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Recurrent Genomic Alterations in Pediatric and Adult Central Nervous System Tumors Detected by Chromosomal Microarray (view source)

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Jennelleh moved page CNS Tumors Table to Recurrent Genomic Alterations in Pediatric and Adult Central Nervous System Tumors Detected by Chromosomal Microarray

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'''Recurrent Genomic Alterations in Pediatric and Adult Central Nervous System Tumors Detected by Chromosomal Microarray'''

−

'''Table 1:''' Pediatric CNS Tumors. ~~Table derived from~~ CGC CNS Workgroup 2015-2018.

+

'''Table 1:''' Pediatric CNS Tumors. CGC CNS Workgroup 2015-2018. Table derived from Neill et al., 2020 [[https://pubmed.ncbi.nlm.nih.gov/32203924/ PMID: 32203924]] with permission from Cancer Genetics.

{| class="wikitable"

|-

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|No diagnostic aberrations

|'''Rearrangement:''' [[MYBL1]] truncating rearrangements and tandem duplication, [[FGFR1]] rearrangements

−

'''Mutation:''' [[FGFR1]]

+

'''Mutation:''' [[FGFR1]]

|Anaplastic features associated with decreased progression free survival

|<ref name=":1" />PMID:25664944; <ref name=":6" />PMID:23633565; <ref name=":8">{{Cite journal|last=Cancer Genome Atlas Research Network|last2=Brat|first2=Daniel J.|last3=Verhaak|first3=Roel G. W.|last4=Aldape|first4=Kenneth D.|last5=Yung|first5=W. K. Alfred|last6=Salama|first6=Sofie R.|last7=Cooper|first7=Lee A. D.|last8=Rheinbay|first8=Esther|last9=Miller|first9=C. Ryan|date=2015-06-25|title=Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas|url=https://pubmed.ncbi.nlm.nih.gov/26061751|journal=The New England Journal of Medicine|volume=372|issue=26|pages=2481–2498|doi=10.1056/NEJMoa1402121|issn=1533-4406|pmc=4530011|pmid=26061751}}</ref>PMID:26061751 <ref name=":9">{{Cite journal|last=Ceccarelli|first=Michele|last2=Barthel|first2=Floris P.|last3=Malta|first3=Tathiane M.|last4=Sabedot|first4=Thais S.|last5=Salama|first5=Sofie R.|last6=Murray|first6=Bradley A.|last7=Morozova|first7=Olena|last8=Newton|first8=Yulia|last9=Radenbaugh|first9=Amie|date=2016-01-28|title=Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma|url=https://pubmed.ncbi.nlm.nih.gov/26824661|journal=Cell|volume=164|issue=3|pages=550–563|doi=10.1016/j.cell.2015.12.028|issn=1097-4172|pmc=4754110|pmid=26824661}}</ref>PMID:26824661; <ref name=":10">{{Cite journal|last=Appin|first=Christina L.|last2=Brat|first2=Daniel J.|date=2015-11|title=Biomarker-driven diagnosis of diffuse gliomas|url=https://pubmed.ncbi.nlm.nih.gov/26004297|journal=Molecular Aspects of Medicine|volume=45|pages=87–96|doi=10.1016/j.mam.2015.05.002|issn=1872-9452|pmid=26004297}}</ref>PMID:26004297; <ref name=":0" />PMID:25461780 <ref name=":3" />PMID:23583981

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'''Loss:''' monosomy 9 / 9p deletion

|'''Mutations:''' [[BRAF]] V600E in ~60%; [[TP53]] (5%)

−

'''Loss:''' [[CDKN2A]]/[[CDKN2B]]

+

'''Loss:''' [[CDKN2A]]/[[CDKN2B]]

|

|<ref name=":0" />PMID:25461780; <ref name=":3" />PMID:23583981; <ref>{{Cite journal|last=Weber|first=R. G.|last2=Hoischen|first2=A.|last3=Ehrler|first3=M.|last4=Zipper|first4=P.|last5=Kaulich|first5=K.|last6=Blaschke|first6=B.|last7=Becker|first7=A. J.|last8=Weber-Mangal|first8=S.|last9=Jauch|first9=A.|date=2007-02-15|title=Frequent loss of chromosome 9, homozygous CDKN2A/p14(ARF)/CDKN2B deletion and low TSC1 mRNA expression in pleomorphic xanthoastrocytomas|url=https://pubmed.ncbi.nlm.nih.gov/16909113|journal=Oncogene|volume=26|issue=7|pages=1088–1097|doi=10.1038/sj.onc.1209851|issn=0950-9232|pmid=16909113}}</ref>PMID:16909113; <ref>{{Cite journal|last=Kaulich|first=Kerstin|last2=Blaschke|first2=Britta|last3=Nümann|first3=Astrid|last4=von Deimling|first4=Andreas|last5=Wiestler|first5=Otmar D.|last6=Weber|first6=Ruthild G.|last7=Reifenberger|first7=Guido|date=2002-12|title=Genetic alterations commonly found in diffusely infiltrating cerebral gliomas are rare or absent in pleomorphic xanthoastrocytomas|url=https://pubmed.ncbi.nlm.nih.gov/12484572|journal=Journal of Neuropathology and Experimental Neurology|volume=61|issue=12|pages=1092–1099|doi=10.1093/jnen/61.12.1092|issn=0022-3069|pmid=12484572}}</ref>PMID:12484572

