Difference between revisions of "Renal Cell Neoplasia Tables: Recurrent Cytogenomic Alterations"

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{{DISPLAYTITLE: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 diagnostic, prognostic and treatment implications in AML.  Table derived from Xu et al., 2018 [PMID: 32434132] with permission from Cancer Genetics.
 
{| class="wikitable"
 
{| class="wikitable"
 
| colspan="8" |'''WHO Classification'''
 
| colspan="8" |'''WHO Classification'''
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|'''Papillary RCC'''
 
|'''Papillary RCC'''
  
'''Type 1'''  
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'''Type 1'''
 
|'''Papillary RCC'''
 
|'''Papillary RCC'''
  
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|15-20%
 
|15-20%
 
|15-20%
 
|15-20%
| colspan="2" |1-5%
+
| colspan="2" | 1-5%
|5%
+
| 5%
|5%
+
| 5%
 
|-
 
|-
 
|'''Origin'''
 
|'''Origin'''
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|1p- (10%) [2; R]
 
|1p- (10%) [2; R]
 
|
 
|
|1p- (25%) [2; R]
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| 1p- (25%) [2; R]
 
| colspan="2" |1p- (30%) [3; R]
 
| colspan="2" |1p- (30%) [3; R]
 
|'''-1''' (90%) '''[1; D]<sup>c</sup>'''
 
|'''-1''' (90%) '''[1; D]<sup>c</sup>'''
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|'''+7/+7,+7''' (84%) '''[1; D]<sup>c</sup>'''
 
|'''+7/+7,+7''' (84%) '''[1; D]<sup>c</sup>'''
 
|'''+7''' (25%) '''[1; D]'''
 
|'''+7''' (25%) '''[1; D]'''
| colspan="2" |+7 (30%) [3; R]
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| colspan="2" | +7 (30%) [3; R]
 
|
 
|
 
|
 
|
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|<nowiki>+12 (52%) [2; R]</nowiki>
 
|<nowiki>+12 (52%) [2; R]</nowiki>
 
|<nowiki>+12 (15%) [3; R]</nowiki>
 
|<nowiki>+12 (15%) [3; R]</nowiki>
| colspan="2" |+12 (35%) [3; R]
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| colspan="2" | +12 (35%) [3; R]
 
|
 
|
 
|
 
|
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|
 
|
 
|<nowiki>-15 (15%) [3; R]</nowiki>
 
|<nowiki>-15 (15%) [3; R]</nowiki>
| colspan="2" |-15 (15%) [3; R]
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| colspan="2" | -15 (15%) [3; R]
 
|
 
|
 
|
 
|
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| colspan="8" |'''Mutations (SNVs, Indels) [level of evidence; clinical significance]'''
 
| colspan="8" |'''Mutations (SNVs, Indels) [level of evidence; clinical significance]'''
 
|-
 
|-
|Mutated
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| Mutated
  
 
in >20%
 
in >20%
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|
 
|
 
|-
 
|-
|Mutated
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| Mutated
  
 
in 10-20%
 
in 10-20%

Revision as of 22:47, 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 diagnostic, prognostic and treatment implications in AML. Table derived from Xu et al., 2018 [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]