | Yes |
| TP53 | c.659A>G | Y220C | COSM10758 | Yes* | Yes | |
| JAK3 | c.2164G>A | V722I | COSM34213 | No** | Yes | |
| FNA F1 | KRAS | c.34G>C | G12R | COSM518 | Yes | Yes |
| TP53 | c.659A>G | Y220C | COSM10758 | Yes | Yes | |
| JAK3 | c.2164G>A | V722I | COSM34213 | Yes* | Yes | |
| FNA F2 | KRAS | c.34G>C | G12R | COSM518 | Yes | Yes |
| TP53 | c.659A>G | Y220C | COSM10758 | Yes | Yes | |
| JAK3 | c.2164G>A | V722I | COSM34213 | Yes* | Yes | |
| EGFR | c.2219_2220insCATCG | I740_P741insHR | Yes | No | ||
| EGFR | c.2236_2250delGAATTAAGAGAAGCA | E746_A750delELREA | COSM6225 | Yes | No | |
| FNA F3 | KRAS | c.34G>C | G12R | COSM518 | Yes | Yes |
| TP53 | c.659A>G | Y220C | COSM10758 | Yes | Yes | |
| JAK3 | c.2164G>A | V722I | COSM34213 | Yes | Yes | |
| EGFR | c.2219_2220insCATCG | I740_P741insHR | Yes | No | ||
| EGFR | c.2236_2250delGAATTAAGAGAAGCA | E746_A750delELREA | COSM6225 | Yes | No | |
| FNA F4 | KRAS | c.34G>C | G12R | COSM518 | Yes | Yes |
| TP53 | c.659A>G | Y220C | COSM10758 | Yes | Yes | |
| JAK3 | c.2164G>A | V722I | COSM34213 | Yes | Yes | |
| FNA F5 | KRAS | c.34G>C | G12R | COSM518 | Yes | Yes |
| TP53 | c.659A>G | Y220C | COSM10758 | Yes | Yes | |
| JAK3 | c.2164G>A | V722I | COSM34213 | Yes | Yes | |
| EGFR | c.2219_2220insCATCG | I740_P741insHR | Yes | No | ||
| EGFR | c.2236_2250delGAATTAAGAGAAGCA | E746_A750delELREA | COSM6225 | Yes | No | |
| M1 F0 | KRAS | c.34G>C | G12R | COSM518 | Yes | n/a |
| TP53 | c.659A>G | Y220C | COSM10758 | Yes | n/a | |
| JAK3 | c.2164G>A | V722I | COSM34213 | Yes | n/a | |
| BRAF | c.1405G>C | G469R | COSM455 | Yes | n/a | |
| M1 F4 | KRAS | c.34G>C | G12R | COSM518 | Yes | n/a |
| TP53 | c.659A>G | Y220C | COSM10758 | Yes | n/a | |
| JAK3 | c.2164G>A | V722I | COSM34213 | Yes | n/a | |
| M2 F0 | KRAS | c.34G>C | G12R | COSM518 | Yes | n/a |
| TP53 | c.659A>G | Y220C | COSM10758 | Yes | n/a | |
| JAK3 | c.2164G>A | V722I | COSM34213 | Yes | n/a | |
| BRAF | c.1405G>C | G469R | COSM455 | Yes | n/a | |
| M2 F4 | KRAS | c.34G>C | G12R | COSM518 | Yes | n/a |
| TP53 | c.659A>G | Y220C | COSM10758 | Yes | n/a | |
| JAK3 | c.2164G>A | V722I | COSM34213 | Yes | n/a | |
| BRAF | c.1405G>C | G469R | COSM455 | Yes | n/a |