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'''Fusions:''' FGFR-[[TACC]]; NTRK fusions

'''Amplification:''' [[PDGFRA]], [[MYCN]], [[MET]], [[CDK4]], [[CDK6]] ([[EGFR]], [[MDM2]] amp rare)

−

'''Mutations:''' [[IDH1]]/[[IDH2]] (rare in pediatric GBM), [[KRAS]], RAS pathway, [[RB1]] pathway, [[TP53]] pathway, [[FGFR1]], H3.3/H3.1-K27M (exclusively in diffuse midline tumors), [[PDGFRA]], [[NF1]], [[SETD2]], [[ATRX]], [[DAXX]]

+

'''Mutations:''' [[IDH1]]/[[IDH2]] (rare in pediatric GBM), [[KRAS]], RAS pathway, [[RB1]] pathway, [[TP53]] pathway, [[FGFR1]], H3.3/H3.1-K27M (exclusively in diffuse midline tumors), [[PDGFRA]], [[NF1]], [[SETD2]], [[ATRX]], [[DAXX]]

|Overall poor prognosis

|<ref>{{Cite journal|last=Korshunov|first=Andrey|last2=Ryzhova|first2=Marina|last3=Hovestadt|first3=Volker|last4=Bender|first4=Sebastian|last5=Sturm|first5=Dominik|last6=Capper|first6=David|last7=Meyer|first7=Jochen|last8=Schrimpf|first8=Daniel|last9=Kool|first9=Marcel|date=2015-05|title=Integrated analysis of pediatric glioblastoma reveals a subset of biologically favorable tumors with associated molecular prognostic markers|url=https://pubmed.ncbi.nlm.nih.gov/25752754|journal=Acta Neuropathologica|volume=129|issue=5|pages=669–678|doi=10.1007/s00401-015-1405-4|issn=1432-0533|pmid=25752754}}</ref>PMID:25752754; <ref name=":14">{{Cite journal|last=Karsy|first=Michael|last2=Neil|first2=Jayson A.|last3=Guan|first3=Jian|last4=Mahan|first4=Mark A.|last5=Mark|first5=Mahan A.|last6=Colman|first6=Howard|last7=Jensen|first7=Randy L.|date=2015-03|title=A practical review of prognostic correlations of molecular biomarkers in glioblastoma|url=https://pubmed.ncbi.nlm.nih.gov/25727226|journal=Neurosurgical Focus|volume=38|issue=3|pages=E4|doi=10.3171/2015.1.FOCUS14755|issn=1092-0684|pmid=25727226}}</ref>PMID:25727226; <ref>{{Cite journal|last=Furgason|first=John M.|last2=Koncar|first2=Robert F.|last3=Michelhaugh|first3=Sharon K.|last4=Sarkar|first4=Fazlul H.|last5=Mittal|first5=Sandeep|last6=Sloan|first6=Andrew E.|last7=Barnholtz-Sloan|first7=Jill S.|last8=Bahassi|first8=El Mustapha|date=2015|title=Whole genome sequence analysis links chromothripsis to EGFR, MDM2, MDM4, and CDK4 amplification in glioblastoma|url=https://pubmed.ncbi.nlm.nih.gov/26328271|journal=Oncoscience|volume=2|issue=7|pages=618–628|doi=10.18632/oncoscience.178|issn=2331-4737|pmc=4549359|pmid=26328271}}</ref>PMID:26328271; <ref>{{Cite journal|last=Singh|first=Devendra|last2=Chan|first2=Joseph Minhow|last3=Zoppoli|first3=Pietro|last4=Niola|first4=Francesco|last5=Sullivan|first5=Ryan|last6=Castano|first6=Angelica|last7=Liu|first7=Eric Minwei|last8=Reichel|first8=Jonathan|last9=Porrati|first9=Paola|date=2012-09-07|title=Transforming fusions of FGFR and TACC genes in human glioblastoma|url=https://pubmed.ncbi.nlm.nih.gov/22837387|journal=Science (New York, N.Y.)|volume=337|issue=6099|pages=1231–1235|doi=10.1126/science.1220834|issn=1095-9203|pmc=3677224|pmid=22837387}}</ref>PMID:22837387; <ref name=":15">{{Cite journal|last=Ramkissoon|first=Shakti H.|last2=Bi|first2=Wenya Linda|last3=Schumacher|first3=Steven E.|last4=Ramkissoon|first4=Lori A.|last5=Haidar|first5=Sam|last6=Knoff|first6=David|last7=Dubuc|first7=Adrian|last8=Brown|first8=Loreal|last9=Burns|first9=Margot|date=2015-10|title=Clinical implementation of integrated whole-genome copy number and mutation profiling for glioblastoma|url=https://pubmed.ncbi.nlm.nih.gov/25754088|journal=Neuro-Oncology|volume=17|issue=10|pages=1344–1355|doi=10.1093/neuonc/nov015|issn=1523-5866|pmc=4578577|pmid=25754088}}</ref>PMID:25754088; <ref name=":0" />PMID:25461780; <ref name=":11" />PMCID:1891902; <ref>{{Cite journal|last=Fontebasso|first=Adam M.|last2=Schwartzentruber|first2=Jeremy|last3=Khuong-Quang|first3=Dong-Anh|last4=Liu|first4=Xiao-Yang|last5=Sturm|first5=Dominik|last6=Korshunov|first6=Andrey|last7=Jones|first7=David T. W.|last8=Witt|first8=Hendrik|last9=Kool|first9=Marcel|date=2013-05|title=Mutations in SETD2 and genes affecting histone H3K36 methylation target hemispheric high-grade gliomas|url=https://pubmed.ncbi.nlm.nih.gov/23417712|journal=Acta Neuropathologica|volume=125|issue=5|pages=659–669|doi=10.1007/s00401-013-1095-8|issn=1432-0533|pmc=3631313|pmid=23417712}}</ref>PMID:23417712; <ref name=":12" />PMCID:5323185; <ref name=":13" />PMID:29687258; <ref>{{Cite journal|last=Paugh|first=Barbara S.|last2=Qu|first2=Chunxu|last3=Jones|first3=Chris|last4=Liu|first4=Zhaoli|last5=Adamowicz-Brice|first5=Martyna|last6=Zhang|first6=Junyuan|last7=Bax|first7=Dorine A.|last8=Coyle|first8=Beth|last9=Barrow|first9=Jennifer|date=2010-06-20|title=Integrated molecular genetic profiling of pediatric high-grade gliomas reveals key differences with the adult disease|url=https://pubmed.ncbi.nlm.nih.gov/20479398|journal=Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology|volume=28|issue=18|pages=3061–3068|doi=10.1200/JCO.2009.26.7252|issn=1527-7755|pmc=2903336|pmid=20479398}}</ref>PMID:20479398; <ref>{{Cite journal|last=Giunti|first=Laura|last2=Pantaleo|first2=Marilena|last3=Sardi|first3=Iacopo|last4=Provenzano|first4=Aldesia|last5=Magi|first5=Alberto|last6=Cardellicchio|first6=Stefania|last7=Castiglione|first7=Francesca|last8=Tattini|first8=Lorenzo|last9=Novara|first9=Francesca|date=2014|title=Genome-wide copy number analysis in pediatric glioblastoma multiforme|url=https://pubmed.ncbi.nlm.nih.gov/24959384|journal=American Journal of Cancer Research|volume=4|issue=3|pages=293–303|issn=2156-6976|pmc=4065410|pmid=24959384}}</ref>PMID:24959384

