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Table 1 Gene expression studies of breast carcinomas aiming to improve clinical management

From: High-throughput genomic technology in research and clinical management of breast cancer. Exploiting the potential of gene expression profiling: is it ready for the clinic?

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]
  1. 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.