Background
Methods
Study objectives
Study design
Study arm 1
Study arm 2
Samples
RNA extraction
MammaTyper® test
Statistical analysis
Results
Intermediate precision
Intersite reproducibility
Analyte | Intersite | Residual | Total | |||
---|---|---|---|---|---|---|
SD | 95% CI | SD | 95% CI | SD | ||
RNA pools Samples 1–8 |
ERBB2
| 0.16 | 0.12–0.21 | 0.24 | 0.22–0.27 | 0.29 |
ESR1
| 0.18 | 0.13–0.29 | 0.40 | 0.37–0.44 | 0.44 | |
PGR
| 0.09 | 0.07–0.13 | 0.16 | 0.15–0.17 | 0.18 | |
MKI67
| 0.21 | 0.17–0.26 | 0.21 | 0.19–0.23 | 0.29 | |
Self-extracted RNAs Samples 9–24 |
ERBB2
| 0.22 | 0.19–0.26 | 0.23 | 0.21–0.24 | 0.31 |
ESR1
| 0.25 | 0.20–0.31 | 0.36 | 0.34–0.39 | 0.44 | |
PGR
| 0.12 | 0.10–0.16 | 0.19 | 0.18–0.20 | 0.23 | |
MKI67
| 0.16 | 0.14–0.20 | 0.19 | 0.18–0.21 | 0.25 | |
RNA pools and self-extracted RNAs Samples 1–24 |
ERBB2
| 0.20 | 0.17–0.23 | 0.23 | 0.22–0.25 | 0.31 |
ESR1
| 0.22 | 0.19–0.27 | 0.38 | 0.36–0.40 | 0.44 | |
PGR
| 0.11 | 0.10–0.14 | 0.18 | 0.17–0.19 | 0.21 | |
MKI67
| 0.18 | 0.16–0.21 | 0.20 | 0.19–0.21 | 0.27 |
Intersite reproducibility including preanalytical variances
Binary single-marker and subtype agreement
ERBB2
|
ESR1
|
PGR
|
MKI67
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample | Counts | Distance to cutoff (Cq) | Counts | Distance to cutoff (Cq) | Counts | Distance to cutoff (Cq) | Counts | Distance to cutoff (Cq) | ||||
Negative | Positive | Negative | Positive | Negative | Positive | Negative | Positive | |||||
1 |
40
| 0 | −1.1 | 0 |
40
| 1.5 | 0 |
40
| 3.2 |
40
| 0 | −3.2 |
2 |
40
| 0 | −1.1 | 0 |
40
| 1.7 | 0 |
40
| 1.8 |
40
| 0 | −0.8 |
3 | 0 |
40
| 0.6 | 0 |
40
| 1.9 | 0 |
40
| 2.5 | 0 |
40
| 0.8 |
4 |
40
| 0 | −1.2 | 0 |
40
| 3.0 | 0 |
40
| 4.6 | 0 |
40
| 0.7 |
5 |
40
| 0 | −1.9 | 0 |
40
| 1.6 | 0 |
40
| 5.6 | 0 |
40
| 0.6 |
6 |
40
| 0 | −2.9 | 0 |
40
| 1.4 | 0 |
40
| 6.0 | 0 |
40
| 0.6 |
7 |
40
| 0 | −3.2 |
40
| 0 | −4.0 |
40
| 0 | −3.0 | 0 |
40
| 2.2 |
8 | 0 |
40
| 1.7 |
12
|
28
| 0.2 | 0 |
40
| 2.9 | 0 |
40
| 1.3 |
9 | 0 |
30
| 1.3 |
30
| 0 | −3.2 |
30
| 0 | −2.3 | 0 |
30
| 1.1 |
10 | 0 |
30
| 3.1 |
30
| 0 | −2.0 |
30
| 0 | −1.7 | 0 |
30
| 1.5 |
11 |
30
| 0 | −1.6 | 0 |
30
| 2.1 | 0 |
30
| 4.9 |
4
|
26
| 0.2 |
12 |
30
| 0 | −1.8 | 0 |
30
| 2.7 | 0 |
30
| 4.7 | 0 |
30
| 1.1 |
13 |
30
| 0 | −1.8 | 0 |
30
| 2.4 | 0 |
30
| 4.6 |
1
|
29
| 0.4 |
14 |
30
| 0 | −2.0 | 0 |
30
| 1.4 | 0 |
30
| 3.2 |
30
| 0 | −0.8 |
15 |
30
| 0 | −1.3 | 0 |
30
| 1.1 | 0 |
30
| 1.0 |
29
|
1
| −1.2 |
16 |
