Dataset: Breast cancer and liver tissue biopsies used to develop and validate an index for liver contamination in metastatic breast cancer
PURPOSE: To develop an index capable of detecting and quantifying the extent of liver RNA contamination in liver biopsies of metastatic...
PURPOSE: To develop an index capable of detecting and quantifying the extent of liver RNA contamination in liver biopsies of metastatic breast cancer METHODS: We developed a microarray-based gene expression liver index by comparing the expression levels of genes in liver tissue biopsies and in primary breast cancer biopsies. The predictive performance of the index was then evaluated in defined mixtures of liver and breast cancer RNA. A calibration curve was established to allow estimation of the liver RNA content in unknown metastatic breast cancer samples. A set of liver biopsies and primary breast cancer biopsies were used to identify genes that were expressed significantly higher in liver tissue. These genes were used in a liver index, which was validated in a new set of liver and primary breast cancer biopsies. A set of liver/breast cancer RNA mixtures was used to establish a calibration curve to allow quantification of liver contamination in metastatic breast cancer samples. The prediction error of the calibration curve was assessed in a new set of liver/breast cancer RNA mixtures and applied to estimate the liver content in a set of unknown metastatic breast cancer biopsies.
- Species:
- human
- Samples:
- 203
- Source:
- E-GEOD-33116
- Updated:
- Dec.12, 2014
- Registered:
- Jul.22, 2014
Factors:
(via ArrayExpress)
| Sample | SAMPLE ID | SAMPLE COHORT | PERCENT LIVER | ORGANISM PART |
|---|---|---|---|---|
| GSM82035 | metbc_23 | met_BC | NA | Metastatic breast cancer biopsy |
| GSM820350 | metbc_22 | met_BC | NA | Metastatic breast cancer biopsy |
| GSM820349 | metbc_21 | met_BC | NA | Metastatic breast cancer biopsy |
| GSM820348 | metbc_20 | met_BC | NA | Metastatic breast cancer biopsy |
| GSM820347 | metbc_19 | met_BC | NA | Metastatic breast cancer biopsy |
| GSM820346 | metbc_18 | met_BC | NA | Metastatic breast cancer biopsy |
| GSM820345 | metbc_17 | met_BC | NA | Metastatic breast cancer biopsy |
| GSM820344 | metbc_16 | met_BC | NA | Metastatic breast cancer biopsy |
| GSM820343 | metbc_15 | met_BC | NA | Metastatic breast cancer biopsy |
| GSM820342 | metbc_14 | met_BC | NA | Metastatic breast cancer biopsy |
| GSM82034 | metbc_13 | met_BC | NA | Metastatic breast cancer biopsy |
| GSM820340 | metbc_12 | met_BC | NA | Metastatic breast cancer biopsy |
| GSM820339 | metbc_11 | met_BC | NA | Metastatic breast cancer biopsy |
| GSM820338 | metbc_10 | met_BC | NA | Metastatic breast cancer biopsy |
| GSM820337 | metbc_9 | met_BC | NA | Metastatic breast cancer biopsy |
| GSM820336 | metbc_8 | met_BC | NA | Metastatic breast cancer biopsy |
| GSM820335 | metbc_7 | met_BC | NA | Metastatic breast cancer biopsy |
| GSM820334 | metbc_6 | met_BC | NA | Metastatic breast cancer biopsy |
| GSM820333 | metbc_5 | met_BC | NA | Metastatic breast cancer biopsy |
| GSM820332 | metbc_4 | met_BC | NA | Metastatic breast cancer biopsy |
| GSM82033 | metbc_3 | met_BC | NA | Metastatic breast cancer biopsy |
| GSM820330 | metbc_2 | met_BC | NA | Metastatic breast cancer biopsy |
