Melanocytic Lesions - Revision history

Jennelleh at 12:56, 26 April 2026

2026-04-26T12:56:20Z

← Older revision		Revision as of 07:56, 26 April 2026
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	\|'''Loci'''		\|'''Loci'''
	\|'''Genes'''		\|'''Genes'''
	\|'''Probes'''		\|'''Number of Probes'''
	\|-		\|-
	\|6, 11		\|6, 11

Jennelleh at 12:50, 26 April 2026

2026-04-26T12:50:26Z

← Older revision		Revision as of 07:50, 26 April 2026
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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 derived from Barron et al., 2026 [<nowiki>PMID 41898865</nowiki><ref name=":0" />; open access].		'''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].
	{\| class="wikitable"		{\| class="wikitable"
	\|'''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 derived from Barron et al., 2026 [<nowiki>PMID 41898865</nowiki><ref name=":0" />; open access].
			'''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"		{\| class="wikitable"
	\|'''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

Jennelleh at 12:23, 26 April 2026

2026-04-26T12:23:51Z

← Older revision		Revision as of 07:23, 26 April 2026
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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.
	{\| class="wikitable"		{\| class="wikitable"
	\|+		\|+
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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].
	{\| class="wikitable"		{\| class="wikitable"
	\|+		\|+
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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].
	{\| class="wikitable"		{\| class="wikitable"
	\|+		\|+
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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].
	{\| class="wikitable"		{\| class="wikitable"
	\|+		\|+
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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].''
	{\| class="wikitable"		{\| class="wikitable"
	\|'''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.''' The symbol “ -”designates data not available. Table derived from Barron et al., 2026 [<nowiki>PMID 41898865</nowiki><ref name=":0" />; open access].
	{\| class="wikitable"		{\| class="wikitable"
	\|'''Region'''		\|'''Region'''
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	'''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"		{\| class="wikitable"
	\|'''Region'''		\|'''Region'''
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	'''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].
	{\| class="wikitable"		{\| class="wikitable"
	\|'''Chromosomes'''		\|'''Chromosomes'''
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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].
	{\| class="wikitable"		{\| class="wikitable"
	\|'''Gene'''		\|'''Gene'''

He.Fang at 23:43, 23 April 2026

2026-04-23T23:43:13Z

← Older revision		Revision as of 18:43, 23 April 2026
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	{\| class="wikitable"		{\| class="wikitable"
	\|'''Gene'''		\|'''Gene'''
	\|'''Function/Potential Role ~~(S11)'''~~		\|'''Function / Potential Role'''
	~~\|'''Gene'''~~
	~~\|'''Function/Potential Role (S12)~~'''
	\|-		\|-
	\|''ADAM30''		\|''ADAM30''
	\|Limited functional evidence		\|Limited functional evidence supporting a driver role in melanoma
	~~\|''CALML5''~~
	~~\|Calcium-binding protein~~
	\|-		\|-
	\|''BPTF''		\|''BPTF''
	\|Chromatin remodeler		\|Chromatin remodeler with context-dependent oncogenic properties
	~~\|''CD274''~~
	~~\|Immune checkpoint regulator~~
	\|-		\|-
	\|''CYP24''		\|''CYP24''
	\|Vitamin D metabolism		\|Vitamin D metabolism gene; indirect relevance to tumor biology
			\|-
			\|''EP300''
			\|Histone acetyltransferase; may function as coactivator or tumor suppressor depending on context
			\|-
			\|''KIRREL''
			\|Limited mechanistic validation as melanoma driver
			\|-
			\|''MKL1''
			\|Transcriptional coactivator; context-dependent oncogenic activity
			\|-
			\|''NOTCH2''
			\|Context-dependent signaling with oncogenic and tumor-suppressive roles depending on cellular context
			\|-
			\|''PDE11A''
			\|Phosphodiesterase with unclear contribution to melanoma progression
			\|-
			\|''PDE4DIP''
			\|Scaffold protein; no consistent evidence of recurrent oncogenic activation in melanoma
			\|-
			\|''PHIP''
			\|Implicated in melanoma progression but mechanistically complex and not a canonical oncogene
			\|-
			\|''PIK3C2G''
			\|PIK3 family member; limited evidence of recurrent activating alterations in melanoma
			\|-
			\|''S100A9, S100A10, S100A11, S100A12''
			\|Inflammatory mediators more commonly implicated in tumor microenvironment modulation than as primary genomic drivers
			\|-
			\|''SS18L1''
			\|Transcriptional regulator without clear melanoma driver validation
			\|-
			\|''CALML5''
			\|Calcium-binding protein; limited oncogenic validation
			\|-
			\|''CD274 (PD-L1)''
			\|Immune checkpoint regulator; deletion effects are context-dependent
			\|-
	\|''CDK10''		\|''CDK10''
	\|Cell-cycle regulator		\|Cell-cycle regulator; limited melanoma-specific driver evidence
	\|-		\|-
	~~\|''EP300''~~
	~~\|Histone acetyltransferase~~
	\|''CHEK1''		\|''CHEK1''
	\|DNA damage kinase		\|DNA damage response kinase; dual context-dependent role
	\|-		\|-
	~~\|''KIRREL''~~
	~~\|Limited driver validation~~
	\|''ETS1''		\|''ETS1''
	\|Transcription factor		\|Transcription factor with context-dependent oncogenic properties
	\|-		\|-
	~~\|''MKL1''~~
	~~\|Transcriptional coactivator~~
	\|''IL15RA''		\|''IL15RA''
	\|Immune regulatory receptor		\|Immune regulatory receptor; indirect tumor role
	\|-		\|-
	~~\|''NOTCH2''~~
	~~\|Signaling (context-dependent)~~
	\|''JAK2''		\|''JAK2''
	\|Oncogenic kinase		\|Oncogenic kinase; loss not typical driver event in melanoma
	\|-		\|-
	~~\|''PDE11A''~~
	~~\|Phosphodiesterase~~
	\|''LARP4B''		\|''LARP4B''
	\|RNA-binding protein		\|RNA-binding protein; insufficient evidence as melanoma driver
	\|-		\|-
	~~\|''PDE4DIP''~~
	~~\|Scaffold protein~~
	\|''MYB''		\|''MYB''
	\|Canonical oncogene		\|Canonical oncogene; loss does not represent typical driver mechanism in melanoma
	\|-		\|-
	~~\|''PHIP''~~
	~~\|Implicated in progression~~
	\|''NET1''		\|''NET1''
	\|RhoA GEF		\|RhoA GEF; limited melanoma-specific evidence
	\|-		\|-
	~~\|''PIK3C2G''~~
	~~\|PIK3 family member~~
	\|''PRDM16''		\|''PRDM16''
	\|~~Transcriptional~~ regulator		\|Context-dependent transcriptional regulator; not established as recurrent melanoma tumor suppressor
	\|-		\|-
	~~\|''S100A9-12''~~
	~~\|Inflammatory mediators~~
	\|''PRKCQ''		\|''PRKCQ''
	\|~~Signaling kinase~~		\|Kinase with signaling roles; melanoma-specific driver role unclear
	\|-		\|-
	~~\|''SS18L1''~~
	~~\|Transcriptional regulator~~
	\|''YAP1''		\|''YAP1''
	\|Hippo pathway oncogene		\|Hippo pathway oncogene; deletion suggests complex regional effects
	\|}		\|}