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'''H3-K27M subgroup:''' [[MYC]], [[PDGFRA]] gains/amp; [[RB1]], [[TP53]] deletions

'''Mutation:''' [[ACVR1]], [[H3F3A]], [[HIST1H3B]], [[TP53]] '''Loss:''' [[CDKN2A]], [[PTEN]], [[RB1]], [[TP53]]

−

'''Amplification:''' [[MYC]], [[MYCN]], [[ID2]], [[PDGFRA]]

+

'''Amplification:''' [[MYC]], [[MYCN]], [[ID2]], [[PDGFRA]]

|Overall poor prognosis regardless of subgroup

|<ref>{{Cite journal|last=Warren|first=Katherine E.|last2=Killian|first2=Keith|last3=Suuriniemi|first3=Miia|last4=Wang|first4=Yonghong|last5=Quezado|first5=Martha|last6=Meltzer|first6=Paul S.|date=2012-3|title=Genomic aberrations in pediatric diffuse intrinsic pontine gliomas|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3280796/|journal=Neuro-Oncology|volume=14|issue=3|pages=326–332|doi=10.1093/neuonc/nor190|issn=1522-8517|pmc=3280796|pmid=22064882}}</ref>PMCID:3280796; <ref>{{Cite journal|last=Buczkowicz|first=Pawel|last2=Hoeman|first2=Christine|last3=Rakopoulos|first3=Patricia|last4=Pajovic|first4=Sanja|last5=Letourneau|first5=Louis|last6=Dzamba|first6=Misko|last7=Morrison|first7=Andrew|last8=Lewis|first8=Peter|last9=Bouffet|first9=Eric|date=2014-05|title=Genomic analysis of diffuse intrinsic pontine gliomas identifies three molecular subgroups and recurrent activating ACVR1 mutations|url=https://pubmed.ncbi.nlm.nih.gov/24705254|journal=Nature Genetics|volume=46|issue=5|pages=451–456|doi=10.1038/ng.2936|issn=1546-1718|pmc=3997489|pmid=24705254}}</ref>PMID:24705254; <ref>{{Cite journal|last=Taylor|first=Kathryn R.|last2=Mackay|first2=Alan|last3=Truffaux|first3=Nathalène|last4=Butterfield|first4=Yaron|last5=Morozova|first5=Olena|last6=Philippe|first6=Cathy|last7=Castel|first7=David|last8=Grasso|first8=Catherine S.|last9=Vinci|first9=Maria|date=2014-05|title=Recurrent activating ACVR1 mutations in diffuse intrinsic pontine glioma|url=https://pubmed.ncbi.nlm.nih.gov/24705252|journal=Nature Genetics|volume=46|issue=5|pages=457–461|doi=10.1038/ng.2925|issn=1546-1718|pmc=4018681|pmid=24705252}}</ref>PMID:24705252 <ref>{{Cite journal|last=Nikbakht|first=Hamid|last2=Panditharatna|first2=Eshini|last3=Mikael|first3=Leonie G.|last4=Li|first4=Rui|last5=Gayden|first5=Tenzin|last6=Osmond|first6=Matthew|last7=Ho|first7=Cheng-Ying|last8=Kambhampati|first8=Madhuri|last9=Hwang|first9=Eugene I.|date=2016-04-06|title=Spatial and temporal homogeneity of driver mutations in diffuse intrinsic pontine glioma|url=https://pubmed.ncbi.nlm.nih.gov/27048880|journal=Nature Communications|volume=7|pages=11185|doi=10.1038/ncomms11185|issn=2041-1723|pmc=4823825|pmid=27048880}}</ref>PMID:27048880; <ref>{{Cite journal|last=Buczkowicz|first=Pawel|last2=Hawkins|first2=Cynthia|date=2015|title=Pathology, Molecular Genetics, and Epigenetics of Diffuse Intrinsic Pontine Glioma|url=https://pubmed.ncbi.nlm.nih.gov/26175967|journal=Frontiers in Oncology|volume=5|pages=147|doi=10.3389/fonc.2015.00147|issn=2234-943X|pmc=4485076|pmid=26175967}}</ref>PMID:26175967; <ref>{{Cite journal|last=Wu|first=Gang|last2=Diaz|first2=Alexander K.|last3=Paugh|first3=Barbara S.|last4=Rankin|first4=Sherri L.