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...

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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	ORGANISM PART	PERCENT LIVER
GSM82035	metbc_23	met_BC	Metastatic breast cancer biopsy	NA
GSM820350	metbc_22	met_BC	Metastatic breast cancer biopsy	NA
GSM820349	metbc_21	met_BC	Metastatic breast cancer biopsy	NA
GSM820348	metbc_20	met_BC	Metastatic breast cancer biopsy	NA
GSM820347	metbc_19	met_BC	Metastatic breast cancer biopsy	NA
GSM820346	metbc_18	met_BC	Metastatic breast cancer biopsy	NA
GSM820345	metbc_17	met_BC	Metastatic breast cancer biopsy	NA
GSM820344	metbc_16	met_BC	Metastatic breast cancer biopsy	NA
GSM820343	metbc_15	met_BC	Metastatic breast cancer biopsy	NA
GSM820342	metbc_14	met_BC	Metastatic breast cancer biopsy	NA
GSM82034	metbc_13	met_BC	Metastatic breast cancer biopsy	NA
GSM820340	metbc_12	met_BC	Metastatic breast cancer biopsy	NA
GSM820339	metbc_11	met_BC	Metastatic breast cancer biopsy	NA
GSM820338	metbc_10	met_BC	Metastatic breast cancer biopsy	NA
GSM820337	metbc_9	met_BC	Metastatic breast cancer biopsy	NA
GSM820336	metbc_8	met_BC	Metastatic breast cancer biopsy	NA
GSM820335	metbc_7	met_BC	Metastatic breast cancer biopsy	NA
GSM820334	metbc_6	met_BC	Metastatic breast cancer biopsy	NA
GSM820333	metbc_5	met_BC	Metastatic breast cancer biopsy	NA
GSM820332	metbc_4	met_BC	Metastatic breast cancer biopsy	NA
GSM82033	metbc_3	met_BC	Metastatic breast cancer biopsy	NA
GSM820330	metbc_2	met_BC	Metastatic breast cancer biopsy	NA
GSM820329	metbc_1	met_BC	Metastatic breast cancer biopsy	NA
GSM820328	mix_11	mix11	breast cancer tumor and liver mixture	100
GSM820327	mix_11	mix11	breast cancer tumor and liver mixture	90
GSM820326	mix_11	mix11	breast cancer tumor and liver mixture	75
GSM820325	mix_11	mix11	breast cancer tumor and liver mixture	50
GSM820324	mix_11	mix11	breast cancer tumor and liver mixture	25
GSM820323	mix_11	mix11	breast cancer tumor and liver mixture	20
GSM820322	mix_11	mix11	breast cancer tumor and liver mixture	15
GSM82032	mix_11	mix11	breast cancer tumor and liver mixture	10
GSM820320	mix_11	mix11	breast cancer tumor and liver mixture	5
GSM820319	mix_11	mix11	breast cancer tumor and liver mixture	not specified
GSM820318	mix_10	mix11	breast cancer tumor and liver mixture	100
GSM820317	mix_10	mix11	breast cancer tumor and liver mixture	90
GSM820316	mix_10	mix11	breast cancer tumor and liver mixture	75
GSM820315	mix_10	mix11	breast cancer tumor and liver mixture	50
GSM820314	mix_10	mix11	breast cancer tumor and liver mixture	25
GSM820313	mix_10	mix11	breast cancer tumor and liver mixture	20
GSM820312	mix_10	mix11	breast cancer tumor and liver mixture	15
GSM8203	mix_10	mix11	breast cancer tumor and liver mixture	10
GSM820310	mix_10	mix11	breast cancer tumor and liver mixture	5
GSM820309	mix_10	mix11	breast cancer tumor and liver mixture	not specified
GSM820308	mix_9	mix11	breast cancer tumor and liver mixture	100
GSM820307	mix_9	mix11	breast cancer tumor and liver mixture	90
GSM820306	mix_9	mix11	breast cancer tumor and liver mixture	75
GSM820305	mix_9	mix11	breast cancer tumor and liver mixture	50
GSM820304	mix_9	mix11	breast cancer tumor and liver mixture	25
