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 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.
'''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 name=":0">{{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>; open access]. 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.
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'''Table 2. Rates in percentage of copy number abnormalities commonly tested on FISH panels across different melanoma subtypes.*'''  
'''Table 2. Rates in percentage of copy number abnormalities commonly tested on FISH panels across different melanoma subtypes.*''' Table derived from Barron et al., 2026 [<nowiki>PMID 41898865</nowiki><ref name=":0" />; open access].
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'''Table 3. Rates of abnormalities detected by FISH panels for each melanoma subtype and 95% confidence intervals for the given rates.*'''
'''Table 3. Rates of abnormalities detected by FISH panels for each melanoma subtype and 95% confidence intervals for the given rates.*''' Table derived from Barron et al., 2026 [<nowiki>PMID 41898865</nowiki><ref name=":0" />; open access].
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'''Table 4. The percentage of melanomas with greater than 3 copy number abnormalities (CNAs) reported by chromosomal microarray (CMA) for each melanoma subtype and the 95% confidence lower bound for the proportion in the given number of reported cases.'''
'''Table 4. The percentage of melanomas with greater than 3 copy number abnormalities (CNAs) reported by chromosomal microarray (CMA) for each melanoma subtype and the 95% confidence lower bound for the proportion in the given number of reported cases.''' Table derived from Barron et al., 2026 [<nowiki>PMID 41898865</nowiki><ref name=":0" />; open access].
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|28
|28
|}
|}
'''''Table 5. Rates of chromosomal abnormalities detected in primary uveal melanoma associated with high risk of metastasis and aggressive clinical behavior.'''''
'''''Table 5. Rates of chromosomal abnormalities detected in primary uveal melanoma associated with high risk of metastasis and aggressive clinical behavior.''' Table derived from Barron et al., 2026 [<nowiki>PMID 41898865</nowiki><ref name=":0" />; open access].''
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|'''Chromosome'''
|'''Chromosome'''
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'''Table 6. Comparison of rates of abnormalities reported in Spitzoid lesions in three or more manuscripts.''' The symbol “ -”designates data not available.
'''Table 6. Comparison of rates of abnormalities reported in Spitzoid lesions in three or more manuscripts.'''* Table derived from Barron et al., 2026 [<nowiki>PMID 41898865</nowiki><ref name=":0" />; open access].
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|'''Region'''
|'''Region'''
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|'''Spitz Nevus (%)'''
|'''Spitz Nevus (%)'''
|'''Spitz Melanocytoma (%)'''
|'''Spitz Melanocytoma (%)'''
|'''Spitzoid Melanoma (%)'''
|'''Spitzoid/Spitz Melanoma (%)'''
|'''Manuscripts'''
|'''Number of Manuscripts'''
|-
|-
|6p25
|6p25
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|FISH
|FISH
|at least 1 CNA
|at least 1 CNA
|''several''
|several
|14
|14
|18
|18
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|CMA
|CMA
|>3 CNAs
|>3 CNAs
|''many''
|many
|2
|2
|16
|16
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|}
|}


<nowiki>*</nowiki>The symbol “-” designates data not available


'''Table 7. CNAs reported in at least 3 manuscripts in at least 50 cases of primary melanomas and 50 cases of metastases with significant difference in rates (P-values given for differences).''' Individual P-values indicate whether each abnormality is significantly greater than 5%. Rates in bold were the greater of the comparison between primary and metastatic melanomas.
 
'''Table 7. CNAs reported in at least 3 manuscripts in at least 50 cases of primary melanomas and 50 cases of metastases with significant difference in rates (P-values given for differences).*''' Individual P-values indicate whether each abnormality is significantly greater than 5%. Rates in bold were the greater of the comparison between primary and metastatic melanomas. Table derived from Barron et al., 2026 [<nowiki>PMID 41898865</nowiki><ref name=":0" />; open access].
{| class="wikitable"
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|'''Region'''
|'''Region'''
|'''Abnormality'''
|'''Abnormality'''
|'''Genes'''
|'''Genes Affected'''
|'''Rate Primary (%)'''
|'''Rate in Primary (%)'''
|'''P-value (P)'''
|'''P-value Primary (P)'''
|'''Rate Metastasis (%)'''
|'''Rate in Metastasis (%)'''
|'''P-value (M)'''
|'''P-value Metastasis'''
|'''P-diff'''
|'''P-value Difference'''
|'''N (P)'''
|'''Number of Primary Melanoma Cases'''
|'''N (M)'''
|'''Number of Metastasis Cases'''
|-
|-
|3p13
|3p13
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|7q31
|7q31
|gain
|gain
|''MET, CAV1''
|''MET, CAV1'', others
|32
|32
|<0.001
|<0.001
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|69
|69
|}
|}
<nowiki>*</nowiki>The symbol “-” designates data not available




'''Table 8. FISH probe sets for analysis of melanocytic lesions with published data included in this study.'''
'''Table 8. FISH probe sets for analysis of melanocytic lesions with published data included in this study.''' Table derived from Barron et al., 2026 [<nowiki>PMID 41898865</nowiki><ref name=":0" />; open access].
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|'''Chromosomes'''
|'''Chromosomes'''
|'''Loci'''
|'''Loci'''
|'''Genes'''
|'''Genes'''
|'''Probes'''
|'''Number of Probes'''
|-
|-
|6, 11
|6, 11
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'''Table 9. Genes classified as other/complex in Table 1.'''
'''Table 9. Genes classified as other/complex in Table 1.''' Table derived from Barron et al., 2026 [<nowiki>PMID 41898865</nowiki><ref name=":0" />; open access].
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|'''Gene'''
|'''Gene'''
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