Compendium of Cancer Genome Aberrations

Melanocytic Lesions: Difference between revisions

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'''Table 1.''' '''Rates of gains and losses significantly higher than 5% for specific chromosome regions in primary melanoma of all subtypes combined''' '''(Literature Review)'''.The is a list of significantly gains and losses selected and evaluated based on a systematic literature search performed on 235 peer-reviewed manuscripts focusing on findings of copy number abnormalities in melanocytic lesions published between 1998 and 2022. Table derived from Barren et al., 2026 [<nowiki>PMID 41898865</nowiki>] with permission from Cancer Genetics. All ''p''-values in the listed CNAs were ≤0.05 and were considered indicative of significance. The abnormalities were reported by at least 3 manuscripts. Possible genes affected by the gain or loss are listed.
{| class="wikitable"
|+
|'''Event Type'''
|'''Region'''
|'''Rate of Gain or Loss (%)'''
|'''Possible Genes Affected'''
|-
| rowspan="45" |Gain
|1p12
|12
|NOTCH2 ***, ADAM30 ***
|-
|1p13
|9
|NRAS *
|-
|1q
|26
|
|-
|1q21
|16
|PDE4DIP ***, BCL9 *, S100A9 ***, S100A10 ***, S100A11 ***, S100A12 ***
|-
|1q23
|28
|NTRK1 *, KIRREL ***
|-
|1q32
|41
|MDM4 *
|-
|2q31
|14
|PDE11A ***
|-
|3p13
|10
|MITF *
|-
|4p
|10
|
|-
|4q12
|17
|KIT *, KDR *, PDGFRA *
|-
|5p
|14
|
|-
|5p15
|32
|TERT *
|-
|5q
|10
|
|-
|6p
|30
|
|-
|6p25
|58
|RREB1 *
|-
|6p21
|25
|CCND3 *
|-
|6q14
|34
|PHIP ***
|-
|7p
|23
|
|-
|7p11
|17
|EGFR *
|-
|7q
|27
|
|-
|7q31
|26
|MET *
|-
|7q34
|27
|BRAF *
|-
|8p
|6
|
|-
|8q
|50
|
|-
|8q24
|39
|MYC *
|-
|11p15
|15
|HRAS *
|-
|11q
|8
|
|-
|11q13
|27
|CCND1 *
|-
|11q14
|11
|GAB2 *
|-
|12p12
|8
|KRAS *, PIK3C2G ***
|-
|12q14
|21
|CDK4 *
|-
|12q15
|11
|HDM2/MDM2 *
|-
|13q14
|10
|RB1 **
|-
|14q32
|37
|AKT1 *
|-
|15q
|14
|
|-
|17p13
|18
|TP53 **
|-
|17q
|18
|
|-
|17q11
|15
|NF1 **
|-
|17q24
|32
|BPTF ***, PRKCA *, PRKAR1A **
|-
|19p13
|37
|MAP2K2 *
|-
|20p11
|11
|
|-
|20q
|23
|
|-
|20q13
|22
|MYBL2 *, ZNF217 *, CYP24 ***, STK6 *, P-REX1 *, SS18L1 ***, GNAS *, SNAI1 *, SNAI2 *
|-
|21q
|14
|
|-
|22q13
|21
|MKL1 ***, EP300 ***
|-
| rowspan="32" |Loss
|1p
|23
|
|-
|1p36
|32
|PRDM16 ***, ARID1A **
|-
|3p21 a
|15
|BAP1 **
|-
|3q
|14
|
|-
|4q
|10
|
|-
|5q
|22
|
|-
|6q
|14
|
|-
|6q23
|29
|MYB ***
|-
|6q25 b
|44
|ARID1B **
|-
|8p
|9
|
|-
|9p
|32
|
|-
|9p21
|38
|CDKN2A **
|-
|9p24
|10
|CD274 ***, JAK2 ***, PTPRD **
|-
|9q
|29
|
|-
|9q12
|13
|
|-
|10p
|19
|
|-
|10p15
|14
|PRKCQ ***, NET1 ***, KLF6 **, IL15RA ***, CALML5 ***, LARP4B ***
|-
|10q
|34
|
|-
|10q23
|25
|PTEN **
|-
|11p11
|23
|CD82 **
|-
|11q
|18
|
|-
|11q22
|9
|YAP1 ***
|-
|11q24
|26
|ETS1 ***, CHEK1 ***
|-
|13q14
|8
|RB1 **
|-
|16p
|14
|
|-
|16q
|25
|
|-
|16q23
|13
|BANP **, CBFA2T3 **, FANCA **, CDK10 ***
|-
|17p
|21
|
|-
|17p13
|12
|TP53 **
|-
|18q
|9
|
|-
|20p11
|18
|
|-
|20q11
|20
|E2F1 ***
|}
'''Table 2. Rates in percentage of CNAs commonly tested on FISH panels across different melanoma subtypes.''' Values in red represent rates calculated from <25 reported cases. The number of reported cases appears in parentheses (). The symbol “-” designates data not available.