GSM820303	mix_9	mix11	breast cancer tumor and liver mixture	20
GSM820302	mix_9	mix11	breast cancer tumor and liver mixture	15
GSM82030	mix_9	mix11	breast cancer tumor and liver mixture	10
GSM820300	mix_9	mix11	breast cancer tumor and liver mixture	5
GSM820299	mix_9	mix11	breast cancer tumor and liver mixture	not specified
GSM820298	mix_8	mix11	breast cancer tumor and liver mixture	100
GSM820297	mix_8	mix11	breast cancer tumor and liver mixture	90
GSM820296	mix_8	mix11	breast cancer tumor and liver mixture	75
GSM820295	mix_8	mix11	breast cancer tumor and liver mixture	50
GSM820294	mix_8	mix11	breast cancer tumor and liver mixture	25
GSM820293	mix_8	mix11	breast cancer tumor and liver mixture	20
GSM820292	mix_8	mix11	breast cancer tumor and liver mixture	15
GSM82029	mix_8	mix11	breast cancer tumor and liver mixture	10
GSM820290	mix_8	mix11	breast cancer tumor and liver mixture	5
GSM820289	mix_8	mix11	breast cancer tumor and liver mixture	not specified
GSM820288	mix_7	mix11	breast cancer tumor and liver mixture	100
GSM820287	mix_7	mix11	breast cancer tumor and liver mixture	90
GSM820286	mix_7	mix11	breast cancer tumor and liver mixture	75
GSM820285	mix_7	mix11	breast cancer tumor and liver mixture	50
GSM820284	mix_7	mix11	breast cancer tumor and liver mixture	25
GSM820283	mix_7	mix11	breast cancer tumor and liver mixture	20
GSM820282	mix_7	mix11	breast cancer tumor and liver mixture	15
GSM82028	mix_7	mix11	breast cancer tumor and liver mixture	10
GSM820280	mix_7	mix11	breast cancer tumor and liver mixture	5
GSM820279	mix_7	mix11	breast cancer tumor and liver mixture	not specified
GSM820278	mix_6	mix11	breast cancer tumor and liver mixture	100
GSM820277	mix_6	mix11	breast cancer tumor and liver mixture	90
GSM820276	mix_6	mix11	breast cancer tumor and liver mixture	75
GSM820275	mix_6	mix11	breast cancer tumor and liver mixture	50
GSM820274	mix_6	mix11	breast cancer tumor and liver mixture	25
GSM820273	mix_6	mix11	breast cancer tumor and liver mixture	20
GSM820272	mix_6	mix11	breast cancer tumor and liver mixture	15
GSM82027	mix_6	mix11	breast cancer tumor and liver mixture	10
GSM820270	mix_6	mix11	breast cancer tumor and liver mixture	5
GSM820269	mix_6	mix11	breast cancer tumor and liver mixture	not specified
GSM820268	mix_5	mix11	breast cancer tumor and liver mixture	100
GSM820267	mix_5	mix11	breast cancer tumor and liver mixture	90
GSM820266	mix_5	mix11	breast cancer tumor and liver mixture	75
GSM820265	mix_5	mix11	breast cancer tumor and liver mixture	50
GSM820264	mix_5	mix11	breast cancer tumor and liver mixture	25
GSM820263	mix_5	mix11	breast cancer tumor and liver mixture	20
GSM820262	mix_5	mix11	breast cancer tumor and liver mixture	15
GSM82026	mix_5	mix11	breast cancer tumor and liver mixture	10
GSM820260	mix_5	mix11	breast cancer tumor and liver mixture	5
GSM820259	mix_5	mix11	breast cancer tumor and liver mixture	not specified
GSM820258	mix_4	mix11	breast cancer tumor and liver mixture	100
GSM820257	mix_4	mix11	breast cancer tumor and liver mixture	90
GSM820256	mix_4	mix11	breast cancer tumor and liver mixture	75
GSM820255	mix_4	mix11	breast cancer tumor and liver mixture	50
