Table 3.
Comparative mutation analysis using blood and tissue samples of the same patients
| AKT1 E17K | PIK3CA | ||||||
|---|---|---|---|---|---|---|---|
| Cohort A | Cohort B | Cohort C | Cohort A | Cohort B | |||
| Total paired samples analyzed, n | 94 | 50 | 35 | 71 | 50 | ||
| Mismatched samples, pairs, n | |||||||
| Tumor | Blood | - | - | ||||
| AKT1 WT | AKT1 E17K | 0 | 0 | 0 | - | - | |
| AKT1 E17K | AKT1 WT | 31 | 1 | 1 | - | - | |
| PIK3CA WT | PIK3CA mut | - | - | - | 1 | 0 | |
| PIK3CA mut | PIK3CA WT | - | - | - | 16 | 0 | |
| PIK3CA mut | PIK3CA mut | - | - | - | 1 | 0 | |
| Total mismatched, pairs, n | 31 | 1 | 1 | 18 | 0 | ||
| Matched samples, pairs, n | |||||||
| AKT1 WT | AKT1 WT | 59 | 47 | 28 | - | - | |
| AKT1 E17K | AKT1 E17K | 4 | 2 | 6 | - | - | |
| PIK3CA WT | PIK3CA WT | - | - | - | 50 | 37 | |
| PIK3CA mut | PIK3CA mut | - | - | - | 5 | 13 | |
| Total matched, pairs, n | 63 | 49 | 34 | 55 | 50 | ||
| Concordance (%) | 67.0 | 98.0 | 97.1 | 75.3a | 100 | ||
| Mutation capture rate in ctDNA (%) | 11.4 | 66.7 | 85.7 | 22.7 | 100 | ||
Cohort A: Analysis of AKT1 E17K mutations using BEAMing for fresh frozen tumor tissue samples and blood samples (serum), and analysis of PIK3CA mutations (H1047R, H1047L, E542K, E545K) using BEAMing for blood samples (serum) and next-generation sequencing for fresh frozen tumor tissue samples. Cohort B: Both AKT1 E17K and PIK3CA mutations (H1047R, H1047L, E542K, E545K) were determined in tissue (FFPE) and blood (plasma) using BEAMing. Cohort C: Analysis of AKT1 E17K using BEAMing for blood samples (plasma) and next-generation sequencing for tissue samples (FFPE). “Matched samples” indicates that the same result was obtained using tissue or blood samples. “Mismatched samples” indicates that different results were obtained using tissue and blood samples. aCalculation was based on total measured events (n = 73), as in one sample, two PIK3CA mutations were detected of which only one matched
Abbreviations: AKT1 v-akt murine thymoma viral oncogene, BEAMing Beads, Emulsions, Amplification, and Magnetics, FFPE formalin-fixed paraffin-embedded, mut mutant, WT wild type