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Line 308: − + − + − + + + + + + + + + + + + + + + + + + + + + + − § ''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''' − |[9, 14, 17, 24, 27, 29, 32, 35, 49, 156-168] − | colspan="2" |[10, 42, 67-71, 73, 74, 98, 169-174] − |[10, 121, 122, 124, 125, 175] − | colspan="2" |[11, 12, 103, 105, 106, 108, 109, 129, 137, 176, 177] − |[12, 76, 102, 103, 105, 129, 132, 135-137, 140, 178-180] − |}
Renal Cell Neoplasia Tables: Recurrent Cytogenomic Alterations (view source)
Revision as of 13:40, 19 May 2021
, 13:40, 19 May 2021Minor tidying of references
{{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'''
|15-20%
|15-20%
|15-20%
|15-20%
| colspan="2" | 1-5%
| colspan="2" |1-5%
| 5%
|5%
| 5%
|5%
|-
|-
|'''Origin'''
|'''Origin'''
|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>'''
|-
|-
|'''chr3'''
|'''chr3'''
|'''-3/3p-''' (''VHL, KDM6A,''
|'''-3/3p-''' (''[[VHL]], [[KDM6A]],''
''KDM5C, SETD2, PBRM1'')
''[[KDM5C]], [[SETD2]], [[PBRM1]]'')
(90%) '''[1; D]'''
(90%) '''[1; D]'''
|
|
|<nowiki>-6 (17%) [3; R]</nowiki>
|<nowiki>-6 (17%) [3; R]</nowiki>
| colspan="2" |'''6p21 (''TFEB'') amp [2; D, P]'''
| colspan="2" |'''6p21 (''[[TFEB]]'') amp [2; D, P]'''
|'''-6''' (90%) '''[1; D]<sup>c</sup>'''
|'''-6''' (90%) '''[1; D]<sup>c</sup>'''
|
|
|8p- (25%) [2; R]
|8p- (25%) [2; R]
|
|
|<nowiki>+8 (</nowiki>''MYC'') (10-33%) [3; R]
|<nowiki>+8 (</nowiki>''[[MYC]]'') (10-33%) [3; R]
| colspan="2" |
| colspan="2" |
|<nowiki>-8 (15%) [3; R]</nowiki><sup>c</sup>
|<nowiki>-8 (15%) [3; R]</nowiki><sup>c</sup>
|-
|-
|'''chr14'''
|'''chr14'''
|'''14q-''' (''HIF1A'') (40%) '''[1; P]'''
|'''14q-''' (''[[HIF1A]]'') (40%) '''[1; P]'''
|
|
|<nowiki>-14 (28%) [2; R]</nowiki>
|<nowiki>-14 (28%) [2; R]</nowiki>
|'''chr17'''
|'''chr17'''
|
|
|'''+17''' (84%) '''[1; D] <sup>c</sup>'''
|'''+17''' (84%) '''[1; D]<sup>c</sup>'''
|17p- (8%) [3; R],
|17p- (8%) [3; R],
|-
|-
|
|
|''TERT'' promoter (5p15) (<10%) [3; R]
|''[[TERT]]'' promoter (5p15) (<10%) [3; R]
|
|
|
|
| colspan="2" |'''''TFE3'' (Xp11)'', TFEB'' (6p21)''' (100%) '''[1; D, P]'''
| colspan="2" |'''''[[TFE3]]'' (Xp11)'', [[TFEB]]'' (6p21)''' (100%) '''[1; D, P]'''
|''TERT'' promoter (5p15) (12%) [3; R]
|''[[TERT]]'' promoter (5p15) (12%) [3; R]
|''CCND1'' (11q13) (40%) [2; D]
|''[[CCND1]]'' (11q13) (40%) [2; D]
|-
|-
| 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%
|''PBRM1'' [2; R]'', '''VHL''''' '''(also promoter methylation) [1; D]'''
|''[[PBRM1]]'' [2; R]'', '''[[VHL]]''''' '''(also promoter methylation) [1; D]'''
|
|
|
|
| colspan="2" |
| colspan="2" |
|''TP53'' [2; R]
|''[[TP53]]'' [2; R]
|
|
|-
|-
| Mutated
|Mutated
in 10-20%
in 10-20%
|''BAP1'' [1; P]'', SETD2'' [2; R]
|''[[BAP1]]'' [1; P]'', [[SETD2]]'' [2; R]
|'''''MET'' [1; D]'''
|'''''[[MET]]'' [1; D]'''
|
|
| colspan="2" |
| colspan="2" |
in 5-10%
in 5-10%
|''KDM5C, MTOR'', ''PTEN,'' ''TP53'' [2; R]
|''[[KDM5C]], [[MTOR]]'', ''[[PTEN]],'' ''[[TP53]]'' [2; R]
|
|
|'''''CDKN2A'' (also promoter hypermethylation) [2; P]'',''''' '''''MET''''' '''[1; D]'''
|'''''[[CDKN2A]]'' (also promoter hypermethylation) [2; P]'',''''' '''''[[MET]]''''' '''[1; D]'''
| colspan="2" |
| colspan="2" |
|''PTEN'' [2; R]
|''[[PTEN]]'' [2; R]
|
|
|-
|-
in 2-5%
in 2-5%
|''ARID1A, CDKN2A, KDMT2C/D, LRP1B, PIK3CA, PTEN, STAG2, TCEB1, TERT''
|''[[ARID1A]], [[CDKN2A]], [[KDMT2C]]/[[KDMT2D]], [[LRP1B]], [[PIK3CA]], [[PTEN]], [[STAG2]], [[TCEB1]], [[TERT]]''
|''CDKN2A/B, KDM6A, MLL3, NF2, NFE2L2, SMARCB1, TERT''
|''[[CDKN2A]]/[[CDKN2B]], [[KDM6A]], [[MLL3]], [[NF2]], [[NFE2L2]], [[SMARCB1]], [[TERT]]''
|''BAP1, FAT1, KDM6A, NF2, NFE2L2, PBRM1, SETD2, STAG2, TERT, TP53''
|''[[BAP1]], [[FAT1]], [[KDM6A]], [[NF2]], [[NFE2L2]], [[PBRM1]], [[SETD2]], [[STAG2]], [[TERT]], [[TP53]]''
| colspan="2" |
| colspan="2" |
|''ARID1A, FAAH2, FAT1/4, FLT4, MICALCL, NIN, PDHB, PDXDC1, TSC1/TSC2, ZNF765''
|''[[ARID1A]], [[FAAH2]], [[FAT1]]/[[FAT4]], [[FLT4]], [[MICALCL]], [[NIN]], [[PDHB]], [[PDXDC1]], [[TSC1]]/[[TSC2]], [[ZNF765]]''
|''ERCC2, C2CD4C''
|''[[ERCC2]], [[C2CD4C]]''
|-
|-
|Mitochondrial DNA
|Mitochondrial DNA
|
|
| colspan="2" |
| colspan="2" |
|''MT-ND5'' [3,D]
|''[[MT-ND5]]'' [3,D]
|''MT-COX1, MT-COX2, MT-COX3, MT-ND5, MT-CYTB'' [2,D]
|''[[MT-COX1]], [[MT-COX2]], [[MT-COX3]], [[MT-ND5]], [[MT-CYTB]]'' [2,D]
|-
|-
| colspan="8" |'''Germline susceptibility'''
| colspan="8" |'''Germline susceptibility'''
|-
|-
|Germline susceptibility
|Germline susceptibility
|§ mainly ''VHL'' (von Hippel-Lindau Syndrome)
|
*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
==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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