|last5=Ju|first5=Bensheng|last6=Li|first6=Yongjin|last7=Zhu|first7=Xiaoyan|last8=Qu|first8=Chunxu|last9=Chen|first9=Xiang|date=2014-05|title=The genomic landscape of diffuse intrinsic pontine glioma and pediatric non-brainstem high-grade glioma|url=https://pubmed.ncbi.nlm.nih.gov/24705251|journal=Nature Genetics|volume=46|issue=5|pages=444–450|doi=10.1038/ng.2938|issn=1546-1718|pmc=4056452|pmid=24705251}}</ref>PMID:24705251; <ref>{{Cite journal|last=Mackay|first=Alan|last2=Burford|first2=Anna|last3=Carvalho|first3=Diana|last4=Izquierdo|first4=Elisa|last5=Fazal-Salom|first5=Janat|last6=Taylor|first6=Kathryn R.|last7=Bjerke|first7=Lynn|last8=Clarke|first8=Matthew|last9=Vinci|first9=Mara|date=2017-10-09|title=Integrated Molecular Meta-Analysis of 1,000 Pediatric High-Grade and Diffuse Intrinsic Pontine Glioma|url=https://pubmed.ncbi.nlm.nih.gov/28966033|journal=Cancer Cell|volume=32|issue=4|pages=520–537.e5|doi=10.1016/j.ccell.2017.08.017|issn=1878-3686|pmc=5637314|pmid=28966033}}</ref>PMID:28966033

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|'''Fusion:''' [[YAP1]] fusions (supratentorial tumors)

'''Mutation:''' [[NF2]] (spinal tumors)

−

'''Loss:''' [[CDKN2A]]

+

'''Loss:''' [[CDKN2A]]

|Intracranial (in children, 90%) or spinal tumors; Histological distinction between WHO grade II and III is of questionable relevance; Prognostic differences among tumors suggested on the basis of methylation analysis

|WHO CNS Tumors (2016)

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'''Loss:''' 3 (in all hypodiploid CPC), 6, 11, 12q, 16, 22

|'''Mutation:''' [[TP53]] in > 50%

−

'''Amplification:''' [[PDGFRB]]

+

'''Amplification:''' [[PDGFRB]]

|80% occur in children; associated with Li-Fraumeni syndrome; Lack of SMARCB1/SMARCA4 aberrations can be used to distinguish CPC from AT/RT

|<ref>{{Cite journal|last=Ruland|first=Vincent|last2=Hartung|first2=Stefan|last3=Kordes|first3=Uwe|last4=Wolff|first4=Johannes E.|last5=Paulus|first5=Werner|last6=Hasselblatt|first6=Martin|date=2014-05|title=Choroid plexus carcinomas are characterized by complex chromosomal alterations related to patient age and prognosis|url=https://pubmed.ncbi.nlm.nih.gov/24478045|journal=Genes, Chromosomes & Cancer|volume=53|issue=5|pages=373–380|doi=10.1002/gcc.22148|issn=1098-2264|pmid=24478045}}</ref>PMID:24478045; <ref>{{Cite journal|last=Gozali|first=Alexa E.|last2=Britt|first2=Barbara|last3=Shane|first3=Lisa|last4=Gonzalez|first4=Ignacio|last5=Gilles|first5=Floyd|last6=McComb|first6=J. Gordon|last7=Krieger|first7=Mark D.|last8=Lavey|first8=Robert S.|last9=Shlien|first9=Adam|date=2012-06|title=Choroid plexus tumors; management, outcome, and association with the Li-Fraumeni syndrome: the Children's Hospital Los Angeles (CHLA) experience, 1991-2010|url=https://pubmed.ncbi.nlm.nih.gov/21990040|journal=Pediatric Blood & Cancer|volume=58|issue=6|pages=905–909|doi=10.1002/pbc.23349|issn=1545-5017|pmid=21990040}}</ref>PMID:21990040; <ref name=":39" />PMID:25575132; <ref>{{Cite journal|last=Nupponen|first=Nina N.|last2=Paulsson|first2=Janna|last3=Jeibmann|first3=Astrid|last4=Wrede|first4=Brigitte|last5=Tanner|first5=Minna|last6=Wolff|first6=Johannes E. A.|last7=Paulus|first7=Werner|last8=Ostman|first8=Arne|last9=Hasselblatt|first9=Martin|date=2008-03|title=Platelet-derived growth factor receptor expression and amplification in choroid plexus carcinomas|url=https://pubmed.ncbi.nlm.nih.gov/18157090|journal=Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc|volume=21|issue=3|pages=265–270|doi=10.1038/modpathol.3800989|issn=0893-3952|pmid=18157090}}</ref>PMID:18157090; <ref name=":40" />PMID:25336695

