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><ref>{{Cite journal|last=Reyes Barron|first=Cynthia|last2=Geiersbach|first2=Katherine B.|last3=Alomari|first3=Ahmed K.|last4=Deak|first4=Kristen L.|last5=Golem|first5=Shivani|last6=Williams|first6=Eli S.|last7=Aypar|first7=Umut|last8=Zou|first8=Ying S.|last9=Wei|first9=Lei|date=2026-03-18|title=Clinical Utility of Copy Number Abnormality Analysis in the Evaluation of Melanocytic Lesions for Diagnosis and Prognosis: An Evidence-Based Review from the Cancer Genomics Consortium Working Group for Melanocytic Lesions|url=https://pubmed.ncbi.nlm.nih.gov/41898865|journal=Genes|volume=17|issue=3|pages=331|doi=10.3390/genes17030331|issn=2073-4425|pmc=13026022|pmid=41898865}}</ref>] 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.
'''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 Barron et al., 2026 [<nowiki>PMID 41898865</nowiki><ref>{{Cite journal|last=Reyes Barron|first=Cynthia|last2=Geiersbach|first2=Katherine B.|last3=Alomari|first3=Ahmed K.|last4=Deak|first4=Kristen L.|last5=Golem|first5=Shivani|last6=Williams|first6=Eli S.|last7=Aypar|first7=Umut|last8=Zou|first8=Ying S.|last9=Wei|first9=Lei|date=2026-03-18|title=Clinical Utility of Copy Number Abnormality Analysis in the Evaluation of Melanocytic Lesions for Diagnosis and Prognosis: An Evidence-Based Review from the Cancer Genomics Consortium Working Group for Melanocytic Lesions|url=https://pubmed.ncbi.nlm.nih.gov/41898865|journal=Genes|volume=17|issue=3|pages=331|doi=10.3390/genes17030331|issn=2073-4425|pmc=13026022|pmid=41898865}}</ref>] 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"
{| class="wikitable"
|+
|+
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|1p12
|1p12
|12
|12
|NOTCH2 ***, ADAM30 ***
|''NOTCH2'' ***, ''ADAM30'' ***
|-
|-
|1p13
|1p13
|9
|9
|NRAS *
|''NRAS'' *
|-
|-
|1q
|1q
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|1q21
|1q21
|16
|16
|PDE4DIP ***, BCL9 *, S100A9 ***, S100A10 ***, S100A11 ***, S100A12 ***
|''PDE4DIP'' ***, ''BCL9'' *, ''S100A9'' ***, ''S100A10'' ***, ''S100A11'' ***, ''S100A12'' ***
|-
|-
|1q23
|1q23
|28
|28
|NTRK1 *, KIRREL ***
|''NTRK1'' *, ''KIRREL'' ***
|-
|-
|1q32
|1q32
|41
|41
|MDM4 *
|''MDM4'' *
|-
|-
|2q31
|2q31
|14
|14
|PDE11A ***
|''PDE11A'' ***
|-
|-
|3p13
|3p13
|10
|10
|MITF *
|''MITF'' *
|-
|-
|4p
|4p
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|4q12
|4q12
|17
|17
|KIT *, KDR *, PDGFRA *
|''KIT'' *, ''KDR'' *, ''PDGFRA'' *
|-
|-
|5p
|5p
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|5p15
|5p15
|32
|32
|TERT *
|''TERT'' *
|-
|-
|5q
|5q
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|6p25
|6p25
|58
|58
|RREB1 *
|''RREB1'' *
|-
|-
|6p21
|6p21
|25
|25
|CCND3 *
|''CCND3'' *
|-
|-
|6q14
|6q14
|34
|34
|PHIP ***
|''PHIP'' ***
|-
|-
|7p
|7p
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|7p11
|7p11
|17
|17
|EGFR *
|''EGFR'' *
|-
|-
|7q
|7q
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|7q31
|7q31
|26
|26
|MET *
|''MET'' *
|-
|-
|7q34
|7q34
|27
|27
|BRAF *
|''BRAF'' *
|-
|-
|8p
|8p
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|8q24
|8q24
|39
|39
|MYC *
|''MYC'' *
|-
|-
|11p15
|11p15
|15
|15
|HRAS *
|''HRAS'' *
|-
|-
|11q
|11q
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|11q13
|11q13
|27
|27
|CCND1 *
|''CCND1'' *
|-
|-
|11q14
|11q14
|11
|11
|GAB2 *
|''GAB2'' *
|-
|-
|12p12
|12p12
|8
|8
|KRAS *, PIK3C2G ***
|''KRAS'' *, ''PIK3C2G'' ***
|-
|-
|12q14
|12q14
|21
|21
|CDK4 *
|''CDK4'' *
|-
|-
|12q15
|12q15
|11
|11
|HDM2/MDM2 *
|''HDM2''/''MDM2'' *
|-
|-
|13q14
|13q14
|10
|10
|RB1 **
|''RB1'' **
|-
|-
|14q32
|14q32
|37
|37
|AKT1 *
|''AKT1'' *
|-
|-
|15q
|15q
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|17p13
|17p13
|18
|18
|TP53 **
|''TP53'' **
|-
|-
|17q
|17q
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|17q11
|17q11
|15
|15
|NF1 **
|''NF1'' **
|-
|-
|17q24
|17q24
|32
|32
|BPTF ***, PRKCA *, PRKAR1A **
|''BPTF'' ***, ''PRKCA'' *, ''PRKAR1A'' **
