Difference between revisions of "Renal Cell Neoplasia Tables: Recurrent Cytogenomic Alterations"
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| + | Note: <sup>a</sup> 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. | ||
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| + | <sup>b</sup> clinical significance, D-diagnosis, P-prognosis, R-recurrence | ||
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| + | <sup>c</sup> alterations in combination | ||
Revision as of 22:50, 14 January 2021
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/D, LRP1B, PIK3CA, PTEN, STAG2, TCEB1, TERT | CDKN2A/B, KDM6A, MLL3, NF2, NFE2L2, SMARCB1, TERT | BAP1, FAT1, KDM6A, NF2, NFE2L2, PBRM1, SETD2, STAG2, TERT, TP53 | ARID1A, FAAH2, FAT1/4, 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, 14, 17, 24, 27, 29, 32, 35, 49, 156-168] | [10, 42, 67-71, 73, 74, 98, 169-174] | [10, 121, 122, 124, 125, 175] | [11, 12, 103, 105, 106, 108, 109, 129, 137, 176, 177] | [12, 76, 102, 103, 105, 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