View source for Recurrent Genomic Alterations in Pediatric and Adult Central Nervous System Tumors Detected by Chromosomal Microarray

'''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 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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!TUMOR
!SUBTYPES
!BROAD ABERRATIONS (>10Mb)
!FOCAL ABERRATIONS (<10Mb)
!CLINICAL FEATURES
!REFERENCES
|-
|'''GLIOMAS'''
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|WHO CNS Tumors (2016)
|-
|Low grade glioma, WHO grade I
|Pilocytic astrocytoma/pilomyxoid astrocytoma
|Some tumors show polysomy 7; other polysomies more common in adult PA
|'''Fusions:''' [[KIAA1549]]-[[BRAF]] fusion (via 3'[[BRAF]] duplication), other [[BRAF]] partners reported; NTRK fusions (rare); [[FGFR1]] fusions (rare) <br>
'''Mutations:''' [[BRAF]] V600E (particularly extra-cerebellar tumors); [[FGFR1]] (midline PA); [[NF1]] (esp. germline), other MAPK pathway mutations <br>
'''Loss:''' [[NF1]] in optic pathway PA
|Classic PA are cerebellar (most commonly associated with BRAF duplication); PA in patients with germline NF1 alterations often develop as optic gliomas;Surgical resection can be curative; PMA generally more aggressive than PA; BRAF fusions and BRAF mutations generally are mutually exclusive
|<ref>{{Cite journal|last=Sievert|first=Angela J.|last2=Jackson|first2=Eric M.|last3=Gai|first3=Xiaowu|last4=Hakonarson|first4=Hakon|last5=Judkins|first5=Alexander R.|last6=Resnick|first6=Adam C.|last7=Sutton|first7=Leslie N.|last8=Storm|first8=Phillip B.|last9=Shaikh|first9=Tamim H.|date=2009-07|title=Duplication of 7q34 in pediatric low-grade astrocytomas detected by high-density single-nucleotide polymorphism-based genotype arrays results in a novel BRAF fusion gene|url=https://pubmed.ncbi.nlm.nih.gov/19016743|journal=Brain Pathology (Zurich, Switzerland)|volume=19|issue=3|pages=449–458|doi=10.1111/j.1750-3639.2008.00225.x|issn=1750-3639|pmc=2850204|pmid=19016743}}</ref>PMID:19016743; <ref>{{Cite journal|last=Jones|first=David T. W.|last2=Ichimura|first2=Koichi|last3=Liu|first3=Lu|last4=Pearson|first4=Danita M.|last5=Plant|first5=Karen|last6=Collins|first6=V. Peter|date=2006-11|title=Genomic Analysis of Pilocytic Astrocytomas at 0.97 Mb Resolution Shows an Increasing Tendency Toward Chromosomal Copy Number Change With Age|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2761618/|journal=Journal of neuropathology and experimental neurology|volume=65|issue=11|pages=1049–1058|doi=10.1097/01.jnen.0000240465.33628.87|issn=0022-3069|pmc=2761618|pmid=17086101}}</ref>PMCID:2761618; <ref>{{Cite journal|last=Bar|first=Eli E.|last2=Lin|first2=Alex|last3=Tihan|first3=Tarik|last4=Burger|first4=Peter C.|last5=Eberhart|first5=Charles G.|date=2008-09|title=Frequent gains at chromosome 7q34 involving BRAF in pilocytic astrocytoma|url=https://pubmed.ncbi.nlm.nih.gov/18716556|journal=Journal of Neuropathology and Experimental Neurology|volume=67|issue=9|pages=878–887|doi=10.1097/NEN.0b013e3181845622|issn=0022-3069|pmid=18716556}}</ref>PMID:18716556 <ref name=":0">{{Cite journal|last=Appin|first=Christina L.|last2=Brat|first2=Daniel J.