{| class="wikitable"
|+
|'''Melanoma Subtype'''
|'''Rate of Gain of 6p25'''
|'''Rate of Loss of 6q23'''
|'''Rate of Gain of 8q24'''
|'''Rate of Loss of 9p21'''
|'''Rate of Gain of 11q13'''
|-
|General cutaneous
|58 (644)
|38 (515)
|33 (567)
|52 (880)
|25 (1871)
|-
|Acral
|72 (149)
|42 (171)
|47 (79)
|28 (222)
|39 (515)
|-
|Blue nevus like
|83 (23)
|61 (23)
| -
| -
|50 (18)
|-
|Desmoplastic
|44 (16)
|33 (3)
| -
| -
|31 (16)
|-
|Mucosal
|97 (33)
|80 (20)
|75 (24)
|39 (233)
|17 (260)
|-
|Nevoid
|66 (41)
|15 (41)
|31 (13)
|69 (13)
|24 (41)
|-
|Spitzoid/Spitz
|54 (99)
|33 (141)
| -
|39 (134)
|33 (146)
|-
|Uveal
| -
|33 (40)
|58 (249)
| -
|0 (83)
|}
'''Table 3. Rates of abnormalities detected by FISH panels for each melanoma subtype and 95% confidence intervals for the given rates.''' The number of cases on which the rates are based is given.
{| class="wikitable"
|+
|Melanoma Subtype
|Rate of FISH Abnormality Detected (%)
|Lower 95% Confidence Limit
|Upper 95% Confidence Limit
|Number of Cases
|-
|General cutaneous
|82
|80
|84
|1682
|-
|Acral
|88
|81
|92
|153
|-
|Blue nevus like
|94
|68
|100
|16
|-
|Mucosal
|100
|86
|100
|30
|-
|Nevoid
|93
|85
|98
|75
|-
|Spitzoid/Spitz
|70
|62
|77
|169
|}
'''Table 4. The percentage of melanomas with greater than 3 CNAs reported by CMA for each melanoma subtype and the 95% confidence lower bound for the proportion in the given number of reported cases.'''
{| class="wikitable"
|+
!Melanoma Subtype
!Percentage of Cases with >3 CNAs by CMA (%)
!Lower 95% Confidence Limit
!Number of Cases
|-
|Overall
|94
|
|769
|-
|General cutaneous
|94
|92
|579
|-
|Acral
|100
|96
|83
|-
|Blue nevus like
|80
|64
|30
|-
|Desmoplastic
|86
|61
|14
|-
|Mucosal
|95
|76
|19
|-
|Nevoid
|85
|58
|13
|-
|Spitzoid/Spitz
|67
|16
|3
|-
|Uveal
|100
|88
|28
|}
Retrieved from "https://content.ccga.io/index.php/Melanocytic_Lesions"