|}

−

'''Table 2:''' Adult CNS Tumors. ~~Table derived from~~ CGC CNS Workgroup 2015-2018.

+

'''Table 2:''' Adult CNS Tumors. CGC CNS Workgroup 2015-2018. Table derived from Neill et al., 2020 [[https://pubmed.ncbi.nlm.nih.gov/32203924/ PMID: 32203924]] with permission from Cancer Genetics.

{| class="wikitable"

|-

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'''Loss:''' 1, 2, 3, 13, 14, 16, 17, 19

|'''Fusion:''' [[KIAA1549]]-[[BRAF]] fusion (via 3'[[BRAF]] duplication), other [[BRAF]] partners reported; NTRK fusions (rare)

−

'''Mutation:''' [[FGFR1]]

+

'''Mutation:''' [[FGFR1]]

|Aneuploidy is more predominant in adult PA; Infratentorial tumors are more likely to have BRAF fusions/dup and be wildtype for BRAF mutations; Extra-cerebellar tumors are more likely to be BRAF V600E+, but negative for fusion; Surgical resection can be curative

|<ref>{{Cite journal|last=Theeler|first=Brett J.|last2=Ellezam|first2=Benjamin|last3=Sadighi|first3=Zsila S.|last4=Mehta|first4=Vidya|last5=Tran|first5=M. Diep|last6=Adesina|first6=Adekunle M.|last7=Bruner|first7=Janet M.|last8=Puduvalli|first8=Vinay K.|date=2014-06|title=Adult pilocytic astrocytomas: clinical features and molecular analysis|url=https://pubmed.ncbi.nlm.nih.gov/24470550|journal=Neuro-Oncology|volume=16|issue=6|pages=841–847|doi=10.1093/neuonc/not246|issn=1523-5866|pmc=4022218|pmid=24470550}}</ref>PMID: 24470550; <ref name=":2" />PMID:26378811; <ref name=":1" />PMID: 25664944; <ref>{{Cite journal|last=Strowd|first=Roy E.|last2=Rodriguez|first2=Fausto J.|last3=McLendon|first3=Roger E.|last4=Vredenburgh|first4=James J.|last5=Chance|first5=Aaron B.|last6=Jallo|first6=George|last7=Olivi|first7=Alessandro|last8=Ahn|first8=Edward S.|last9=Blakeley|first9=Jaishri O.|date=2016-06|title=Histologically benign, clinically aggressive: Progressive non-optic pathway pilocytic astrocytomas in adults with NF1|url=https://pubmed.ncbi.nlm.nih.gov/26992069|journal=American Journal of Medical Genetics. Part A|volume=170|issue=6|pages=1455–1461|doi=10.1002/ajmg.a.37622|issn=1552-4833|pmc=4938896|pmid=26992069}}</ref>PMID:26992069

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|'''Gain:''' 7, 19

'''Loss:''' 4, 9p 10

−

'''Amplification:''' [[EGFR]], [[MDM4]], [[CDK4]]

+

'''Amplification:''' [[EGFR]], [[MDM4]], [[CDK4]]

|'''Loss:''' homozygous [[CDKN2A]]/[[CDKN2B]]

'''Mutation:''' [[EGFR]], [[NF1]], [[PTEN]]

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'''Chromothripsis'''

|'''Gain or Amplification:''' [[CDK4]], [[CDK6]], cyclin E2 ([[CCNE2]])

−

'''Loss:''' [[PTEN]]

+

'''Loss:''' [[PTEN]]

|About 10% of glioblastomas; correspond closely to secondary glioblastoma with history of prior glioma. These cases often involve loss of 10q , gain of CDK4, CDK6, cyclin E2, and increase in copy number alterations.

