Table 1 |
|||||
|
Gene expression studies of breast carcinomas aiming to improve clinical management |
|||||
| Gene expression profiles and classifiers |
Tissue/population included |
Samples (n) |
Platform |
Number of differentially expressed cDNAs/oligos/probe sets (total) |
Ref. |
|
|
|||||
| Overall outcome/metastasis |
PBC (node -ve, age <55 years) |
117 |
oligo Agilent Hu25k |
70 (24,479) |
[7] |
| PBC (node ±ve, age <53 years) |
295 |
oligo Agilent Hu25k |
70 (24,479) |
[8] |
|
| PBC (node -ve, any age) |
287 |
Affymetrix U133A |
76 (22,283) |
[9] |
|
| PBC (node -ve, ER+ only) |
668 |
qRT-PCR |
21 genes |
[32,33] |
|
| PBC (population and validation cohorts) |
448 |
Affymetrix U133 set |
64 (44,792) |
[37] |
|
| Tumour classification |
PBC (+benign tissues) |
65 |
cDNA (Stanford) |
476 (8102) |
[3] |
| PBC (+benign tissues) |
78 |
cDNA (Stanford) |
476 (8102) |
[4] |
|
| PBC (+benign tissues) |
122 |
cDNA (Stanford) |
476 (8102) |
[5] |
|
| PBC (node ±ve) |
20 |
Agilent, Applied Biosystems, cDNA (Stanford) |
[6] |
||
| PBC + metastases |
105 |
Agilent oligo (1Av1, 1Av2) |
1300 (>17,000) |
[11] |
|
| PBC (node ±) |
99 |
cDNA (NCI) |
706 (7650) |
[38] |
|
| ER status |
PBC (2–5 cm, node -ve) |
47 |
cDNA |
100 (6728) |
[39] |
| PBC (1.5–5 cm, node ±ve, ER/PR +ve or -ve) |
49 |
Affymetrix HuGeneFL |
100 (5600) |
[40] |
|
| PRC (stage I-II, node -ve, ER and PR +ve) |
26 |
SAGE |
520 (>50,000) |
[41] |
|
| Nodal status |
PBC (ER ±ve, node ±ve) |
49 |
Affymetrix U95A |
100 (12,626) |
[42] |
| Apocrine |
PBC (large operable/advanced inoperable/inflammatory) |
49 |
Affymetrix U133A |
520 (22,283) |
[10] |
| Wound Response |
PBC (node ±ve, age <55 years) |
295 |
Oligo Agilent Hu25k |
442 (24,479) |
[16] |
| Proliferation |
PBC (node ±ve, age <55 years) |
311 |
Oligo Agilent Hu25k |
50 (24,479) |
[17] |
| Grade |
PBC (node ±ve, ER ±ve) |
189 |
Affymetrix U133A |
128 (22,283) |
[12] |
| Grade/progression |
Normal breast, ADH, DCIS, IDC (LCM) |
61 |
cDNA (Research Genetics) |
200 (1940) |
[43] |
| Hereditary breast cancer |
PBC (sporadic, BRCA1, BRCA2) |
22 |
DNA clones |
176 (6512) |
[18] |
| Fibroblasts from normal breast (BRCA1, normal controls) |
28 |
cDNA (IMAGE) |
47 (5603) |
[44] |
|
| Tamoxifen resistant |
PBC (responsive and nonresponsive to tamoxifen) |
112 |
cDNA (NKI) |
81 (19,200) |
[21] |
| ER response |
MCF-7 cells and luminal breast tumours |
65 |
cDNA (Agilent) |
822 (>17,000) |
[13] |
| Neoadjuvant chemotherapy response |
PBC (docetaxel) |
24 |
Affymetrix U95A |
92 (12,626) |
[20] |
| PBC (doxorubicin/cyclophosphamide) |
40 |
Affymetrix U133A |
253 (22,283) |
[19] |
|
| PBC (doxorubicin) |
36 |
Affymetrix U133A plus2.0 |
38 (54,678) |
[14] |
|
| PBC (gemcitabine/epirubicin/docetaxel) |
100 |
Custom made oligo |
512 (21,329) |
[45] |
|
| PBC (doxorubicin/cyclophosphamide) |
16 |
cDNA (NCI) |
137 (7650) |
[46] |
|
|
|
|||||
|
Whilst we have endeavoured to highlight the major studies in this field, we regret any offence to authors of other important work not included in this table. ADH, atypical ductal hyperplasia; DCIS, ductal carcinoma in situ; ER, oestrogen receptor; IDC, invasive ductal carcinoma; LCM, laser capture microdissection; PBC, primary breast carcinoma; PR, progesterone receptor; qRT-PCR, quantitative reverse transcription polymerase chain reaction. |
|||||
|
Sims et al. Breast Cancer Research 2006 8:214 doi:10.1186/bcr1605 |
|||||