Table 5.
Comparison of mutant allelic frequency from two laboratories using different next-generation sequencing platforms.
| Sample | p.L858R | p.E746_A750del (exon 19 deletion) | p.T790M | p.A767_V769dup (exon 20 insertion) | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Expected mutant allele frequency (%) | Lab F | Lab C | Expected mutant allele frequency (%) | Lab F | Lab C | Expected mutant allele frequency (%) | Lab F | Lab C | Expected mutant allele frequency (%) | Lab F | Lab C | |||||
| Molecular coverage depth, total/mutant (allele frequency, %) | Read coverage depth, total/mutant (allele frequency, %) | Read coverage depth, total/mutant (allele frequency, %) | Molecular coverage depth, total/mutant (allele frequency, %) | Read coverage depth, total/mutant (allele frequency, %) | Read coverage depth, total/mutant (allele frequency, %) | Molecular coverage depth, total/mutant (allele frequency, %) | Read coverage depth, total/mutant (allele frequency, %) | Read coverage depth, total/mutant (allele frequency, %) | Molecular coverage depth, total/mutant (allele frequency, %) | Read coverage depth, total/mutant (allele frequency, %) | Read coverage depth, total/mutant (allele frequency, %) | |||||
| Level 1 | 4.29 | 1970/67 (3.40) | 74088/2440 (3.29) | 4594/171 (3.72) | 5.19 | 3360/131 (3.90) | 60991/1272 (2.09) | 5819/231 (3.97) | 4.01 | 3182/124 (3.90) | 59366/2276 (3.83) | 1717/71 (4.14) | 3.85 | 3258/130 (3.99) | 38689/1707 (4.41) | 1091/30 (2.75) |
| Level 2 | 2.13 | 1755/41 (2.34) | 70894/1707 (2.41) | 4385/84 (1.92) | 2.13 | 2855/65 (2.28) | 61723/753 (1.22) | 10001/130 (1.30) | 2.05 | 2680/51 (1.90) | 56596/983 (1.74) | 2572/87 (3.38) | 1.94 | 2670/53 (1.99) | 37564/541 (2.37) | 2341/24 (1.03) |
| Level 3 | 0.80 | 1912/15 (0.78) | 107664/791 (0.73) | 4681/52 (1.11) | 1.10 | 3095/22 (0.71) | 94144/378 (0.40) | 9416/57 (0.61) | 0.81 | 2902/26 (0.90) | 84166/754 (0.90) | NDa | 0.72 | 3667/21 (0.57) | 57591/541 (0.94) | NDa |
| Level 4 | 0.12 | 1804/0 (ND) | 70849/0 (ND) | NDa | 0.10 | 3158/3 (0.09) | 73836/114 (0.15) | NDa | 0.11 | 2980/0 (ND) | 65455/0 (ND) | NDa | 0.05 | 3296/3 (0.09) | 49234/115 (0.23) | NDa |
| Precision materials (P-1~P-3)b | 3.00 | 2250/89 (3.96) | 97519/3743 (3.84) | 4067/148 (3.64) | 3.00 | 2306/68 (2.95) | 45162/1336 (2.96) | 9157/250 (2.73) | 3.00 | 3132/126 (4.02) | 60226/1396 (2.32) | 2131/111 (5.21) | - | - | - | - |
| 3.00 | 2259/94 (4.16) | 124662/5042 (4.04) | 6335/344 (5.43) | 3.00 | 3326/114 (3.43) | 110580/3431 (3.1) | 8823/274 (3.11) | 3.00 | 2980/112 (3.76) | 88684/3164 (3.57) | 2904/126 (4.34) | - | - | - | - | |
| 3.00 | 2200/72 (3.27) | 87890/2799 (3.18) | 4638/139 (2.99) | 3.00 | 3462/134 (3.87) | 81882/1905 (2.33) | 14136/242 (1.71) | 3.00 | 3380/123 (3.64) | 89937/3303 (3.67) | Invalidc | - | - | - | - | |
aCoverage depth was not provided by the laboratory. bOnly positive results from precision materials were summarized in the table. cOne measurement of P-1 material showed invalid result using next-generation sequencing from a laboratory. ND, not detected.