Renal Table: Recurrent Genomic Alterations Detected by Chromosomal Microarray

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Table 1 - Recurrent Genomic Alterations in Renal Cell Neoplasia Detected by Chromosomal Microarray (Literature Review). Genetic alterations and their associated clinical significance in major types of renal cell neoplasia. Table derived from Liu et al., 2020 [PMID 32434132] with permission from Cancer Genetics.

WHO Classification
Subtype Clear Cell RCC Papillary RCC

Type 1

Papillary RCC

Type 2

(heterogeneous group)

MiTF-Translocation RCC Chromophobe RCC Oncocytoma
Percentage 70-75% 15-20% 15-20% 1-5% 5% 5%
Origin Proximal    Tubules Collecting   Ducts
Copy Number Alterations [level of evidencea; clinical significanceb]
Whole genome Mostly gains Mostly losses No CNAs (~50%) [1; R]
chr1 1p- (10%) [2; R] 1p- (25%) [2; R] 1p- (30%) [3; R] -1 (90%) [1; D]c -1/1p- soly (50%) [1; R]
chr2 +2 (18%) [2; R] -2 (80%) [1; D]c
chr3 -3/3p- (VHL, KDM6A,

KDM5C, SETD2, PBRM1)

(90%) [1; D]

+3 (40%) [2; R] 3p-/cnLOH(3p) (21%) [2; R], 3p+ (12%) [3; R], 3q+ (21%) [3; R] -3 (25%) [3; R]
chr4 4p- (10%) [2; R] -4 (21%) [3; R] +4 (10%) [3; R]
chr5 5p+ (24%) [2; R],

5q+ (SQSTM1) (40-60%) [2; R]

5q+/+5 (20%) [2; R] -5 (25%) [3; R]
chr6 6q- (20%) [2; R] -6 (17%) [3; R] 6p21 (TFEB) amp [2; D, P] -6 (90%) [1; D]c
chr7 +7 (25%) [2; R] +7/+7,+7 (84%) [1; D]c +7 (25%) [1; D] +7 (30%) [3; R]
chr8 8p- (25%) [2; R] +8 (MYC) (10-33%) [3; R] -8 (15%) [3; R]c
chr9 9p- (20%) [1; P]

9q- (20%) [2; R]

9p- (19%) [2; R],

9q- (17%) [3; R]

9p- (30%) [3; R] -9 (35%) [3; R]
chr10 10q- (10%) [2; R] 10q- (17%) [3; R] -10 (90%) [1; D]c
chr11 11q- (19%) [3; R] -11 (10%) [3; R]
chr12 +12 (15%) [2; R] +12 (52%) [2; R] +12 (15%) [3; R] +12 (35%) [3; R]
chr13 +13 (13%) [2; R] -13 (20%) [3; R] -13 (85%) [1; D]c
chr14 14q- (HIF1A) (40%) [1; P] -14 (28%) [2; R] -14 (10%) [2; R]
chr15 -15 (15%) [3; R] -15 (15%) [3; R]
chr16 16p+ (12%) [2; R],

16q+ (10%) [2; R]

+16 (55%) [2; R] 16p+ (40%) [2; R],

16q+ (35%) [2; R]

chr17 +17 (84%) [1; D]c 17p- (8%) [3; R],

+17/17q+ (50%) [1; D]

17p- (20%) [3; R],

17q+ (40%) [3; R]

-17 (90%) [1; D]c
chr18 -18 (10%) [2; R] -18 (26%) [2; R] -18 (15%) [3; R]
chr19
chr20 +20 (13%) [2; R] +20 (40%) [2; R]
chr21 -21 (19%) [3; R] -21 (70%) [1; D]c -21 (15%) [3; R]
chr22 -22 (40%) [2; R]
X -X (10%) [3;R]
Y -Y (40%) [1; R with -1]c
Rearrangements [level of evidence; clinical significance]
TERT promoter (5p15) (<10%) [3; R] TFE3 (Xp11), TFEB (6p21) (100%) [1; D, P] TERT promoter (5p15) (12%) [3; R] CCND1 (11q13) (40%) [2; D]
Mutations (SNVs, Indels) [level of evidence; clinical significance]
Mutated

in >20%

PBRM1 [2; R], VHL (also promoter methylation) [1; D] TP53 [2; R]
Mutated

in 10-20%

BAP1 [1; P], SETD2 [2; R] MET [1; D]
Mutated

in 5-10%

KDM5C, MTOR, PTEN, TP53 [2; R] CDKN2A (also promoter hypermethylation) [2; P], MET [1; D] PTEN [2; R]
Mutated

