A Comparative Study for Detection of EGFR Mutations in Plasma Cell-Free DNA in Korean Clinical Diagnostic Laboratories

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)

0.72

3667/21 (0.57)

57591/541 (0.94)

Level 4

0.12

1804/0 (ND)

70849/0 (ND)

0.10

3158/3 (0.09)

73836/114 (0.15)

0.11

2980/0 (ND)

65455/0 (ND)

0.05

3296/3 (0.09)

49234/115 (0.23)

Precision materials (P-1~P-3

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)

-

-

-

-

depth was not provided by the laboratory. positive results from precision materials were summarized in the table. measurement of P-1 material showed invalid result using next-generation sequencing from a laboratory. ND, not detected.