|<ref name=":44" />PMID:26061754; <ref name=":15" />PMID:25754088; <ref name=":45" />PMID:28535583 <ref name=":47">{{Cite journal|last=Geisenberger|first=Christoph|last2=Mock|first2=Andreas|last3=Warta|first3=Rolf|last4=Rapp|first4=Carmen|last5=Schwager|first5=Christian|last6=Korshunov|first6=Andrey|last7=Nied|first7=Ann-Katrin|last8=Capper|first8=David|last9=Brors|first9=Benedikt|date=2015-09|title=Molecular profiling of long-term survivors identifies a subgroup of glioblastoma characterized by chromosome 19/20 co-gain|url=https://pubmed.ncbi.nlm.nih.gov/25931051|journal=Acta Neuropathologica|volume=130|issue=3|pages=419–434|doi=10.1007/s00401-015-1427-y|issn=1432-0533|pmid=25931051}}</ref>PMID:25931051; <ref name=":46" />PMID:26091668; <ref name=":0" />PMID:25461780; <ref name=":48">{{Cite journal|last=Louis|first=David N.|last2=Perry|first2=Arie|last3=Reifenberger|first3=Guido|last4=von Deimling|first4=Andreas|last5=Figarella-Branger|first5=Dominique|last6=Cavenee|first6=Webster K.|last7=Ohgaki|first7=Hiroko|last8=Wiestler|first8=Otmar D.|last9=Kleihues|first9=Paul|date=2016-06|title=The 2016 World Health Organization Classification of Tumors of the Central Nervous System: a summary|url=https://pubmed.ncbi.nlm.nih.gov/27157931|journal=Acta Neuropathologica|volume=131|issue=6|pages=803–820|doi=10.1007/s00401-016-1545-1|issn=1432-0533|pmid=27157931}}</ref>PMID:27157931; <ref name=":14" />PMID:25727226; <ref>{{Cite journal|last=Liu|first=Qun|last2=Liu|first2=Yuexin|last3=Li|first3=Wenliang|last4=Wang|first4=Xiaoguang|last5=Sawaya|first5=Raymond|last6=Lang|first6=Frederick F.|last7=Yung|first7=W. K. Alfred|last8=Chen|first8=Kexin|last9=Fuller|first9=Gregory N.|date=2015-10|title=Genetic, epigenetic, and molecular landscapes of multifocal and multicentric glioblastoma|url=https://pubmed.ncbi.nlm.nih.gov/26323991|journal=Acta Neuropathologica|volume=130|issue=4|pages=587–597|doi=10.1007/s00401-015-1470-8|issn=1432-0533|pmc=4776337|pmid=26323991}}</ref>PMID:26323991 <ref name=":8" />PMID:26061751; <ref name=":13" />PMID:29687258

Line 381: Line 381:

|'''Loss:''' 4, 9p, 10, 13, 14, 15, 22 , (3, 4q, 19q, 16p, 21q, 5p loss in age <40)

'''Gain:''' 7, 19, 20 (1q, 12p, 11q, 9q, 4, 10p gain in age <40)

−

'''Amplification:''' [[EGFR]], [[MDM4]], [[CDK4]], [[MET]]

+

'''Amplification:''' [[EGFR]], [[MDM4]], [[CDK4]], [[MET]]

|'''Loss:''' homozygous [[CDKN2A]]/[[CDKN2B]], [[PTEN]], [[RB1]]

'''Mutation:''' [[TERT]], [[EGFR]], [[PTEN]], [[NF1]], [[RB1]], [[PIK3CA]] or [[PIK3R1]], [[TP53]]

−

'''Amplification:''' [[EGFR]], [[MDM4]], [[MDM2]], [[CDK4]], [[PDGFRA]], [[MET]]

+

'''Amplification:''' [[EGFR]], [[MDM4]], [[MDM2]], [[CDK4]], [[PDGFRA]], [[MET]]

|Overall poor prognosis. Gain of 19q, amplification of EGFR, and homozygous loss of CDKN2A are seen primarily in patients over age 40. Co-gain of 19 and 20 may be associated with longer survival.

|<ref name=":44" />PMID:26061754; <ref name=":15" />PMID:25754088; <ref name=":45" />PMID:28535583 <ref name=":47" />PMID:25931051; <ref name=":46" />PMID:26091668; <ref name=":0" />PMID:25461780; <ref name=":48" />PMID:27157931; <ref name=":14" />PMID:25727226; <ref name=":8" />PMID:26061751

Line 397: Line 397:

'''CN-LOH:''' 1p, 14q

|'''Loss:''' [[NF2]], [[CDKN2A]], [[PTEN]]

−

'''Mutation:''' [[NF2]], [[PI3K]], [[SMO]], [[AKT1]], [[KLF4]], [[TRAF7]], [[TERT]], [[ARID1A]]

+

'''Mutation:''' [[NF2]], [[PI3K]], [[SMO]], [[AKT1]], [[KLF4]], [[TRAF7]], [[TERT]], [[ARID1A]]

|Array findings characteristic of higher grade tumors when histology supports lower grade may suggest increased likelihood of recurrence. Polysomy, particularly involving chromosome 5, are seen in angiomatous meningiomas. LOH 1p and/or LOH 1p/14q correlated with anaplastic transformation.