29
| 0 | −1.5 | 0 |
29
| 2.5 | 0 |
29
| 2.9 | 0 |
29
| 0.7 |
17 |
30
| 0 | −1.1 | 0 |
30
| 1.4 | 0 |
30
| 0.8 | 0 |
30
| 1.1 |
18 |
30
| 0 | −1.3 | 0 |
30
| 2.5 | 0 |
30
| 4.2 |
30
| 0 | −1.2 |
19 |
30
| 0 | −1.5 | 0 |
30
| 2.8 | 0 |
30
| 2.8 |
1
|
29
| 0.4 |
20 |
30
| 0 | −2.6 |
30
| 0 | −0.9 | 0 |
30
| 3.3 |
29
|
1
| −0.6 |
21 |
30
| 0 | −2.8 |
20
|
10
| 0.0 | 0 |
30
| 3.4 |
29
|
1
| −0.5 |
22 |
30
| 0 | −3.1 |
30
| 0 | −3.4 |
30
| 0 | −3.1 | 0 |
30
| 2.1 |
23 |
30
| 0 | −3.1 |
30
| 0 | −2.3 |
16
|
14
| 0.0 | 0 |
30
| 2.2 |
24 | 0 |
30
| 1.9 |
30
| 0 | −5.2 |
30
| 0 | −3.3 |
1
|
29
| 0.4 |
kappa Statistic | 1.00 | 0.91 | 0.94 | 0.94 |
Sample | Not defined | HER2-positive (nonluminal) | Luminal B-like (HER2-positive) | Luminal B-like (HER2-negative) | Triple-negative (ductal) | Luminal A-like |
---|---|---|---|---|---|---|
1 | 0 | 0 | 0 | 0 | 0 |
40
|
2 | 0 | 0 | 0 | 0 | 0 |
40
|
3 | 0 | 0 |
40
| 0 | 0 | 0 |
4 | 0 | 0 | 0 |
40
| 0 | 0 |
5 | 0 | 0 | 0 |
40
| 0 | 0 |
6 | 0 | 0 | 0 |
40
| 0 | 0 |
7 | 0 | 0 | 0 | 0 |
40
| 0 |
8 |
12
| 0 |
28
| 0 | 0 | 0 |
9 | 0 |
30
| 0 | 0 | 0 | 0 |
10 | 0 |
30
| 0 | 0 | 0 | 0 |
11 | 0 | 0 | 0 |
26
| 0 |
4
|
12 | 0 | 0 | 0 |
30
| 0 | 0 |
13 | 0 | 0 | 0 |
29
| 0 |
1
|
14 | 0 | 0 | 0 | 0 | 0 |
30
|
15 | 0 | 0 | 0 |
1
| 0 |
29
|
16 | 0 | 0 | 0 |
29
| 0 | 0 |
17 | 0 | 0 | 0 |
30
| 0 | 0 |
18 | 0 | 0 | 0 | 0 | 0 |
30
|
19 | 0 | 0 | 0 |
29
| 0 |
1
|
20 |
30
| 0 | 0 | 0 | 0 | 0 |
21 |
20
| 0 | 0 | 0 | 0 |
10
|
22 | 0 | 0 | 0 | 0 |
30
| 0 |
23 |
14
| 0 | 0 | 0 |
16
| 0 |
24 | 0 |
30
| 0 | 0 | 0 | 0 |
kappa Statistic | 0.90 |
Intra- and interclass correlation
Analyte | Intersite variance | Intersample variance | Residual variance | ICC_intra | ICC_inter | kappa Statistic | |
ERBB2
| 0.039 | 2.886 | 0.054 |
0.982
|
0.987
|
1.00
| |
ESR1
| 0.049 | 5.889 | 0.144 |
0.976
|
0.992
|
0.91
| |
PGR
| 0.013 | 8.279 | 0.031 |
0.996
|
0.998
|
0.94
| |
MKI67
| 0.032 | 1.565 | 0.039 |
0.976
|
0.980
|
0.94
| |
Subtype | N/A |
0.90
| |||||
Analyte | Intersite variance (present study) | Intersample variance (FinHer data) | Residual variance (present study) | ICC_intra | ICC_inter | kappa Statistic (median) | 2.5–97.5% percentile |
ERBB2
| 0.039 | 3.723 | 0.054 |
0.986
|
0.990
|
0.95
| 0.92–0.97 |
ESR1
| 0.049 | 5.941 | 0.144 |
0.977
|
0.992
|
0.97
| 0.96–0.99 |
PGR
| 0.013 | 7.461 | 0.031 |
0.996
|
0.998
|
0.97
| 0.96–0.99 |
MKI67
| 0.032 | 1.739 | 0.039 |
0.978
|
0.982
|
0.85
| 0.82–0.88 |
Subtype | N/A |
0.91
| 0.89-0.93 |