| GSM820329 | metbc_1 | met_BC | NA | Metastatic breast cancer biopsy |
| GSM820328 | mix_11 | mix11 | 100 | breast cancer tumor and liver mixture |
| GSM820327 | mix_11 | mix11 | 90 | breast cancer tumor and liver mixture |
| GSM820326 | mix_11 | mix11 | 75 | breast cancer tumor and liver mixture |
| GSM820325 | mix_11 | mix11 | 50 | breast cancer tumor and liver mixture |
| GSM820324 | mix_11 | mix11 | 25 | breast cancer tumor and liver mixture |
| GSM820323 | mix_11 | mix11 | 20 | breast cancer tumor and liver mixture |
| GSM820322 | mix_11 | mix11 | 15 | breast cancer tumor and liver mixture |
| GSM82032 | mix_11 | mix11 | 10 | breast cancer tumor and liver mixture |
| GSM820320 | mix_11 | mix11 | 5 | breast cancer tumor and liver mixture |
| GSM820319 | mix_11 | mix11 | not specified | breast cancer tumor and liver mixture |
| GSM820318 | mix_10 | mix11 | 100 | breast cancer tumor and liver mixture |
| GSM820317 | mix_10 | mix11 | 90 | breast cancer tumor and liver mixture |
| GSM820316 | mix_10 | mix11 | 75 | breast cancer tumor and liver mixture |
| GSM820315 | mix_10 | mix11 | 50 | breast cancer tumor and liver mixture |
| GSM820314 | mix_10 | mix11 | 25 | breast cancer tumor and liver mixture |
| GSM820313 | mix_10 | mix11 | 20 | breast cancer tumor and liver mixture |
| GSM820312 | mix_10 | mix11 | 15 | breast cancer tumor and liver mixture |
| GSM8203 | mix_10 | mix11 | 10 | breast cancer tumor and liver mixture |
| GSM820310 | mix_10 | mix11 | 5 | breast cancer tumor and liver mixture |
| GSM820309 | mix_10 | mix11 | not specified | breast cancer tumor and liver mixture |
| GSM820308 | mix_9 | mix11 | 100 | breast cancer tumor and liver mixture |
| GSM820307 | mix_9 | mix11 | 90 | breast cancer tumor and liver mixture |
| GSM820306 | mix_9 | mix11 | 75 | breast cancer tumor and liver mixture |
| GSM820305 | mix_9 | mix11 | 50 | breast cancer tumor and liver mixture |
| GSM820304 | mix_9 | mix11 | 25 | breast cancer tumor and liver mixture |
| GSM820303 | mix_9 | mix11 | 20 | breast cancer tumor and liver mixture |
| GSM820302 | mix_9 | mix11 | 15 | breast cancer tumor and liver mixture |
| GSM82030 | mix_9 | mix11 | 10 | breast cancer tumor and liver mixture |
| GSM820300 | mix_9 | mix11 | 5 | breast cancer tumor and liver mixture |
| GSM820299 | mix_9 | mix11 | not specified | breast cancer tumor and liver mixture |
| GSM820298 | mix_8 | mix11 | 100 | breast cancer tumor and liver mixture |
| GSM820297 | mix_8 | mix11 | 90 | breast cancer tumor and liver mixture |
| GSM820296 | mix_8 | mix11 | 75 | breast cancer tumor and liver mixture |
| GSM820295 | mix_8 | mix11 | 50 | breast cancer tumor and liver mixture |
| GSM820294 | mix_8 | mix11 | 25 | breast cancer tumor and liver mixture |
| GSM820293 | mix_8 | mix11 | 20 | breast cancer tumor and liver mixture |
| GSM820292 | mix_8 | mix11 | 15 | breast cancer tumor and liver mixture |
| GSM82029 | mix_8 | mix11 | 10 | breast cancer tumor and liver mixture |
| GSM820290 | mix_8 | mix11 | 5 | breast cancer tumor and liver mixture |
| GSM820289 | mix_8 | mix11 | not specified | breast cancer tumor and liver mixture |
| GSM820288 | mix_7 | mix11 | 100 | breast cancer tumor and liver mixture |
| GSM820287 | mix_7 | mix11 | 90 | breast cancer tumor and liver mixture |
| GSM820286 | mix_7 | mix11 | 75 | breast cancer tumor and liver mixture |