|<ref name=":24" />PMID:23528542; <ref name=":49">{{Cite journal|last=Och|first=Waldemar|last2=Szmuda|first2=Tomasz|last3=Sikorska|first3=Beata|last4=Springer|first4=Janusz|last5=Jaskólski|first5=Dariusz|last6=Zakrzewska|first6=Magdalena|last7=Liberski|first7=Paweł P.|date=2016-11-XX|title=Recurrence-associated chromosomal anomalies in meningiomas: Single-institution study and a systematic review with meta-analysis|url=https://pubmed.ncbi.nlm.nih.gov/27575681|journal=Neurologia I Neurochirurgia Polska|volume=50|issue=6|pages=439–448|doi=10.1016/j.pjnns.2016.08.003|issn=0028-3843|pmid=27575681}}</ref>PMID:27575681; <ref name=":50">{{Cite journal|last=Lee|first=Yohan|last2=Liu|first2=Jason|last3=Patel|first3=Shilpa|last4=Cloughesy|first4=Timothy|last5=Lai|first5=Albert|last6=Farooqi|first6=Haumith|last7=Seligson|first7=David|last8=Dong|first8=Jun|last9=Liau|first9=Linda|date=2010-07|title=Genomic landscape of meningiomas|url=https://pubmed.ncbi.nlm.nih.gov/20015288|journal=Brain Pathology (Zurich, Switzerland)|volume=20|issue=4|pages=751–762|doi=10.1111/j.1750-3639.2009.00356.x|issn=1750-3639|pmc=3167483|pmid=20015288}}</ref>PMID:20015288 <ref>{{Cite journal|last=Jansen|first=M.|last2=Mohapatra|first2=G.|last3=Betensky|first3=R. A.|last4=Keohane|first4=C.|last5=Louis|first5=D. N.|date=2012-04|title=Gain of chromosome arm 1q in atypical meningioma correlates with shorter progression-free survival|url=https://pubmed.ncbi.nlm.nih.gov/21988727|journal=Neuropathology and Applied Neurobiology|volume=38|issue=2|pages=213–219|doi=10.1111/j.1365-2990.2011.01222.x|issn=1365-2990|pmc=3563294|pmid=21988727}}</ref>PMID:21988727; <ref name=":51">{{Cite journal|last=Gabeau-Lacet|first=Darlene|last2=Engler|first2=David|last3=Gupta|first3=Sumeet|last4=Scangas|first4=George A.|last5=Betensky|first5=Rebecca A.|last6=Barker|first6=Fred G.|last7=Loeffler|first7=Jay S.|last8=Louis|first8=David N.|last9=Mohapatra|first9=Gayatry|date=2009-10|title=Genomic profiling of atypical meningiomas associates gain of 1q with poor clinical outcome|url=https://pubmed.ncbi.nlm.nih.gov/19918127|journal=Journal of Neuropathology and Experimental Neurology|volume=68|issue=10|pages=1155–1165|doi=10.1097/NEN.0b013e3181ba3952|issn=1554-6578|pmc=2847373|pmid=19918127}}</ref>PMID19918127; <ref name=":52">{{Cite journal|last=Abedalthagafi|first=Malak S.|last2=Merrill|first2=Parker H.|last3=Bi|first3=Wenya Linda|last4=Jones|first4=Robert T.|last5=Listewnik|first5=Marc L.|last6=Ramkissoon|first6=Shakti H.|last7=Thorner|first7=Aaron R.|last8=Dunn|first8=Ian F.|last9=Beroukhim|first9=Rameen|date=2014-11-15|title=Angiomatous meningiomas have a distinct genetic profile with multiple chromosomal polysomies including polysomy of chromosome 5|url=https://pubmed.ncbi.nlm.nih.gov/25347344|journal=Oncotarget|volume=5|issue=21|pages=10596–10606|doi=10.18632/oncotarget.2517|issn=1949-2553|pmc=4279396|pmid=25347344}}</ref>PMID:25347344 <ref name=":53">{{Cite journal|last=Brastianos|first=Priscilla K.|last2=Horowitz|first2=Peleg M.|last3=Santagata|first3=Sandro|last4=Jones|first4=Robert T.|last5=McKenna|first5=Aaron|last6=Getz|first6=Gad|last7=Ligon|first7=Keith L.|last8=Palescandolo|first8=Emanuele|last9=Van Hummelen|first9=Paul|date=2013-03|title=Genomic sequencing of meningiomas identifies oncogenic SMO and AKT1 mutations|url=https://pubmed.ncbi.nlm.nih.gov/23334667|journal=Nature Genetics|volume=45|issue=3|pages=285–289|doi=10.1038/ng.2526|issn=1546-1718|pmc=3739288|pmid=23334667}}</ref>PMID:23334667; <ref name=":54">{{Cite journal|last=Abedalthagafi|first=Malak S.|last2=Bi|first2=Wenya Linda|last3=Merrill|first3=Parker H.|last4=Gibson|first4=William J.|last5=Rose|first5=Matthew F.|last6=Du|first6=Ziming|last7=Francis|first7=Joshua M.|last8=Du|first8=Rose|last9=Dunn|first9=Ian F.|date=2015-06|title=ARID1A and TERT promoter mutations in dedifferentiated meningioma|url=https://pubmed.ncbi.nlm.nih.gov/25963524|journal=Cancer Genetics|volume=208|issue=6|pages=345–350|doi=10.1016/j.cancergen.2015.03.005|issn=2210-7762|pmc=4882906|pmid=25963524}}</ref>PMID:25963524; <ref name=":55">{{Cite journal|last=Abedalthagafi|first=Malak|last2=Bi|first2=Wenya Linda|last3=Aizer|first3=Ayal A.|last4=Merrill|first4=Parker H.|last5=Brewster|first5=Ryan|last6=Agarwalla|first6=Pankaj K.|last7=Listewnik|first7=Marc L.|last8=Dias-Santagata|first8=Dora|last9=Thorner|first9=Aaron R.|date=2016-05|title=Oncogenic PI3K mutations are as common as AKT1 and SMO mutations in meningioma|url=https://pubmed.ncbi.nlm.nih.gov/26826201|journal=Neuro-Oncology|volume=18|issue=5|pages=649–655|doi=10.1093/neuonc/nov316|issn=1523-5866|pmc=4827048|pmid=26826201}}</ref>PMID:26826201 <ref name=":56">{{Cite journal|last=Harmancı|first=Akdes Serin|last2=Youngblood|first2=Mark W.|last3=Clark|first3=Victoria E.|last4=Coşkun|first4=Süleyman|last5=Henegariu|first5=Octavian|last6=Duran|first6=Daniel|last7=Erson-Omay|first7=E. Zeynep|last8=Kaulen|first8=Leon D.|last9=Lee|first9=Tong Ihn|date=2017-02-14|title=Integrated genomic analyses of de novo pathways underlying atypical meningiomas|url=https://pubmed.ncbi.nlm.nih.gov/28195122|journal=Nature Communications|volume=8|pages=14433|doi=10.1038/ncomms14433|issn=2041-1723|pmc=5316884|pmid=28195122}}</ref>PMID:28195122; <ref name=":57">{{Cite journal|last=Aizer|first=Ayal A.|last2=Abedalthagafi|first2=Malak|last3=Bi|first3=Wenya Linda|last4=Horvath|first4=Margaret C.|last5=Arvold|first5=Nils D.|last6=Al-Mefty|first6=Ossama|last7=Lee|first7=Eudocia Q.|last8=Nayak|first8=Lakshmi|last9=Rinne|first9=Mikael L.|date=2016-02|title=A prognostic cytogenetic scoring system to guide the adjuvant management of patients with atypical meningioma|url=https://pubmed.ncbi.nlm.nih.gov/26323607|journal=Neuro-Oncology|volume=18|issue=2|pages=269–274|doi=10.1093/neuonc/nov177|issn=1523-5866|pmc=4724184|pmid=26323607}}</ref>PMID:26323607;

