Table 2 Discordant results between SSS and AVENIO assays for PIK3CA mutation detection

From: Clinical impact of single-gene vs. panel sequencing in advanced HR + /HER2− breast cancer: insights and implications

Sample ID

z-score

Variant count (hVAF)

Variant

VAF AVENIO (%)

VAF SSS (%)

B195_4

3.36

2 (5.1)

H1047R

not detected

2.97

B201_1

3.65

0

E542K

not detected

0.46

B207_1

6.74

4 (6.3)

H1047R

not detected

0.97

B211_6a

3.21

11 (14.2)

H1047R

not detected

0.33

B303_1

0.88

1 (0.3)

H1047R

not detected

0.42

B350_1

1.31

2 (3.5)

H1047R

not detected

0.47

B538_1

1.48

0

E545K

not detected

2.94

B341_1

2.78

1 (0.6)

E545K

0.59

below LOD (0.37; 4 reads)

B475_1

1.59

2 (0.4)

N345K

0.39

below LOD (0.31;2 reads)

B485_1

0.61

1 (0.4)

H1047R

0.37

below LOD (0.24;6 reads)

B620_1

1.51

1 (0.2)

H1047R

0.17

below LOD (0.18;8 reads)

B518_1

7.36

1 (10.4)

E545A

10.38

not detected*

  1. aA second variant was detected in this sample in both assays; *AVENIO result was confirmed by repeating the assay twice. Variant count refers to the total number of pathogenic or likely pathogenic variants identified in the sample, with the corresponding highest variant allele frequency (hVAF) shown in parentheses.
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