in 2-5%

ARID1A, CDKN2A, KDMT2C/KDMT2D, LRP1B, PIK3CA, PTEN, STAG2, TCEB1, TERT CDKN2A/CDKN2B, KDM6A, MLL3, NF2, NFE2L2, SMARCB1, TERT BAP1, FAT1, KDM6A, NF2, NFE2L2, PBRM1, SETD2, STAG2, TERT, TP53 ARID1A, FAAH2, FAT1/FAT4, FLT4, MICALCL, NIN, PDHB, PDXDC1, TSC1/TSC2, ZNF765 ERCC2, C2CD4C
Mitochondrial  DNA MT-ND5 [3,D] MT-COX1, MT-COX2, MT-COX3, MT-ND5, MT-CYTB [2,D]
Germline susceptibility
Germline susceptibility
  • mainly VHL (von Hippel-Lindau Syndrome)
  • PTEN (Cowden Syndrome)
  • FLCN (Birt-Hogg-Dube syndrome)
  • TSC1 and TSC2 (tuberous sclerosis)
  • SDHB (most common), SDHC (less common), SDHA (rare), SDHD (rare) (succinate dehydrogenase deficient RCC)
  • MET (Hereditary papillary RCC)
  • FH (Hereditary leiomyomatosis and RCC)
 FCLN (Birt-Hogg-Dube syndrome) FCLN (Birt-Hogg-Dube syndrome)
References [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20][21][22] [23][24][25][26][27][28][29][30][31][32][33][34][35][36][37][38] [1][39][40][41][42][43] [44][45][46][47][48][49][50][51][52][53][54] [45][55][56][46][47][51][57][58][59][52][60][61][62][63]

Note: a level of evidence (ranges from level 1 to 3 as specified in the methods). Level 1, established clinical significance and present in current WHO classification and/or professional practice guidelines such as NCCN, ASCO, CAP guidelines or FDA approval; Level 2, recurrent clinical significance based on large studies with outcomes; and Level 3, recurrent but uncertain clinical significance based on smaller studies and multiple case reports.

          b clinical significance, D-diagnosis, P-prognosis, R-recurrence

          c alterations in combination

Reference

1. Liu YJ, Houldsworth J, Emmadi R, Dyer L, Wolff DJ. Assessing Genomic Copy Number Alterations as Best Practice for Renal Cell Neoplasia: An Evidence-Based Review from the Cancer Genomics Consortium Workgroup. Cancer Genet. 2020 Jun;244:40-54. doi: 10.1016/j.cancergen.2020.04.004. Epub 2020 May 1. PMID 32434132.

