Table 3.

The range of tumor biomarker technologies used to generate cancer predictors and prognosticators, with references to examples discussed in this review.

Measurement target	Technology	Reference
Single genes	FISH	[Lebeau et al. 2001]
	CISH and SISH	[Penault-Llorca et al. 2009]
Sets of genes	FISH	[Davis et al. 2007]
	DNA sequencing	[Ley et al. 2008]
	DNA SNP analysis	[Tenesa and Dunlop, 2009;  Easton et al. 2007]
Methylated gene promoters	Methylation-specific  quantitative PCR	[Huang et al. 2009]
Pairs of mRNAs	Quantitative PCR	[Ma et al. 2004]
Sets of mRNAs	Quantitative PCR	[Paik et al. 2004 #2974]
	Microarrays	[Liu et al. 2007; Sotiriou et al. 2006;  Wang et al. 2005; Van ‘t Veer et al. 2002]
	RNA-seq	[Shah et al. 2009]
	Microelectrodes	[Fang et al. 2009]
Tumor classification inferred from mRNAs	Microarrays	[Sorlie et al. 2001; Perou et al. 2000]
Tumor grade inferred from mRNAs	Microarrays	[Sotiriou et al. 2006a]
Tumor signaling pathways  inferred from mRNAs	Microarrays	[Bild et al. 2006a; West et al. 2001]
Exon usage	Exon-specific micorarrays	[Andre et al. 2009]
Sets of miRNAs and ncRNAs	Quantitative PCR	[Zhu et al. 2009]
Single proteins	Immunohistochemistry	[Pertschuk et al. 1979]
Sets of proteins	Immunohistochemistry	[Ring et al. 2006]
Metabolites	Biochemical assays	[Sreekumar et al. 2009]
Tumor functional pathways	Image-based probes such as PET	[Contractor and Aboagye, 2009]
Clinical data	Decision support tools	[Ravdin et al. 2001]
Clinical and mRNA data	Integrative models	[Acharya et al. 2008; Cardoso et al. 2008]

CISH, chromogenic in situ hybridization; FISH, fluorescent in situ hybridization; miRNAs, micro-RNAs; ncRNAs, noncoding RNAs; PCR, polymerase chain reaction; PET, positron-emission tomography; SISH, silver-enhanced in situ hybridization; SNP, single nucleotide polymorphisms.