Table 2. SNV/CNA tracking in nine metastatic breast cancer patients by NGS.
Patient ID | Study Sample (months) | Age | ER | PR | Her2 | CA15-3 (U/ml) | cfDNA genomic copies/ml | SNV (AA mutation) and VAF | COSMIC ID | Gene amplification | |||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Gene | Mutation | VAF (%) | Coverage | ||||||||||
1 | Baseline | 52 | pos | pos | pos | 602 | 2,076 | PIK3CA | p.H1047R | 7.8 | 1988 | COSM775 | NOMO2 and ERBB2 |
5 | 376 | 2,727 | PIK3CA | p.H1047R | 4.9 | 1100 | COSM775 | ERBB2 | |||||
2 | Baseline | 45 | pos | pos | neg | 25 | 4,697 |
PIK3CA TP53 |
p.H1047R p.R248Q | 2.5 6.5 |
1260 876 |
COSM775 COSM10662 | ERBB2 |
20 | 131 | 5,515 | - | ||||||||||
3 | Baseline | 74 | pos | pos | neg | 29 | 3,545 | PIK3CA | p.H1047R | 5 | 2145 | COSM775 | - |
14 | 24 | 5,742 | - | - | |||||||||
4 | Baseline | 80 | pos | pos | neg | 150 | 13,041 |
PIK3CA ESR1 |
p.N345K p.Y537N | 11.7 10.9 |
1357 457 |
COSM36200 COSM1074635 | - |
2 | 194 | 3,655 |
PIK3CA ESR1 |
p.N345K p.Y537N | 1 0.5 |
1660 528 |
COSM754 COSM1074635 | - | |||||
5 | Baseline | 49 | pos | pos | pos | 23 | 12,621 | - | |||||
2 | 23 | 13,970 | - | ||||||||||
6 | Baseline | 27 | pos | pos | neg | 23 | 4,455 | - | |||||
11 | 23 | 9,212 | - | ||||||||||
17 | 25 | 2,115 | PIK3CA | p.H1047R | 1 | 1181 | COSM775 | - | |||||
24 | 56 | 7,318 |
PIK3CA TP53 |
p.H1047R p.E271G | 10.1 6.2 |
1738 64 |
COSM775 COSM43879 | - | |||||
7 | Baseline | 72 | pos | NA | neg | 314 | 6,409 | - | - | ||||
1 | 395 | 31,364 | LMTK3 | p.E1251V | 3.5 | 1995 | - | ||||||
8 | Baseline | 51 | pos | pos | neg | 20 | 1,515 | - | |||||
7 | 46 | 2,621 | - | ||||||||||
9 | 221 | 4,864 | - | ||||||||||
10 | 567 | 11,727 | ERBB2 and MYC | ||||||||||
13 | 252 | 9,818 | - | ||||||||||
9 | Baseline | 43 | pos | pos | neg | 74 | 2,197 | - | - | ||||
3 | 110 | 4,803 | - | - | |||||||||
6 | 168 | 504,545 |
PIK3CA ESR1 |
p.E545K p.D538G | 17.8 28.6 |
1159 353 |
COSM763 COSM94250 | CCND1 | |||||
12 | 147 | 96,970 | - | - | |||||||||
13 | 138 | 86,667 | - | - |
Age is the age at the time of the first blood sample.