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  44. ↑ Davis, Caleb F.; et al. (2014-09-08). "The somatic genomic landscape of chromophobe renal cell carcinoma". Cancer Cell. 26 (3): 319–330. doi:10.1016/j.ccr.2014.07.014. ISSN 1878-3686. PMC 4160352. PMID 25155756.
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  47. ↑ 47.0 47.1 Yusenko, Maria V.; et al. (2009-05-18). "High-resolution DNA copy number and gene expression analyses distinguish chromophobe renal cell carcinomas and renal oncocytomas". BMC cancer. 9: 152. doi:10.1186/1471-2407-9-152. ISSN 1471-2407. PMC 2686725. PMID 19445733.
  48. ↑ Kang, Xue-Ling; et al. (2015). "Chromosomal imbalances revealed in primary renal cell carcinomas by comparative genomic hybridization". International Journal of Clinical and Experimental Pathology. 8 (4): 3636–3647. ISSN 1936-2625. PMC 4466932. PMID 26097545.
  49. ↑ Sperga, Maris; et al. (2013-10). "Chromophobe renal cell carcinoma--chromosomal aberration variability and its relation to Paner grading system: an array CGH and FISH analysis of 37 cases". Virchows Archiv: An International Journal of Pathology. 463 (4): 563–573. doi:10.1007/s00428-013-1457-6. ISSN 1432-2307. PMID 23913167. Check date values in: |date= (help)
  50. ↑ Casuscelli, Jozefina; et al. (2017-06-15). "Genomic landscape and evolution of metastatic chromophobe renal cell carcinoma". JCI insight. 2 (12). doi:10.1172/jci.insight.92688. ISSN 2379-3708. PMC 5470887. PMID 28614790.
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  52. ↑ 52.0 52.1 Tan, Min-Han; et al. (2010-05-12). "Genomic expression and single-nucleotide polymorphism profiling discriminates chromophobe renal cell carcinoma and oncocytoma". BMC cancer. 10: 196. doi:10.1186/1471-2407-10-196. ISSN 1471-2407. PMC 2883967. PMID 20462447.
  53. ↑ Abbosh, Philip; et al. (12 2018). "Molecular and Genomic Profiling to Identify Actionable Targets in Chromophobe Renal Cell Cancer". European Urology Focus. 4 (6): 969–971. doi:10.1016/j.euf.2017.01.003. ISSN 2405-4569. PMID 28753842. Check date values in: |date= (help)
  54. ↑ Hammer, B. E. (1989-03). "Proton decoupled 13C NMR imaging". Magnetic Resonance Imaging. 7 (2): 235–240. doi:10.1016/0730-725x(89)90710-8. ISSN 0730-725X. PMID 2541301. Check date values in: |date= (help)
  55. ↑ Durinck, Steffen; et al. (2015-01). "Spectrum of diverse genomic alterations define non-clear cell renal carcinoma subtypes". Nature Genetics. 47 (1): 13–21. doi:10.1038/ng.3146. ISSN 1546-1718. PMC 4489427. PMID 25401301. Check date values in: |date= (help)
  56. ↑ Gowrishankar, Banumathy; et al. (2015-05). "A genomic algorithm for the molecular classification of common renal cortical neoplasms: development and validation". The Journal of Urology. 193 (5): 1479–1485. doi:10.1016/j.juro.2014.11.099. ISSN 1527-3792. PMID 25498568. Check date values in: |date= (help)
  57. ↑ Joshi, Shilpy; et al. (2015-12-01). "The Genomic Landscape of Renal Oncocytoma Identifies a Metabolic Barrier to Tumorigenesis". Cell Reports. 13 (9): 1895–1908. doi:10.1016/j.celrep.2015.10.059. ISSN 2211-1247. PMC 4779191. PMID 26655904.
  58. ↑ Lindgren, Valerie; et al. (2004-02). "Cytogenetic analysis of a series of 13 renal oncocytomas". The Journal of Urology. 171 (2 Pt 1): 602–604. doi:10.1097/01.ju.0000109172.07081.16. ISSN 0022-5347. PMID 14713769. Check date values in: |date= (help)
  59. ↑ Paner, Gladell P.; et al. (2007-01). "High incidence of chromosome 1 abnormalities in a series of 27 renal oncocytomas: cytogenetic and fluorescence in situ hybridization studies". Archives of Pathology & Laboratory Medicine. 131 (1): 81–85. doi:10.1043/1543-2165(2007)131[81:HIOCAI]2.0.CO;2. ISSN 1543-2165. PMID 17227127. Check date values in: |date= (help)
  60. ↑ Boris, Ronald S.; et al. (2011-06). "The impact of germline BHD mutation on histological concordance and clinical treatment of patients with bilateral renal masses and known unilateral oncocytoma". The Journal of Urology. 185 (6): 2050–2055. doi:10.1016/j.juro.2011.02.051. ISSN 1527-3792. PMC 3164767. PMID 21496834. Check date values in: |date= (help)
  61. ↑ Michalova, Kvetoslava; et al. (2018-08). "Papillary renal cell carcinoma with cytologic and molecular genetic features overlapping with renal oncocytoma: Analysis of 10 cases". Annals of Diagnostic Pathology. 35: 1–6. doi:10.1016/j.anndiagpath.2018.01.010. ISSN 1532-8198. PMID 30072012. Check date values in: |date= (help)
  62. ↑ He, Huiying; et al. (2018-12). ""High-grade oncocytic renal tumor": morphologic, immunohistochemical, and molecular genetic study of 14 cases". Virchows Archiv: An International Journal of Pathology. 473 (6): 725–738. doi:10.1007/s00428-018-2456-4. ISSN 1432-2307. PMID 30232607. Check date values in: |date= (help)
  63. ↑ Dvorakova, Marie; et al. (2010-05-24). "Renal oncocytoma: a comparative clinicopathologic study and fluorescent in-situ hybridization analysis of 73 cases with long-term follow-up". Diagnostic Pathology. 5: 32. doi:10.1186/1746-1596-5-32. ISSN 1746-1596. PMC 2881070. PMID 20497539.
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