|date=2015-01|title=Molecular pathways in gliomagenesis and their relevance to neuropathologic diagnosis|url=https://pubmed.ncbi.nlm.nih.gov/25461780|journal=Advances in Anatomic Pathology|volume=22|issue=1|pages=50–58|doi=10.1097/PAP.0000000000000048|issn=1533-4031|pmid=25461780}}</ref>PMID:25461780  <ref name=":1">{{Cite journal|last=Venneti|first=Sriram|last2=Huse|first2=Jason T.|date=2015-03|title=The evolving molecular genetics of low-grade glioma|url=https://pubmed.ncbi.nlm.nih.gov/25664944|journal=Advances in Anatomic Pathology|volume=22|issue=2|pages=94–101|doi=10.1097/PAP.0000000000000049|issn=1533-4031|pmc=4667550|pmid=25664944}}</ref>PMID:25664944; <ref name=":2">{{Cite journal|last=Fontebasso|first=Adam M.|last2=Shirinian|first2=Margret|last3=Khuong-Quang|first3=Dong-Anh|last4=Bechet|first4=Denise|last5=Gayden|first5=Tenzin|last6=Kool|first6=Marcel|last7=De Jay|first7=Nicolas|last8=Jacob|first8=Karine|last9=Gerges|first9=Noha|date=2015-10-13|title=Non-random aneuploidy specifies subgroups of pilocytic astrocytoma and correlates with older age|url=https://pubmed.ncbi.nlm.nih.gov/26378811|journal=Oncotarget|volume=6|issue=31|pages=31844–31856|doi=10.18632/oncotarget.5571|issn=1949-2553|pmc=4741644|pmid=26378811}}</ref>PMID:26378811 <ref>{{Cite journal|last=Rodriguez|first=Fausto J.|last2=Ligon|first2=Azra H.|last3=Horkayne-Szakaly|first3=Iren|last4=Rushing|first4=Elisabeth J.|last5=Ligon|first5=Keith L.|last6=Vena|first6=Natalie|last7=Garcia|first7=Denise I.|last8=Cameron|first8=J. Douglas|last9=Eberhart|first9=Charles G.|date=2012-9|title=BRAF Duplications and MAPK Pathway Activation Are Frequent in Gliomas of the Optic Nerve Proper|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3429698/|journal=Journal of neuropathology and experimental neurology|volume=71|issue=9|pages=789–794|doi=10.1097/NEN.0b013e3182656ef8|issn=0022-3069|pmc=3429698|pmid=22892521}}</ref>PMCID:3429698; <ref>{{Cite journal|last=Jones|first=David T. W.|last2=Hutter|first2=Barbara|last3=Jäger|first3=Natalie|last4=Korshunov|first4=Andrey|last5=Kool|first5=Marcel|last6=Warnatz|first6=Hans-Jörg|last7=Zichner|first7=Thomas|last8=Lambert|first8=Sally R.|last9=Ryzhova|first9=Marina|date=2013-08|title=Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma|url=https://pubmed.ncbi.nlm.nih.gov/23817572|journal=Nature Genetics|volume=45|issue=8|pages=927–932|doi=10.1038/ng.2682|issn=1546-1718|pmc=3951336|pmid=23817572}}</ref>PMID:23817572; <ref name=":3">{{Cite journal|last=Zhang|first=Jinghui|last2=Wu|first2=Gang|last3=Miller|first3=Claudia P.|last4=Tatevossian|first4=Ruth G.|last5=Dalton|first5=James D.|last6=Tang|first6=Bo|last7=Orisme|first7=Wilda|last8=Punchihewa|first8=Chandanamali|last9=Parker|first9=Matthew|date=2013-06|title=Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas|url=https://pubmed.ncbi.nlm.nih.gov/23583981|journal=Nature Genetics|volume=45|issue=6|pages=602–612|doi=10.1038/ng.2611|issn=1546-1718|pmc=3727232|pmid=23583981}}</ref>PMID:23583981 <ref>{{Cite journal|last=Jones|first=David T. W.|last2=Kocialkowski|first2=Sylvia|last3=Liu|first3=Lu|last4=Pearson|first4=Danita M.