View source for Renal Cell Neoplasia Tables: Recurrent Cytogenomic Alterations

{{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.
{| class="wikitable"
| colspan="8" |'''WHO Classification'''
|-
|'''Subtype'''
|'''Clear Cell RCC'''
|'''Papillary RCC'''

'''Type 1'''
|'''Papillary RCC'''

'''Type 2'''

(heterogeneous group)
| colspan="2" |'''MiTF-Translocation RCC'''
|'''Chromophobe RCC'''
|'''Oncocytoma'''
|-
|'''Percentage'''
|70-75%
|15-20%
|15-20%
| colspan="2" | 1-5%
| 5%
| 5%
|-
|'''Origin'''
| colspan="5" |Proximal    Tubules
| colspan="2" |Collecting   Ducts
|-
| colspan="8" |'''Copy Number Alterations [level of evidence<sup>a</sup>; clinical significance<sup>b</sup>]'''
|-
|'''Whole genome'''
|
|Mostly gains
|
| colspan="2" |
|Mostly losses
|'''No CNAs''' (~50%) '''[1; R]'''
|-
|'''chr1'''
|1p- (10%) [2; R]
|
| 1p- (25%) [2; R]
| colspan="2" |1p- (30%) [3; R]
|'''-1''' (90%) '''[1; D]<sup>c</sup>'''
|'''-1/1p-''' soly (50%) '''[1; R]'''
|-
|'''chr2'''
|
|<nowiki>+2 (18%) [2; R]</nowiki>
|
| colspan="2" |
|'''-2''' (80%) '''[1; D]<sup>c</sup>'''
|
|-
|'''chr3'''
|'''-3/3p-''' (''[[VHL]], [[KDM6A]],''

''[[KDM5C]], [[SETD2]], [[PBRM1]]'')

(90%) '''[1; D]'''
|<nowiki>+3 (40%) [2; R]</nowiki>
|3p-/cnLOH(3p) (21%) [2; R], 3p+ (12%) [3; R], 3q+ (21%) [3; R]
| colspan="2" |
|<nowiki>-3 (25%) [3; R]</nowiki>
|
|-
|'''chr4'''
|4p- (10%) [2; R]
|
|<nowiki>-4 (21%) [3; R]</nowiki>
| colspan="2" |
|<nowiki>+4 (10%) [3; R]</nowiki>
|
|-
|'''chr5'''
|5p+ (24%) [2; R],

5q+ (''SQSTM1'') (40-60%) [2; R]
|
|5q+/+5 (20%) [2; R]
| colspan="2" |
|<nowiki>-5 (25%) [3; R]</nowiki>
|
|-
|'''chr6'''
|6q- (20%) [2; R]
|
|<nowiki>-6 (17%) [3; R]</nowiki>
| colspan="2" |'''6p21 (''[[TFEB]]'') amp [2; D, P]'''
|'''-6''' (90%) '''[1; D]<sup>c</sup>'''
|
|-
|'''chr7'''
|<nowiki>+7 (25%) [2; R]</nowiki>
|'''+7/+7,+7''' (84%) '''[1; D]<sup>c</sup>'''
|'''+7''' (25%) '''[1; D]'''
| colspan="2" | +7 (30%) [3; R]
|
|
|-
|'''chr8'''
|8p- (25%) [2; R]
|
|<nowiki>+8 (</nowiki>''[[MYC]]'') (10-33%) [3; R]
| colspan="2" |
|<nowiki>-8 (15%) [3; R]</nowiki><sup>c</sup>
|
|-
|'''chr9'''
|'''9p-''' (20%) '''[1; P]'''

9q- (20%) [2; R]
|
|9p- (19%) [2; R],

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

16q+ (10%) [2; R]
|<nowiki>+16 (55%) [2; R]</nowiki>
|16p+ (40%) [2; R],

16q+ (35%) [2; R]
| colspan="2" |
|
|
|-
|'''chr17'''
|
|'''+17''' (84%) '''[1; D] <sup>c</sup>'''
|17p- (8%) [3; R],