	==Reference==		==Reference==

He.Fang: change fond for the tables

2026-04-23T23:40:11Z

change fond for the tables

← Older revision		Revision as of 18:40, 23 April 2026
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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.'''''
	{\| class="wikitable"		{\| class="wikitable"
	\|'''Chromosome'''		\|'''Chromosome'''

He.Fang: add supplemental tables from the paper

2026-04-23T23:39:07Z

add supplemental tables from the paper

Show changes

Jennelleh at 13:58, 14 April 2026

2026-04-14T13:58:12Z

← Older revision		Revision as of 08:58, 14 April 2026
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	'''Table 2. Rates in percentage of copy number ~~Aabnormalities~~ 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.*'''
	{\| class="wikitable"		{\| class="wikitable"
	\|+		\|+

Jennelleh at 20:19, 13 April 2026

2026-04-13T20:19:42Z

← Older revision		Revision as of 15:19, 13 April 2026
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	\|0 (83)		\|0 (83)
	\|}		\|}
	<nowiki>*</nowiki>The symbol “-” designates data not available~~; Values in red represent rates calculated from <25 reported cases~~; The number of reported cases appears in parentheses ().		<nowiki>*</nowiki>The symbol “-” designates data not available; The number of reported cases appears in parentheses ().

Jennelleh at 20:13, 13 April 2026

2026-04-13T20:13:43Z

← Older revision		Revision as of 15:13, 13 April 2026
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	\|28		\|28
	\|}		\|}

			==Reference==

Jennelleh at 20:12, 13 April 2026

2026-04-13T20:12:36Z

← Older revision		Revision as of 15:12, 13 April 2026
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	'''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 copy number Aabnormalities commonly tested on FISH panels across different melanoma subtypes.*'''
	{\| class="wikitable"		{\| class="wikitable"
	\|+		\|+
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	\|0 (83)		\|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.~~		<nowiki>*</nowiki>The symbol “-” designates data not available; Values in red represent rates calculated from <25 reported cases; The number of reported cases appears in parentheses ().


			'''Table 3. Rates of abnormalities detected by FISH panels for each melanoma subtype and 95% confidence intervals for the given rates.*'''
	{\| class="wikitable"		{\| class="wikitable"
	\|+		\|+
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	\|169		\|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.'''		<nowiki>*</nowiki>The number of cases on which the rates are based is given.


			'''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.'''
	{\| class="wikitable"		{\| class="wikitable"
	\|+		\|+