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}}
 
{{DISPLAYTITLE:Renal Table: Recurrent Genomic Alterations Detected by Chromosomal Microarray}}
  
'''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.
+
'''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.
 
{| class="wikitable"
 
{| class="wikitable"
 
| colspan="8" |'''WHO Classification'''
 
| colspan="8" |'''WHO Classification'''
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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]
+
|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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|'''chr17'''
 
|'''chr17'''
 
|
 
|
|'''+17''' (84%) '''[1; D] <sup>c</sup>'''
+
|'''+17''' (84%) '''[1; D]<sup>c</sup>'''
 
|17p- (8%) [3; R],
 
|17p- (8%) [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
+
|Mutated
  
 
in >20%
 
in >20%
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|
 
|
 
|-
 
|-
| Mutated
+
|Mutated
  
 
in 10-20%
 
in 10-20%
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|-
 
|-
 
|Germline susceptibility
 
|Germline susceptibility
|§ mainly ''[[VHL]]'' (von Hippel-Lindau Syndrome)
+
|
 
+
*mainly ''[[VHL]]'' (von Hippel-Lindau Syndrome)
§ ''[[PTEN]]'' (Cowden Syndrome)
+
*''[[PTEN]]'' (Cowden Syndrome)
 
+
*''[[FLCN]]'' (Birt-Hogg-Dube 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)
§ ''[[TSC1]]'' and ''[[TSC2]]'' (tuberous sclerosis)
+
|
 
+
*''[[MET]]'' (Hereditary papillary RCC)
§ ''[[SDHB]] (most common), [[SDHC]] (less common), [[SDHA]] (rare), [[SDHD]] (rare)'' (succinate dehydrogenase deficient RCC)
+
|
|§ ''[[MET]]'' (Hereditary papillary RCC)
+
*''[[FH]]'' (Hereditary leiomyomatosis and RCC)
|§ ''[[FH]]'' (Hereditary leiomyomatosis and RCC)
 
 
|
 
|
 
| colspan="2" |''[[FCLN]]'' (Birt-Hogg-Dube syndrome)
 
| colspan="2" |''[[FCLN]]'' (Birt-Hogg-Dube syndrome)
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|-
 
|-
 
|'''References'''
 
|'''References'''
|[9<ref
+
|<ref name=
 
|}
 
|}
 
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.
 
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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==Reference==
 
==Reference==
  
1. Xu X, Bryke C, Sukhanova M, Huxley E, Dash DP, Dixon-Mciver A, Fang M, Griepp PT, Hodge JC, Iqbal A, Jeffries S, Kanagal-Shamanna R, Quintero-Rivera F, Shetty S, Slovak ML, Yenamandra A, Lennon PA, Raca G. (2018). Assessing copy number abnormalities and copy-neutral loss-of-heterozygosity across the genome as best practice in diagnostic evaluation of acute myeloid leukemia: An evidence-based review from the cancer genomics consortium (CGC) myeloid neoplasms working group. Cancer Genet [Epub ahead of print], PMID 30344013.
+
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.
 
<references />
 
<references />

Latest revision as of 13:40, 19 May 2021


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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