'''+17/17q+''' (50%) '''[1; D]'''
| colspan="2" |17p- (20%) [3; R],

17q+ (40%) [3; R]
|'''-17''' (90%) '''[1; D]<sup>c</sup>'''
|
|-
|'''chr18'''
|<nowiki>-18 (10%) [2; R]</nowiki>
|
|<nowiki>-18 (26%) [2; R]</nowiki>
| colspan="2" |
|<nowiki>-18 (15%) [3; R]</nowiki>
|
|-
|'''chr19'''
|
|
|
| colspan="2" |
|
|
|-
|'''chr20'''
|<nowiki>+20 (13%) [2; R]</nowiki>
|<nowiki>+20 (40%) [2; R]</nowiki>
|
| colspan="2" |
|
|
|-
|'''chr21'''
|
|
|<nowiki>-21 (19%) [3; R]</nowiki>
| colspan="2" |
|'''-21''' (70%) '''[1; D]<sup>c</sup>'''
|<nowiki>-21 (15%) [3; R]</nowiki>
|-
|'''chr22'''
|
|
|<nowiki>-22 (40%) [2; R]</nowiki>
| colspan="2" |
|
|
|-
|X
|
|
|
| colspan="2" |
|
|<nowiki>-X (10%) [3;R]</nowiki>
|-
|Y
|
|
|
| colspan="2" |
|
|<nowiki>-Y (40%) [1; R with -1]</nowiki><sup>c</sup>
|-
| colspan="8" |'''Rearrangements [level of evidence; clinical significance]'''
|-
|
|''[[TERT]]'' promoter (5p15) (<10%) [3; R]
|
|
| colspan="2" |'''''[[TFE3]]'' (Xp11)'', [[TFEB]]'' (6p21)''' (100%) '''[1; D, P]'''
|''[[TERT]]'' promoter (5p15) (12%) [3; R]
|''[[CCND1]]'' (11q13) (40%) [2; D]
|-
| colspan="8" |'''Mutations (SNVs, Indels) [level of evidence; clinical significance]'''
|-
| Mutated

in >20%
|''[[PBRM1]]'' [2; R]'', '''[[VHL]]''''' '''(also promoter methylation) [1; D]'''
|
|
| colspan="2" |
|''[[TP53]]'' [2; R]
|
|-
| Mutated

in 10-20%
|''[[BAP1]]'' [1; P]'', [[SETD2]]'' [2; R]
|'''''[[MET]]'' [1; D]'''
|
| colspan="2" |
|
|
|-
|Mutated

in 5-10%
|''[[KDM5C]], [[MTOR]]'', ''[[PTEN]],'' ''[[TP53]]'' [2; R]
|
|'''''[[CDKN2A]]'' (also promoter hypermethylation) [2; P]'',''''' '''''[[MET]]''''' '''[1; D]'''
| colspan="2" |
|''[[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]]''
| colspan="2" |
|''[[ARID1A]], [[FAAH2]], [[FAT1]]/[[FAT4]], [[FLT4]], [[MICALCL]], [[NIN]], [[PDHB]], [[PDXDC1]], [[TSC1]]/[[TSC2]], [[ZNF765]]''
|''[[ERCC2]], [[C2CD4C]]''
|-
|Mitochondrial  DNA
|
|
|
| colspan="2" |
|''[[MT-ND5]]'' [3,D]
|''[[MT-COX1]], [[MT-COX2]], [[MT-COX3]], [[MT-ND5]], [[MT-CYTB]]'' [2,D]
|-
| colspan="8" |'''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)
|
| colspan="2" |''[[FCLN]]'' (Birt-Hogg-Dube syndrome)
|''[[FCLN]]'' (Birt-Hogg-Dube syndrome)
|-
|'''References'''
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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.

          <sup>b</sup> clinical significance, D-diagnosis, P-prognosis, R-recurrence

          <sup>c</sup> alterations in combination