GSM820254	mix_4	mix11	breast cancer tumor and liver mixture	25
GSM820253	mix_4	mix11	breast cancer tumor and liver mixture	20
GSM820252	mix_4	mix11	breast cancer tumor and liver mixture	15
GSM82025	mix_4	mix11	breast cancer tumor and liver mixture	10
GSM820250	mix_4	mix11	breast cancer tumor and liver mixture	5
GSM820249	mix_4	mix11	breast cancer tumor and liver mixture	not specified
GSM820248	mix_3	mix11	breast cancer tumor and liver mixture	100
GSM820247	mix_3	mix11	breast cancer tumor and liver mixture	90
GSM820246	mix_3	mix11	breast cancer tumor and liver mixture	75
GSM820245	mix_3	mix11	breast cancer tumor and liver mixture	50
GSM820244	mix_3	mix11	breast cancer tumor and liver mixture	25
GSM820243	mix_3	mix11	breast cancer tumor and liver mixture	20
GSM820242	mix_3	mix11	breast cancer tumor and liver mixture	15
GSM82024	mix_3	mix11	breast cancer tumor and liver mixture	10
GSM820240	mix_3	mix11	breast cancer tumor and liver mixture	5
GSM820239	mix_3	mix11	breast cancer tumor and liver mixture	not specified
GSM820238	mix_2	mix11	breast cancer tumor and liver mixture	100
GSM820237	mix_2	mix11	breast cancer tumor and liver mixture	90
GSM820236	mix_2	mix11	breast cancer tumor and liver mixture	75
GSM820235	mix_2	mix11	breast cancer tumor and liver mixture	50
GSM820234	mix_2	mix11	breast cancer tumor and liver mixture	25
GSM820233	mix_2	mix11	breast cancer tumor and liver mixture	20
GSM820232	mix_2	mix11	breast cancer tumor and liver mixture	15
GSM82023	mix_2	mix11	breast cancer tumor and liver mixture	10
GSM820230	mix_2	mix11	breast cancer tumor and liver mixture	5
GSM820229	mix_2	mix11	breast cancer tumor and liver mixture	not specified
GSM820228	mix_1	mix11	breast cancer tumor and liver mixture	100
GSM820227	mix_1	mix11	breast cancer tumor and liver mixture	90
GSM820226	mix_1	mix11	breast cancer tumor and liver mixture	75
GSM820225	mix_1	mix11	breast cancer tumor and liver mixture	50
GSM820224	mix_1	mix11	breast cancer tumor and liver mixture	25
GSM820223	mix_1	mix11	breast cancer tumor and liver mixture	20
GSM820222	mix_1	mix11	breast cancer tumor and liver mixture	15
GSM82022	mix_1	mix11	breast cancer tumor and liver mixture	10
GSM820220	mix_1	mix11	breast cancer tumor and liver mixture	5
GSM820219	mix_1	mix11	breast cancer tumor and liver mixture	not specified
GSM820218	mix_0_R3	mix1tripl	breast cancer tumor and liver mixture	5
GSM820217	mix_0_R3	mix1tripl	breast cancer tumor and liver mixture	10
GSM820216	mix_0_R3	mix1tripl	breast cancer tumor and liver mixture	15
GSM820215	mix_0_R3	mix1tripl	breast cancer tumor and liver mixture	20
GSM820214	mix_0_R3	mix1tripl	breast cancer tumor and liver mixture	not specified
GSM820213	mix_0_R3	mix1tripl	breast cancer tumor and liver mixture	25
GSM820212	mix_0_R3	mix1tripl	breast cancer tumor and liver mixture	50
GSM8202	mix_0_R3	mix1tripl	breast cancer tumor and liver mixture	70
GSM820210	mix_0_R3	mix1tripl	breast cancer tumor and liver mixture	75
GSM820209	mix_0_R3	mix1tripl	breast cancer tumor and liver mixture	80
GSM820208	mix_0_R3	mix1tripl	breast cancer tumor and liver mixture	85
GSM820207	mix_0_R3	mix1tripl	breast cancer tumor and liver mixture	90
GSM820206	mix_0_R3	mix1tripl	breast cancer tumor and liver mixture	100