|-
|-
|19p13
|19p13
|37
|37
|MAP2K2 *
|''MAP2K2'' *
|-
|-
|20p11
|20p11
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|20q13
|20q13
|22
|22
|MYBL2 *, ZNF217 *, CYP24 ***, STK6 *, P-REX1 *, SS18L1 ***, GNAS *, SNAI1 *, SNAI2 *
|''MYBL2'' *, ''ZNF217'' *, ''CYP24'' ***, ''STK6'' *, ''P-REX1'' *, ''SS18L1'' ***, ''GNAS'' *, ''SNAI1'' *, ''SNAI2'' *
|-
|-
|21q
|21q
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|22q13
|22q13
|21
|21
|MKL1 ***, EP300 ***
|''MKL1'' ***, ''EP300'' ***
|-
|-
| rowspan="32" |Loss
| rowspan="32" |Loss
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|1p36
|1p36
|32
|32
|PRDM16 ***, ARID1A **
|''PRDM16'' ***, ''ARID1A'' **
|-
|-
|3p21 a
|3p21 a
|15
|15
|BAP1 **
|''BAP1'' **
|-
|-
|3q
|3q
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|6q23
|6q23
|29
|29
|MYB ***
|''MYB'' ***
|-
|-
|6q25 b
|6q25 b
|44
|44
|ARID1B **
|''ARID1B'' **
|-
|-
|8p
|8p
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|9p21
|9p21
|38
|38
|CDKN2A **
|''CDKN2A'' **
|-
|-
|9p24
|9p24
|10
|10
|CD274 ***, JAK2 ***, PTPRD **
|''CD274'' ***, ''JAK2'' ***, ''PTPRD'' **
|-
|-
|9q
|9q
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|10p15
|10p15
|14
|14
|PRKCQ ***, NET1 ***, KLF6 **, IL15RA ***, CALML5 ***, LARP4B ***
|''PRKCQ'' ***, ''NET1'' ***, ''KLF6'' **, ''IL15RA'' ***, ''CALML5'' ***, ''LARP4B'' ***
|-
|-
|10q
|10q
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|10q23
|10q23
|25
|25
|PTEN **
|''PTEN'' **
|-
|-
|11p11
|11p11
|23
|23
|CD82 **
|''CD82'' **
|-
|-
|11q
|11q
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|11q22
|11q22
|9
|9
|YAP1 ***
|''YAP1'' ***
|-
|-
|11q24
|11q24
|26
|26
|ETS1 ***, CHEK1 ***
|''ETS1'' ***, ''CHEK1'' ***
|-
|-
|13q14
|13q14
|8
|8
|RB1 **
|''RB1'' **
|-
|-
|16p
|16p
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|16q23
|16q23
|13
|13
|BANP **, CBFA2T3 **, FANCA **, CDK10 ***
|''BANP'' **, ''CBFA2T3'' **, ''FANCA'' **, ''CDK10'' ***
|-
|-
|17p
|17p
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|17p13
|17p13
|12
|12
|TP53 **
|''TP53'' **
|-
|-
|18q
|18q
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|20q11
|20q11
|20
|20
|E2F1 ***
|''E2F1'' ***
|}
|}
<nowiki>*</nowiki>Oncogene; **Tumor suppressor gene; ***Other/complex (context-dependent function, dual role, limited melanoma-specific evidence, or gene located within amplified locus without definitive driver status)
'''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.
'''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"
{| class="wikitable"

Revision as of 15:02, 13 April 2026

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 Barron et al., 2026 [PMID 41898865[1]] 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.

Event Type Region Rate of Gain or Loss (%) Possible Genes Affected
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 ***
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 ***

*Oncogene; **Tumor suppressor gene; ***Other/complex (context-dependent function, dual role, limited melanoma-specific evidence, or gene located within amplified locus without definitive driver status)


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.

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.

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.

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
  1. ↑ Reyes Barron, Cynthia; Geiersbach, Katherine B.; Alomari, Ahmed K.; Deak, Kristen L.; Golem, Shivani; Williams, Eli S.; Aypar, Umut; Zou, Ying S.; Wei, Lei (2026-03-18). "Clinical Utility of Copy Number Abnormality Analysis in the Evaluation of Melanocytic Lesions for Diagnosis and Prognosis: An Evidence-Based Review from the Cancer Genomics Consortium Working Group for Melanocytic Lesions". Genes. 17 (3): 331. doi:10.3390/genes17030331. ISSN 2073-4425. PMC 13026022. PMID 41898865.{{cite journal}}: CS1 maint: unflagged free DOI (link)
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