Table 4. List of published comparative genomic hybridization (CGH) studies of kidney and renal cell carcinoma (RCC).
| Manuscript | Sporadic ccRCC Cases | Other tissues evalauted | Method | Factors evaluated | Finding |
|---|---|---|---|---|---|
| Wilhelm et al.22 | 16 | 13 Papillary, 5 chromophobe, | Array CGH-329 clones | RCC subtype segregation | Segregation of kidney tumor histological sub-types by copy number variation (CNV) differences |
| 6 Oncocytoma, 2 normal kidney | ccRCC 3p−, 5q+, and 6q−, 8p−, 9p− or 14q− | ||||
| Toma et al.17 | 22 | 22 Matched normal tissue | Affymetrix 10k chip | Survival | CNV most frequent at 3p−, 5q+, 14q−, 9−,7q+, 6q− |
| qPCR, immunohistochemistry (IHC) | Novel microdeletions at Chr1 , Chr 4, Chr6, Chr8 and Chr 9 | ||||
| Some alterations validated using gene and immunohistochemical (IHC) protein expression assays | |||||
| Arai et al.18 | 51 | NA | array CGH (4361 BACs) | Survival, grade, stage, vascular InvolvementPromoter methylation in 9 genes | CNV most frequent at 3p−, 5q+, 7+Genetic cluster profiles associated with survivial, independent of grade, stage |
| Chen et al.20 | 80 | NA | Illumina 317K SNP array | Stage, grade, telomere length | CNV most frequent at 3p−, 5q+, 8p12-pter, 6q23.3-27, 14q24.1-qter, 9q32-qter, |
| Demographics, smoking, alcohol, medical Hx | 10q22.3-qter, 9p13.3-pter, 4q28.3-qter, 1q25.1-qter, 7q21.13-qter, 8q24.12-qterLoss of heterozygosity (LOH) 9p, 9q, 14q, 18q associated with grade | ||||
| LOH 14q, 18p, 21q associated with stage | |||||
| LOH 2q, 6p, 6q, 9p, 9q, 17p associated with short telomere length | |||||
| Beroukhim et al.19 | 49, 5 Metastases | 36 Tumors/12 VHL patients | Affymetrix 250K StyI | Von Hippel–Lindau (VHL) disease, VHL inactivation, grade, | CNV most frequent at 3p−, 14q−, 5q+CNV higher in VHL WT compared with VHL disease cases |
| Gene expression differences | LOH 1p, 3p (VHL), 4q, 6q, 8p, 9p (CDKN2A, 2B) and 14q | ||||
| Amplification 1q, 2q, 5q, 7q, 8q (MYC), 12p and 20q | |||||
| Shuib et al.21 (data combined with Beroukim et al.) | 22 VHL wild-type (WT) | 57 VHL patients | Affymetrix 250K | VHL disease (germline) | CNV most frequent at 3p−, 14q−, 5q+7p+, 8p− (TNFRSF10C, DUSP4) associated with germline VHL clear cell RCC17p− (TP53), 2p+ (HIF2A) associated with VHL wild-type ccRCC |
| Moore et al., current study | 412 Clear cell RCC | Array CGH (2464 BACs) | VHL inactivation, age, sex, stage, grade | CN loss most frequent at 3p, 14q, 8p, 4q, 9p, 9q, 6q, 3q, 10q, 13q, 1q, | |
| Body mass index, hypertension, family cancer Hx, | CN gain at 5q, 7q, 7p, 5p, 20q, 12q, 12pStage and grade associated with 1p−, 9p−, 9q− 13q−, 14q−, 12q+ | ||||
| Occupational solvent, lead, pesticide, exposures | CNV higher among VHL wild-type compared to hypermethylated casesLOH across 3p varied by VHL inactivation status | ||||
| LINE1 methylation | CNV higher in male compared to females cases, independent of grade, stage | ||||
| CNV higher in cases without positive family Hx cancer | |||||
| Smoking associated with 16p11.2-13.2 gain |
Abbreviations: ccRCC, clear cell renal cell carcinoma; CGH, array comparative genomic hybridization; NA, not applicable.