Line 408: Line 408:

'''Loss:''' 1p, 3p, 6q, 7p, 14/14q, 9p, 10, 11p, 18/18q, 19q, 22/loss 22q

|'''Loss:''' [[NF2]], [[CDKN2A]], [[PTEN]]

−

'''Mutation:''' [[NF2]], [[CDKN2A]]/[[CDKN2C]], [[SMARCE1]], [[SMARCB1]], [[TERT]]

+

'''Mutation:''' [[NF2]], [[CDKN2A]]/[[CDKN2C]], [[SMARCE1]], [[SMARCB1]], [[TERT]]

|Gain of 1q is assocociated with a shorter PFS; Loss of 1p, 9p and 10 appear with greater frequency as tumor grade increases.

|<ref name=":24" />PMID:23528542; <ref name=":49" />PMID:27575681; <ref name=":50" />PMID:20015288 <ref name=":50" />PMID:21988727; <ref name=":51" />PMID19918127; <ref name=":52" />PMID:25347344 <ref name=":53" />PMID:23334667; <ref name=":54" />PMID:25963524; <ref name=":55" />PMID:26826201 <ref name=":56" />PMID:28195122; <ref name=":57" />PMID:26323607; <ref name=":58" />PMID:11958368; <ref name=":59" />PMID:25965831; <ref name=":60" />PMID:24536048; <ref name=":61" />PMID:24722350 <ref name=":62" />PMID:12568317; <ref name=":63" />PMID:26771848; <ref name=":64" />PMID:27012381; <ref name=":65" />PMID:27480481; <ref name=":66" />PMID:27624470; <ref name=":67" />PMID:27458586; <ref name=":68" />PMID:17225936

Line 428: Line 428:

|'''Fusion:''' [[YAP1]] fusions (supratentorial tumors)

'''Mutation:''' [[NF2]] (spinal tumors)

−

'''Loss:''' [[CDKN2A]]

+

'''Loss:''' [[CDKN2A]]

|Intracranial (in children, 90%) or spinal tumors; Histological distinction between WHO grade II and III is not reliable; Prognostic differences among tumors suggested on the basis of methylation analysis

|WHO CNS Tumors (2016)

Line 478: Line 478:

|<ref name=":16" />PMID: 25965575; <ref>{{Cite journal|last=Wu|first=Jing|last2=Armstrong|first2=Terri S.|last3=Gilbert|first3=Mark R.|date=2016-07|title=Biology and management of ependymomas|url=https://pubmed.ncbi.nlm.nih.gov/27022130|journal=Neuro-Oncology|volume=18|issue=7|pages=902–913|doi=10.1093/neuonc/now016|issn=1523-5866|pmc=4896548|pmid=27022130}}</ref>PMID:27022130

|}

+

==Reference==

+

1. Neill SG, Hauenstein J, Li MM, Liu YJ, Luo M, Saxe DF, Ligon AH. (2020-05). Copy number assessment in the genomic analysis of CNS neoplasia: An evidence-based review from the cancer genomics consortium (CGC) working group on primary CNS tumors. Cancer Genetics. 243: 19–47. PMID 32203924.

Jennelleh

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