GSM820205	mix_0_R2	mix1tripl	breast cancer tumor and liver mixture	5
GSM820204	mix_0_R2	mix1tripl	breast cancer tumor and liver mixture	10
GSM820203	mix_0_R2	mix1tripl	breast cancer tumor and liver mixture	15
GSM820202	mix_0_R2	mix1tripl	breast cancer tumor and liver mixture	20
GSM82020	mix_0_R2	mix1tripl	breast cancer tumor and liver mixture	not specified
GSM820200	mix_0_R2	mix1tripl	breast cancer tumor and liver mixture	25
GSM820199	mix_0_R2	mix1tripl	breast cancer tumor and liver mixture	50
GSM820198	mix_0_R2	mix1tripl	breast cancer tumor and liver mixture	70
GSM820197	mix_0_R2	mix1tripl	breast cancer tumor and liver mixture	75
GSM820196	mix_0_R2	mix1tripl	breast cancer tumor and liver mixture	80
GSM820195	mix_0_R2	mix1tripl	breast cancer tumor and liver mixture	85
GSM820194	mix_0_R2	mix1tripl	breast cancer tumor and liver mixture	90
GSM820193	mix_0_R2	mix1tripl	breast cancer tumor and liver mixture	100
GSM820192	mix_0_R1	mix1tripl	breast cancer tumor and liver mixture	5
GSM82019	mix_0_R1	mix1tripl	breast cancer tumor and liver mixture	10
GSM820190	mix_0_R1	mix1tripl	breast cancer tumor and liver mixture	15
GSM820189	mix_0_R1	mix1tripl	breast cancer tumor and liver mixture	20
GSM820188	mix_0_R1	mix1tripl	breast cancer tumor and liver mixture	not specified
GSM820187	mix_0_R1	mix1tripl	breast cancer tumor and liver mixture	25
GSM820186	mix_0_R1	mix1tripl	breast cancer tumor and liver mixture	50
GSM820185	mix_0_R1	mix1tripl	breast cancer tumor and liver mixture	70
GSM820184	mix_0_R1	mix1tripl	breast cancer tumor and liver mixture	75
GSM820183	mix_0_R1	mix1tripl	breast cancer tumor and liver mixture	80
GSM820182	mix_0_R1	mix1tripl	breast cancer tumor and liver mixture	85
GSM82018	mix_0_R1	mix1tripl	breast cancer tumor and liver mixture	90
GSM820180	mix_0_R1	mix1tripl	breast cancer tumor and liver mixture	100
GSM820179	liver_31	li_val	Liver biopsy	100
GSM820178	liver_30	li_val	Liver biopsy	100
GSM820177	liver_29	li_val	Liver biopsy	100
GSM820176	liver_28	li_val	Liver biopsy	100
GSM820175	liver_27	li_val	Liver biopsy	100
GSM820174	liver_26	li_val	Liver biopsy	100
GSM820173	liver_25	li_val	Liver biopsy	100
GSM820172	liver_24	li_val	Liver biopsy	100
GSM82017	liver_23	li_val	Liver biopsy	100
GSM820170	liver_22	li_val	Liver biopsy	100
GSM820169	liver_21	li_dev	Liver biopsy	100
GSM820168	liver_20	li_dev	Liver biopsy	100
GSM820167	liver_19	li_dev	Liver biopsy	100
GSM820166	liver_18	li_dev	Liver biopsy	100
GSM820165	liver_17	li_dev	Liver biopsy	100
GSM820164	liver_16	li_dev	Liver biopsy	100
GSM820163	liver_15	li_dev	Liver biopsy	100
GSM820162	liver_14	li_dev	Liver biopsy	100
GSM82016	liver_13	li_dev	Liver biopsy	100
GSM820160	liver_12	li_dev	Liver biopsy	100
GSM820159	liver_11	li_dev	Liver biopsy	100
GSM820158	liver_10	li_dev	Liver biopsy	100
GSM820157	liver_9	li_dev	Liver biopsy	100
GSM820156	liver_8	li_dev	Liver biopsy	100
GSM820155	liver_7	li_dev	Liver biopsy	100
GSM820154	liver_6	li_dev	Liver biopsy	100
GSM820153	liver_5	li_dev	Liver biopsy	100
GSM820152	liver_4	li_dev	Liver biopsy	100
GSM82015	liver_3	li_dev	Liver biopsy	100
GSM820150	liver_2	li_dev	Liver biopsy	100
GSM820149	liver_1	li_dev	Liver biopsy	100