Table 1.
Histology, RNA, and Microarray Quality Control Measures
| Patient Sample | Histology QC |
RNA QC |
Microarray QC |
|||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Histology | Size | Grade | ER | PR | HER2 | CA (%) | Other Features | Concentration (μg/μL) | 260/280 | 260/230 | % P | Actin | GAPDH | |
| A1 | Ductal | 2.3 | 3 | + | + | − | 90 | 0.339 | 2.08 | 2.03 | 54.2 | 1.49 | 1.44 | |
| A2 | 80 | 0.097 | 2.09 | 2.37 | 49.7 | 2.09 | 2.09 | |||||||
| A3 | 65 | 0.162 | 2.09 | 2.08 | 53.9 | 2.04 | 1.77 | |||||||
| B1 | Lobular | 3.6 | 2 | + | + | − | 50 | 0.068 | 2.02 | 2.24 | 53.4 | 1.34 | 1.26 | |
| B2 | 85 | 0.08 | 2.09 | 2.44 | 50.6 | 1.21 | 1.12 | |||||||
| B3 | 70 | 0.068 | 2.11 | 1.86 | 53 | 1.81 | 1.36 | |||||||
| C1 | Ductal | 2 | 2 | + | + | − | 10 | Biopsy site | 0.042 | 1.98 | 2.39 | 54.3 | 1.49 | 1.14 |
| C2 | 80 | Biopsy site | 0.093 | 2.06 | 1.63 | 56 | 1.37 | 1.01 | ||||||
| C3 | 40 | Biopsy site | 0.07 | 2.04 | 0.84 | 57 | 1.24 | 1 | ||||||
| D1 | Ductal | 2.8 | 2 | + | + | − | 30 | 0.158 | 2.08 | 2.27 | 55.3 | 1.54 | 1.31 | |
| D2 | 50 | 0.147 | 2.08 | 1.59 | 50.4 | 1.35 | 1.28 | |||||||
| D3 | 70 | 0.182 | 2.1 | 2.22 | 52 | 1.21 | 1.23 | |||||||
| E1 | Ductal | 2.1 | 3 | − | − | − | 25 | 0.269 | 2.08 | 1.82 | 52.7 | 1.17 | 1.03 | |
| E2 | 75 | 0.324 | 2.08 | 2.27 | 50.9 | 1.14 | 1.05 | |||||||
| E3 | 50 | 0.26 | 2.08 | 2.2 | 53.5 | 1.08 | 1.09 | |||||||
| F1 | Ductal/micropapillary | Multi-focal | 2 | + | − | − | 25 | 0.06 | 2.11 | 1.8 | 54.1 | 1.89 | 1.17 | |
| F2 | 60 | 0.292 | 2.06 | 2.19 | 54 | 1.19 | 1.13 | |||||||
| F3 | 25 | 0.079 | 2.04 | 2.13 | 54.2 | 1.18 | 0.99 | |||||||
| G1 | Ductal | 3.4 | 3 | − | − | − | 70 | 0.515 | 2.08 | 2.19 | 51.3 | 3.31 | 1.31 | |
| G2 | 30 | 0.076 | 2.03 | 2.39 | 56.1 | 1.13 | 0.98 | |||||||
| G3 | 70 | 0.331 | 2.07 | 2.24 | 54.4 | 1.21 | 1.04 | |||||||
| H1 | Ductal | 1.6 | 3 | − | − | − | 30 | 0.112 | 2.11 | 1.59 | 50.3 | 2.94 | 1.12 | |
| H2 | 30 | 0.096 | 1.92 | 0.92 | 54.1 | 2.21 | 1.09 | |||||||
| H3 | 30 | 0.072 | 2.12 | 1.29 | 49.7 | 1.49 | 1.09 | |||||||
| H4 | 20 | 0.285 | 2.09 | 1.98 | 49.6 | 6.66 | 1.95 | |||||||
| I1 | Ductal/lobular | > 2 | 2 | + | + | − | 70 | 0.237 | 2.11 | 1.96 | 52.5 | 2.35 | 1.19 | |
| I2 | 70 | 0.331 | 2.09 | 2.03 | 51 | 2.17 | 1.15 | |||||||
