Table 1:
Cancer gene panel sequencing of two glioblastoma cases
| Case | Mutation type | Storage period (years) | Sample type | DNA extraction method | DNA yield per slice (µg)a | First experiment |
Second experiment |
||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Input DNA (ng) | Library yield (fmol) | Mean coverageb | Input DNA (ng) | Library yield (fmol)c | Mean coverageb | ||||||
| 1 | BRAF V600E | 4.4 | Bloodd | QIAamp | – | 30 | 279.8 | 86.3 | – | – | |
| Fresh frozen | QIAamp | – | 30 | 84.1 | 55.6 | – | – | ||||
| FFPE | HiTE | 3.25 | 30 | 9.9 | 19.1 | 1600 | 67.7 | 119 | |||
| FFPE | DNeasy | 0.97 | 30 | 4.2 | 6.2 | 980 | 17.4e | 29.3 | |||
| 2 | IDH1 R132H | 5.7 | Bloodd | QIAamp | – | 30 | 202.8 | 91.1 | – | – | |
| Fresh frozen | QIAamp | – | 30 | 205.4 | 83.5 | – | – | ||||
| FFPE | HiTE | 0.96 | 30 | 18.7 | 14.1 | 980 | 77.4 | 77.4 | |||
| FFPE | DNeasy | 0.30 | 30 | 9.1 | 5.5 | 130 | 10.8e | 20.5 | |||
a
DNA yield was determined with the Qubit dsDNA BR kit. The mean value for the two experiments is shown.
b
Mean coverage of target regions (after removal of duplicated reads).
c
Yield of library prepared in an attempt to acquire the same amount of library with the fresh frozen tissue sample.
d
DNA obtained from peripheral blood of the same patient (no mutation control).
e
Because of limited DNA yield, a comparable amount of library as obtained from fresh frozen samples could not be prepared.