Table 1.

Gene expression studies in RCC

Study	Year	Samples	Analytical focus	Results
Clinically driven analyses
Takahashi et al. [24]	2001	29 cc 29 normal	5-year survival	51 probes associate with survival, 96% accuracy
Vasselli et al. [25]	2003	51 cc 6 papillary 1 unknown	Survival	45 genes most associated with survival; VCAM-1 alone can stratify patients by survival
Jones et al. [28]	2005	22 cc 10 metastases 37 other 24 normal	Progression and metastases	31 genes that are continuously deregulated in disease progression; 155 genes that associate with metastases, 88.9% accuracy
Kosari et al. [29]	2005	10 aggressive cc 9 non-aggressive cc 9 metastatic cc 12 normal	Tumor aggressiveness	35 genes distinguish between non-aggressive and aggressive tumors; survivin expression associated with survival by multivariate analysis in 183 patients
Zhao et al. [32•]	2006	177 cc	Unsupervised	2 primary clusters composed of 5 subclusters with survival difference
Yao et al. [27]	2008	25 cc (14 metastatic) 2 metastases	Metastatic vs nonmetastatic	3 genes (VCAM-1, EDNRB, RGS5) that by qRT-PCR associate with survival
Biology-driven analyses
Vasselli et al. [25]	2003	51 cc 6 papillary 1 unknown	Unsupervised	2 clusters of metastatic tumors with survival difference
Skubitz et al. [35]	2006	16 cc 21 normal	Unsupervised	2 subtypes distinguishable by 546 genes, with possible pathway differences
Zhao et al. [32•]	2006	177 cc	Survival	259 genes associated with survival by univariate and multivariate analysis
Gordan et al. [16••]	2008	21 cc	Wild-type VHL vs H1H2 vs H2 tumors	3 groups have distinct biological pathways; H2 tumors overexpress c-Myc, leading to increased proliferation
Zhao et al. [33]	2009	177 cc	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 et al. [36]	2010	48 cc 18 normal	Unsupervised consensus clustering	2 subtypes of cc (ccA and ccB) with pathway and survival differences, differentiable by < 120 probes
Gene expression and cytogenetics/sequencing analyses
Furge et al. [18]	2004	60 cc 5 papillary 16 chromophobe	Histological classification by virtual cytogenetics	1018 gene classifier and cytogenetic classifier to distinguish between 3 subtypes, 99% and 81% accuracy, respectively
Sultmann et al. [19]	2005	65 cc 13 papillary 9 chromophobe 25 normal	Cytogenetics; metastases and survival	136 genes significantly associated with cytogenetic abnormalities; 45 genes associated with survival; 85 genes associated with metastasis formation
Beroukhim et al. [21•]	2009	49 sporadic cc 5 metastases 36 VHL tumors	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
Dalgliesh et al. [17••]	2010	96 cc	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; PCR—polymerase chain reaction; RCC—renal cell carcinoma; VCAM—vascular cell adhesion molecule; VHL—von Hippel Lindau.