Table 1.

Gene expression studies in RCC (reproduced with kind permission from Springer Science+Business Media: Curr Oncol Rep: Renal cell carcinoma: where will the state-of-the-art lead us? Volume 12 (2010) 193–201, Brannon AR, Rathmell WK, Table X[116]).

Study	Year	Samples	Analytical focus	Results
Clinically driven analyses
Takahashi [39]	2001	29 clear cell	5 year survival	51 probes associate with survival, 96% accuracy
		29 normal
Vasselli[40]	2003	51 clear cell	Survival	45 genes most associated with survival. VCAM-1 alone can stratify patients by survival.
		6 papillary
		1 unknown
Jones [117]	2005	22 clear cell	Progression and metastases	31 genes that are continuously deregulated in disease progression. 155 genes that associate with metastases, 88.9% accuracy
		10 metastases
		37 other
		24 normal
Kosari [118]	2005	10 aggressive cc	Tumor aggressiveness	35 genes distinguish between non-aggressive and aggressive tumors. Survivin expression associated with survival by multivariate analysis in 183 patients
		9 non-aggressive cc
		9 metastatic cc
		12 normal
Zhao [47]	2006	177 clear cell	Unsupervised	2 primary clusters composed of 5 subclusters with survival difference.
Yao [119]	2008	25 clear cell (14 metastatic)	Metastatic vs non- metastatic	3 genes (VCAM-1, EDNRB, RGS5) that by qRT-PCR associate with survival
		2 metastases
Wuttig[51]	2009	20 metastatic clear cell	Disease-free interval Number of metastases	306 differentially expressed genes differentiate early (≤ 9 months) versus late (≥5 years) occurring metastases 163 probe sets differentiate patients with multiple (≥16) and “few”( ≤8) metastases
Biology-driven analyses
Vasselli [40]	2003	51 clear cell	Unsupervised	2 clusters of metastatic tumors with survival difference
		6 papillary
		1 unknown
Skubitz [49]	2006	16 clear cell	Unsupervised	2 subtypes distinguishable by 546 genes, with possible pathway differences
		21 normal
Zhao [47]	2006	177 clear cell	Survival	259 genes associated with survival by univariate and multivariate analysis
Gordan [27]	2008	21 clear cell	Wild-type VHL vs H1H2 vs H2 tumors	3 groups have distinct biological pathways. H2 tumors overexpress c-Myc, leading to increased proliferation
Zhao [48]	2009	177 clear cell	Biology of survival gene set	Good prognosis tumors resemble normal renal cortex or glomerulus. Poor prognosis tumors associated with wound healing and loss of differentiation gene sets.
Brannon [50]	2010	48 clear cell	Unsupervised consensus clustering	2 subtypes of clear cell (ccA and ccB) with pathway and survival differences, differentiable by <120 probes
		18 normal
Gene Expression and Cytogenetics/Sequencing Analyses
Furge [31]	2004	60 clear cell	Histological classification by virtual cytogenetics	1018 gene classifier and cytogenetic classifier to distinguish between 3 subtypes, 99% and 81% accuracy, respectively.
		5 papillary
		16 chromophobe
Sultmann [34]	2005	65 clear cell	Cytogenetics; Metastases and survival	136 genes significantly associated with cytogenetic abnormalities. 45 genes associated with survival. 85 genes associated with metastasis formation.
		13 papillary
		9 chromophobe
		25 normal
Beroukhim [30]	2009	49 sporadic cc	VHL disease vs sporadic clear cell	VHL disease and sporadic clear cell tumors have similar gene expression and cytogenetic profiles, but sporadic cases have more frequent alterations.
		5 metastases
		36 VHL tumors
Dalgliesh [29]	2010	96 clear cell	Genetics by sequencing	Mutations in histone modification and DNA damage repair genes may be important in RCC development or progression

cc, Clear Cell; H1H2, HIF-1 and HIF-2 overexpressing; H2, HIF-2 only overexpressing; VHL, von Hippel Lindau