| GSM820285 | mix_7 | mix11 | 50 | breast cancer tumor and liver mixture |
| GSM820284 | mix_7 | mix11 | 25 | breast cancer tumor and liver mixture |
| GSM820283 | mix_7 | mix11 | 20 | breast cancer tumor and liver mixture |
| GSM820282 | mix_7 | mix11 | 15 | breast cancer tumor and liver mixture |
| GSM82028 | mix_7 | mix11 | 10 | breast cancer tumor and liver mixture |
| GSM820280 | mix_7 | mix11 | 5 | breast cancer tumor and liver mixture |
| GSM820279 | mix_7 | mix11 | not specified | breast cancer tumor and liver mixture |
| GSM820278 | mix_6 | mix11 | 100 | breast cancer tumor and liver mixture |
| GSM820277 | mix_6 | mix11 | 90 | breast cancer tumor and liver mixture |
| GSM820276 | mix_6 | mix11 | 75 | breast cancer tumor and liver mixture |
| GSM820275 | mix_6 | mix11 | 50 | breast cancer tumor and liver mixture |
| GSM820274 | mix_6 | mix11 | 25 | breast cancer tumor and liver mixture |
| GSM820273 | mix_6 | mix11 | 20 | breast cancer tumor and liver mixture |
| GSM820272 | mix_6 | mix11 | 15 | breast cancer tumor and liver mixture |
| GSM82027 | mix_6 | mix11 | 10 | breast cancer tumor and liver mixture |
| GSM820270 | mix_6 | mix11 | 5 | breast cancer tumor and liver mixture |
| GSM820269 | mix_6 | mix11 | not specified | breast cancer tumor and liver mixture |
| GSM820268 | mix_5 | mix11 | 100 | breast cancer tumor and liver mixture |
| GSM820267 | mix_5 | mix11 | 90 | breast cancer tumor and liver mixture |
| GSM820266 | mix_5 | mix11 | 75 | breast cancer tumor and liver mixture |
| GSM820265 | mix_5 | mix11 | 50 | breast cancer tumor and liver mixture |
| GSM820264 | mix_5 | mix11 | 25 | breast cancer tumor and liver mixture |
| GSM820263 | mix_5 | mix11 | 20 | breast cancer tumor and liver mixture |
| GSM820262 | mix_5 | mix11 | 15 | breast cancer tumor and liver mixture |
| GSM82026 | mix_5 | mix11 | 10 | breast cancer tumor and liver mixture |
| GSM820260 | mix_5 | mix11 | 5 | breast cancer tumor and liver mixture |
| GSM820259 | mix_5 | mix11 | not specified | breast cancer tumor and liver mixture |
| GSM820258 | mix_4 | mix11 | 100 | breast cancer tumor and liver mixture |
| GSM820257 | mix_4 | mix11 | 90 | breast cancer tumor and liver mixture |
| GSM820256 | mix_4 | mix11 | 75 | breast cancer tumor and liver mixture |
| GSM820255 | mix_4 | mix11 | 50 | breast cancer tumor and liver mixture |
| GSM820254 | mix_4 | mix11 | 25 | breast cancer tumor and liver mixture |
| GSM820253 | mix_4 | mix11 | 20 | breast cancer tumor and liver mixture |
| GSM820252 | mix_4 | mix11 | 15 | breast cancer tumor and liver mixture |
| GSM82025 | mix_4 | mix11 | 10 | breast cancer tumor and liver mixture |
| GSM820250 | mix_4 | mix11 | 5 | breast cancer tumor and liver mixture |
| GSM820249 | mix_4 | mix11 | not specified | breast cancer tumor and liver mixture |
| GSM820248 | mix_3 | mix11 | 100 | breast cancer tumor and liver mixture |
| GSM820247 | mix_3 | mix11 | 90 | breast cancer tumor and liver mixture |
| GSM820246 | mix_3 | mix11 | 75 | breast cancer tumor and liver mixture |
| GSM820245 | mix_3 | mix11 | 50 | breast cancer tumor and liver mixture |
| GSM820244 | mix_3 | mix11 | 25 | breast cancer tumor and liver mixture |
| GSM820243 | mix_3 | mix11 | 20 | breast cancer tumor and liver mixture |
| GSM820242 | mix_3 | mix11 | 15 | breast cancer tumor and liver mixture |
