Renal Table: Recurrent Genomic Alterations Detected by Chromosomal Microarray

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Table 1 - Recurrent Genomic Alterations in AML Detected by Chromosomal Microarray (Literature Review). This is a comprehensive list of CNAs and CN-LOH detectable by CMA testing with strong 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 [9[1], 14[2], 17[3], 24[4], 27[5], 29[6], 32[7], 35[8], 49[9], 156-168] [10, 42[10], 67-71[11][12][13][14][15], 73[16], 74[17], 98[18], 169-174] [10, 121, 122, 124, 125, 175] [11[19], 12[20], 103[21], 105[22], 106[23], 108[24], 109[25], 129, 137, 176, 177] [12[20], 76, 102[26], 103[21], 105[22], 129, 132, 135-137, 140, 178-180]

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

  1. ↑ Cancer Genome Atlas Research Network (2013-07-04). "Comprehensive molecular characterization of clear cell renal cell carcinoma". Nature. 499 (7456): 43–49. doi:10.1038/nature12222. ISSN 1476-4687. PMC 3771322. PMID 23792563.
  2. ↑ Klatte, Tobias; et al. (2009-02-10). "Cytogenetic profile predicts prognosis of patients with clear cell renal cell carcinoma". Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology. 27 (5): 746–753. doi:10.1200/JCO.2007.15.8345. ISSN 1527-7755. PMID 19124809.
  3. ↑ Mitchell, Thomas J.; et al. (04 19, 2018). "Timing the Landmark Events in the Evolution of Clear Cell Renal Cell Cancer: TRACERx Renal". Cell. 173 (3): 611–623.e17. doi:10.1016/j.cell.2018.02.020. ISSN 1097-4172. PMC 5927631. PMID 29656891. Check date values in: |date= (help)
  4. ↑ Chen, Meng; et al. (2009-11-15). "Genome-wide profiling of chromosomal alterations in renal cell carcinoma using high-density single nucleotide polymorphism arrays". International Journal of Cancer. 125 (10): 2342–2348. doi:10.1002/ijc.24642. ISSN 1097-0215. PMC 2768265. PMID 19521957.
  5. ↑ Gerlinger, Marco; et al. (2012-03-08). "Intratumor heterogeneity and branched evolution revealed by multiregion sequencing". The New England Journal of Medicine. 366 (10): 883–892. doi:10.1056/NEJMoa1113205. ISSN 1533-4406. PMC 4878653. PMID 22397650.
  6. ↑ Sato, Yusuke; et al. (2013-08). "Integrated molecular analysis of clear-cell renal cell carcinoma". Nature Genetics. 45 (8): 860–867. doi:10.1038/ng.2699. ISSN 1546-1718. PMID 23797736. Check date values in: |date= (help)
  7. ↑ Beroukhim, Rameen; et al. (2009-06-01). "Patterns of gene expression and copy-number alterations in von-hippel lindau disease-associated and sporadic clear cell carcinoma of the kidney". Cancer Research. 69 (11): 4674–4681. doi:10.1158/0008-5472.CAN-09-0146. ISSN 1538-7445. PMC 2745239. PMID 19470766.
  8. ↑ Arai, Eri; et al. (2008-09-01). "Genetic clustering of clear cell renal cell carcinoma based on array-comparative genomic hybridization: its association with DNA methylation alteration and patient outcome". Clinical Cancer Research: An Official Journal of the American Association for Cancer Research. 14 (17): 5531–5539. doi:10.1158/1078-0432.CCR-08-0443. ISSN 1078-0432. PMID 18765545.
  9. ↑ Kroeger, Nils; et al. (2013-04-15). "Deletions of chromosomes 3p and 14q molecularly subclassify clear cell renal cell carcinoma". Cancer. 119 (8): 1547–1554. doi:10.1002/cncr.27947. ISSN 1097-0142. PMID 23335244.
  10. ↑ Antonelli, Alessandro; et al. (2010-06). "Cytogenetic features, clinical significance and prognostic impact of type 1 and type 2 papillary renal cell carcinoma". Cancer Genetics and Cytogenetics. 199 (2): 128–133. doi:10.1016/j.cancergencyto.2010.02.013. ISSN 1873-4456. PMID 20471516. Check date values in: |date= (help)
