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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.
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Breast Cancer Research

ISSN: 1465-542X

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