| GSM82024 | mix_3 | mix11 | 10 | breast cancer tumor and liver mixture |
| GSM820240 | mix_3 | mix11 | 5 | breast cancer tumor and liver mixture |
| GSM820239 | mix_3 | mix11 | not specified | breast cancer tumor and liver mixture |
| GSM820238 | mix_2 | mix11 | 100 | breast cancer tumor and liver mixture |
| GSM820237 | mix_2 | mix11 | 90 | breast cancer tumor and liver mixture |
| GSM820236 | mix_2 | mix11 | 75 | breast cancer tumor and liver mixture |
| GSM820235 | mix_2 | mix11 | 50 | breast cancer tumor and liver mixture |
| GSM820234 | mix_2 | mix11 | 25 | breast cancer tumor and liver mixture |
| GSM820233 | mix_2 | mix11 | 20 | breast cancer tumor and liver mixture |
| GSM820232 | mix_2 | mix11 | 15 | breast cancer tumor and liver mixture |
| GSM82023 | mix_2 | mix11 | 10 | breast cancer tumor and liver mixture |
| GSM820230 | mix_2 | mix11 | 5 | breast cancer tumor and liver mixture |
| GSM820229 | mix_2 | mix11 | not specified | breast cancer tumor and liver mixture |
| GSM820228 | mix_1 | mix11 | 100 | breast cancer tumor and liver mixture |
| GSM820227 | mix_1 | mix11 | 90 | breast cancer tumor and liver mixture |
| GSM820226 | mix_1 | mix11 | 75 | breast cancer tumor and liver mixture |
| GSM820225 | mix_1 | mix11 | 50 | breast cancer tumor and liver mixture |
| GSM820224 | mix_1 | mix11 | 25 | breast cancer tumor and liver mixture |
| GSM820223 | mix_1 | mix11 | 20 | breast cancer tumor and liver mixture |
| GSM820222 | mix_1 | mix11 | 15 | breast cancer tumor and liver mixture |
| GSM82022 | mix_1 | mix11 | 10 | breast cancer tumor and liver mixture |
| GSM820220 | mix_1 | mix11 | 5 | breast cancer tumor and liver mixture |
| GSM820219 | mix_1 | mix11 | not specified | breast cancer tumor and liver mixture |
| GSM820218 | mix_0_R3 | mix1tripl | 5 | breast cancer tumor and liver mixture |
| GSM820217 | mix_0_R3 | mix1tripl | 10 | breast cancer tumor and liver mixture |
| GSM820216 | mix_0_R3 | mix1tripl | 15 | breast cancer tumor and liver mixture |
| GSM820215 | mix_0_R3 | mix1tripl | 20 | breast cancer tumor and liver mixture |
| GSM820214 | mix_0_R3 | mix1tripl | not specified | breast cancer tumor and liver mixture |
| GSM820213 | mix_0_R3 | mix1tripl | 25 | breast cancer tumor and liver mixture |
| GSM820212 | mix_0_R3 | mix1tripl | 50 | breast cancer tumor and liver mixture |
| GSM8202 | mix_0_R3 | mix1tripl | 70 | breast cancer tumor and liver mixture |
| GSM820210 | mix_0_R3 | mix1tripl | 75 | breast cancer tumor and liver mixture |
| GSM820209 | mix_0_R3 | mix1tripl | 80 | breast cancer tumor and liver mixture |
| GSM820208 | mix_0_R3 | mix1tripl | 85 | breast cancer tumor and liver mixture |
| GSM820207 | mix_0_R3 | mix1tripl | 90 | breast cancer tumor and liver mixture |
| GSM820206 | mix_0_R3 | mix1tripl | 100 | breast cancer tumor and liver mixture |
| GSM820205 | mix_0_R2 | mix1tripl | 5 | breast cancer tumor and liver mixture |
| GSM820204 | mix_0_R2 | mix1tripl | 10 | breast cancer tumor and liver mixture |
| GSM820203 | mix_0_R2 | mix1tripl | 15 | breast cancer tumor and liver mixture |
| GSM820202 | mix_0_R2 | mix1tripl | 20 | breast cancer tumor and liver mixture |
| GSM82020 | mix_0_R2 | mix1tripl | not specified | breast cancer tumor and liver mixture |
| GSM820200 | mix_0_R2 | mix1tripl | 25 | breast cancer tumor and liver mixture |