  11. ↑ Jiang, F.; et al. (1998-11). "Chromosomal imbalances in papillary renal cell carcinoma: genetic differences between histological subtypes". The American Journal of Pathology. 153 (5): 1467–1473. doi:10.1016/S0002-9440(10)65734-3. ISSN 0002-9440. PMC 1853413. PMID 9811338. Check date values in: |date= (help)
  12. ↑ Klatte, Tobias; et al. (2009-02-15). "Cytogenetic and molecular tumor profiling for type 1 and type 2 papillary renal cell carcinoma". Clinical Cancer Research: An Official Journal of the American Association for Cancer Research. 15 (4): 1162–1169. doi:10.1158/1078-0432.CCR-08-1229. ISSN 1078-0432. PMID 19228721.
  13. ↑ Sanders, Melinda E.; et al. (2002-09). "Unique patterns of allelic imbalance distinguish type 1 from type 2 sporadic papillary renal cell carcinoma". The American Journal of Pathology. 161 (3): 997–1005. doi:10.1016/S0002-9440(10)64260-5. ISSN 0002-9440. PMC 1867241. PMID 12213728. Check date values in: |date= (help)
  14. ↑ Yu, Wenjuan; et al. (2013-06). "Clinicopathological, genetic, ultrastructural characterizations and prognostic factors of papillary renal cell carcinoma: new diagnostic and prognostic information". Acta Histochemica. 115 (5): 452–459. doi:10.1016/j.acthis.2012.10.009. ISSN 1618-0372. PMID 23219441. Check date values in: |date= (help)
  15. ↑ Schraml, P.; et al. (2000-03). "Allelic loss at the D9S171 locus on chromosome 9p13 is associated with progression of papillary renal cell carcinoma". The Journal of Pathology. 190 (4): 457–461. doi:10.1002/(SICI)1096-9896(200003)190:43.0.CO;2-C. ISSN 0022-3417. PMID 10699995. Check date values in: |date= (help)
  16. ↑ Hughson, M. D.; et al. (1998-10-15). "Clear-cell and papillary carcinoma of the kidney: an analysis of chromosome 3, 7, and 17 abnormalities by microsatellite amplification, cytogenetics, and fluorescence in situ hybridization". Cancer Genetics and Cytogenetics. 106 (2): 93–104. doi:10.1016/s0165-4608(98)00068-5. ISSN 0165-4608. PMID 9797772.
  17. ↑ Velickovic, M.; et al. (2001-06-15). "VHL and FHIT locus loss of heterozygosity is common in all renal cancer morphotypes but differs in pattern and prognostic significance". Cancer Research. 61 (12): 4815–4819. ISSN 0008-5472. PMID 11406557.
  18. ↑ Przybycin, Christopher G.; et al. (2013-07). "Hereditary syndromes with associated renal neoplasia: a practical guide to histologic recognition in renal tumor resection specimens". Advances in Anatomic Pathology. 20 (4): 245–263. doi:10.1097/PAP.0b013e318299b7c6. ISSN 1533-4031. PMID 23752087. Check date values in: |date= (help)
  19. ↑ 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.
  20. ↑ 20.0 20.1 Chen, Fengju; et al. (2016-03-15). "Multilevel Genomics-Based Taxonomy of Renal Cell Carcinoma". Cell Reports. 14 (10): 2476–2489. doi:10.1016/j.celrep.2016.02.024. ISSN 2211-1247. PMC 4794376. PMID 26947078.
  21. ↑ 21.0 21.1 Krill-Burger, John M.; et al. (2012-06). "Renal cell neoplasms contain shared tumor type-specific copy number variations". The American Journal of Pathology. 180 (6): 2427–2439. doi:10.1016/j.ajpath.2012.01.044. ISSN 1525-2191. PMC 3378847. PMID 22483639. Check date values in: |date= (help)
  22. ↑ 22.0 22.1 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.
  23. ↑ 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.
  24. ↑ 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)
  25. ↑ 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.
  26. ↑ 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)
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