| I3 | 70 | 0.173 | 2.12 | 2.07 | 51.5 | 1.79 | 1.1 | |||||||
| J1 | Ductal | 3.5 | 3 | + | + | − | 80 | 0.682 | 2.08 | 1.93 | 49.8 | 3.85 | 1.47 | |
| J2 | 80 | 0.941 | 2.08 | 2.11 | 51.3 | 2.91 | 1.42 | |||||||
| J3 | 80 | 0.561 | 2.07 | 2.17 | 50.8 | 3.49 | 1.57 | |||||||
| K1 | Ductal | 2.4 | 2 | + | + | − | 15 | DCIS | 0.068 | 2.12 | 1.66 | 51.4 | 1.88 | 1.22 |
| K2 | 75 | DCIS | 0.044 | 2.06 | 1.85 | 55 | 1.85 | 1.04 | ||||||
| L1 | Ductal | 1.3 | 3 | + | + | − | 0 | DCIS | 0.055 | 2.1 | 1.31 | 51.2 | 1.55 | 1.17 |
| L2 | 15 | DCIS | 0.083 | 2.11 | 1.84 | 50.7 | 1.39 | 0.92 | ||||||
| L3 | 15 | DCIS | 0.099 | 2.09 | 1.21 | 51 | 1.69 | 1.06 | ||||||
| M1 | Ductal | 1.9 | 2 | + | + | − | 50 | 0.116 | 2.1 | 1.74 | 50.3 | 2.49 | 1.75 | |
| M2 | 50 | Necrosis | 0.09 | 2.08 | 1.74 | 49.1 | 1.58 | 1.1 | ||||||
| M3 | 30 | 0.084 | 2.12 | 1.65 | 45.5 | 2.06 | 1.35 | |||||||
| N1 | Ductal | 1.8 | 2 | + | + | − | 20 | 0.077 | 2.14 | 1.8 | 50.5 | 1.57 | 1.19 | |
| N2 | 70 | 0.068 | 2.06 | 1.96 | 52.9 | 1.28 | 1.09 | |||||||
| N3 | 70 | 0.069 | 2.13 | 0.67 | 51.6 | 1.74 | 1.33 | |||||||
| O1 | Ductal | 3 | 1 | + | + | − | 20 | Carcinoma + papilloma | 0.261 | 2.11 | 2.2 | 53.7 | 2 | 0.95 |
| O2 | 50 | Carcinoma + papilloma | 0.143 | 2.13 | 1.24 | 55.5 | 2.06 | 1.13 | ||||||
| P1 | Ductal | 0.9 | 3 | − | − | − | 60 | 0.05 | 2.11 | 1.89 | 54.4 | 1.34 | 1.06 | |
| P2 | 10 | 0.044 | 2.15 | 1.61 | 56.6 | 1.34 | 1.05 | |||||||
| Q1 | Ductal | 1.8 | 3 | − | + | − | 70 | Biopsy site | 0.474 | 2.07 | 2.03 | 51.9 | 2.13 | 1.08 |
| Q2 | 30 | Biopsy site | 0.226 | 2.11 | 2.03 | 55.1 | 2.02 | 1.02 | ||||||
| R1 | Ductal | 2.8 | 3 | + | − | − | 70 | Biopsy site | 0.156 | 2.07 | 2.1 | 52.8 | 1.66 | 1.12 |
| R2 | 20 | Biopsy site | 0.132 | 2.1 | 2.14 | 52.8 | 2.33 | 1.26 | ||||||
NOTE. 260/280 and 260/230 are optical density ratios; CA is the tumor content in percent; % P is the percent of probe sets present; actin and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) are the 3′ to 5′ probe set ratios for the actin and GAPDH probe sets, respectively.
Abbreviations: QC, quality control; ER, estrogen receptor; PR, progesterone receptor; HER2, human epidermal growth factor receptor 2; DCIS, ductal carcinoma-in-situ.