| GSM820199 | mix_0_R2 | mix1tripl | 50 | breast cancer tumor and liver mixture |
| GSM820198 | mix_0_R2 | mix1tripl | 70 | breast cancer tumor and liver mixture |
| GSM820197 | mix_0_R2 | mix1tripl | 75 | breast cancer tumor and liver mixture |
| GSM820196 | mix_0_R2 | mix1tripl | 80 | breast cancer tumor and liver mixture |
| GSM820195 | mix_0_R2 | mix1tripl | 85 | breast cancer tumor and liver mixture |
| GSM820194 | mix_0_R2 | mix1tripl | 90 | breast cancer tumor and liver mixture |
| GSM820193 | mix_0_R2 | mix1tripl | 100 | breast cancer tumor and liver mixture |
| GSM820192 | mix_0_R1 | mix1tripl | 5 | breast cancer tumor and liver mixture |
| GSM82019 | mix_0_R1 | mix1tripl | 10 | breast cancer tumor and liver mixture |
| GSM820190 | mix_0_R1 | mix1tripl | 15 | breast cancer tumor and liver mixture |
| GSM820189 | mix_0_R1 | mix1tripl | 20 | breast cancer tumor and liver mixture |
| GSM820188 | mix_0_R1 | mix1tripl | not specified | breast cancer tumor and liver mixture |
| GSM820187 | mix_0_R1 | mix1tripl | 25 | breast cancer tumor and liver mixture |
| GSM820186 | mix_0_R1 | mix1tripl | 50 | breast cancer tumor and liver mixture |
| GSM820185 | mix_0_R1 | mix1tripl | 70 | breast cancer tumor and liver mixture |
| GSM820184 | mix_0_R1 | mix1tripl | 75 | breast cancer tumor and liver mixture |
| GSM820183 | mix_0_R1 | mix1tripl | 80 | breast cancer tumor and liver mixture |
| GSM820182 | mix_0_R1 | mix1tripl | 85 | breast cancer tumor and liver mixture |
| GSM82018 | mix_0_R1 | mix1tripl | 90 | breast cancer tumor and liver mixture |
| GSM820180 | mix_0_R1 | mix1tripl | 100 | breast cancer tumor and liver mixture |
| GSM820179 | liver_31 | li_val | 100 | Liver biopsy |
| GSM820178 | liver_30 | li_val | 100 | Liver biopsy |
| GSM820177 | liver_29 | li_val | 100 | Liver biopsy |
| GSM820176 | liver_28 | li_val | 100 | Liver biopsy |
| GSM820175 | liver_27 | li_val | 100 | Liver biopsy |
| GSM820174 | liver_26 | li_val | 100 | Liver biopsy |
| GSM820173 | liver_25 | li_val | 100 | Liver biopsy |
| GSM820172 | liver_24 | li_val | 100 | Liver biopsy |
| GSM82017 | liver_23 | li_val | 100 | Liver biopsy |
| GSM820170 | liver_22 | li_val | 100 | Liver biopsy |
| GSM820169 | liver_21 | li_dev | 100 | Liver biopsy |
| GSM820168 | liver_20 | li_dev | 100 | Liver biopsy |
| GSM820167 | liver_19 | li_dev | 100 | Liver biopsy |
| GSM820166 | liver_18 | li_dev | 100 | Liver biopsy |
| GSM820165 | liver_17 | li_dev | 100 | Liver biopsy |
| GSM820164 | liver_16 | li_dev | 100 | Liver biopsy |
| GSM820163 | liver_15 | li_dev | 100 | Liver biopsy |
| GSM820162 | liver_14 | li_dev | 100 | Liver biopsy |
| GSM82016 | liver_13 | li_dev | 100 | Liver biopsy |
| GSM820160 | liver_12 | li_dev | 100 | Liver biopsy |
| GSM820159 | liver_11 | li_dev | 100 | Liver biopsy |
| GSM820158 | liver_10 | li_dev | 100 | Liver biopsy |
| GSM820157 | liver_9 | li_dev | 100 | Liver biopsy |
| GSM820156 | liver_8 | li_dev | 100 | Liver biopsy |
| GSM820155 | liver_7 | li_dev | 100 | Liver biopsy |
| GSM820154 | liver_6 | li_dev | 100 | Liver biopsy |
| GSM820153 | liver_5 | li_dev | 100 | Liver biopsy |
| GSM820152 | liver_4 | li_dev | 100 | Liver biopsy |
| GSM82015 | liver_3 | li_dev | 100 | Liver biopsy |
| GSM820150 | liver_2 | li_dev | 100 | Liver biopsy |
| GSM820149 | liver_1 | li_dev | 100 | Liver biopsy |