|last5=Bäcklund|first5=L. Magnus|last6=Ichimura|first6=Koichi|last7=Collins|first7=V. Peter|date=2008-11-01|title=Tandem duplication producing a novel oncogenic BRAF fusion gene defines the majority of pilocytic astrocytomas|url=https://pubmed.ncbi.nlm.nih.gov/18974108|journal=Cancer Research|volume=68|issue=21|pages=8673–8677|doi=10.1158/0008-5472.CAN-08-2097|issn=1538-7445|pmc=2577184|pmid=18974108}}</ref>PMID:18974108; <ref>{{Cite journal|last=Colin|first=C.|last2=Padovani|first2=L.|last3=Chappé|first3=C.|last4=Mercurio|first4=S.|last5=Scavarda|first5=D.|last6=Loundou|first6=A.|last7=Frassineti|first7=F.|last8=André|first8=N.|last9=Bouvier|first9=C.|date=2013-10|title=Outcome analysis of childhood pilocytic astrocytomas: a retrospective study of 148 cases at a single institution|url=https://pubmed.ncbi.nlm.nih.gov/23278243|journal=Neuropathology and Applied Neurobiology|volume=39|issue=6|pages=693–705|doi=10.1111/nan.12013|issn=1365-2990|pmid=23278243}}</ref>PMID:23278243; <ref name=":4">{{Cite journal|last=Schindler|first=Genevieve|last2=Capper|first2=David|last3=Meyer|first3=Jochen|last4=Janzarik|first4=Wibke|last5=Omran|first5=Heymut|last6=Herold-Mende|first6=Christel|last7=Schmieder|first7=Kirsten|last8=Wesseling|first8=Pieter|last9=Mawrin|first9=Christian|date=2011-03|title=Analysis of BRAF V600E mutation in 1,320 nervous system tumors reveals high mutation frequencies in pleomorphic xanthoastrocytoma, ganglioglioma and extra-cerebellar pilocytic astrocytoma|url=https://pubmed.ncbi.nlm.nih.gov/21274720|journal=Acta Neuropathologica|volume=121|issue=3|pages=397–405|doi=10.1007/s00401-011-0802-6|issn=1432-0533|pmid=21274720}}</ref>PMID:21274720
|-
|
|Angiocentric glioma
|Aberrations involving 6q24-q25
|'''Fusions:''' [[MYB]]-[[QKI]] rearrangement/deletion (classic histology)<br>
'''Rearrangement:''' [[MYB]] alone (atypical histology)<br>
'''Amplification:''' [[MYB]] (atypical histology)
|Generally indolent tumors; surgical resection can be curative
|<ref name=":5">{{Cite journal|last=Bandopadhayay|first=Pratiti|last2=Ramkissoon|first2=Lori A.|last3=Jain|first3=Payal|last4=Bergthold|first4=Guillaume|last5=Wala|first5=Jeremiah|last6=Zeid|first6=Rhamy|last7=Schumacher|first7=Steven E.|last8=Urbanski|first8=Laura|last9=O'Rourke|first9=Ryan|date=2016-03|title=MYB-QKI rearrangements in angiocentric glioma drive tumorigenicity through a tripartite mechanism|url=https://pubmed.ncbi.nlm.nih.gov/26829751|journal=Nature Genetics|volume=48|issue=3|pages=273–282|doi=10.1038/ng.3500|issn=1546-1718|pmc=4767685|pmid=26829751}}</ref>PMID:26829751; <ref name=":6">{{Cite journal|last=Ramkissoon|first=Lori A.|last2=Horowitz|first2=Peleg M.|last3=Craig|first3=Justin M.|last4=Ramkissoon|first4=Shakti H.|last5=Rich|first5=Benjamin E.|last6=Schumacher|first6=Steven E.|last7=McKenna|first7=Aaron|last8=Lawrence|first8=Michael S.|last9=Bergthold|first9=Guillaume|date=2013-05-14|title=Genomic analysis of diffuse pediatric low-grade gliomas identifies recurrent oncogenic truncating rearrangements in the transcription factor MYBL1|url=https://pubmed.ncbi.nlm.nih.gov/23633565|journal=Proceedings of the National Academy of Sciences of the United States of America|volume=110|issue=20|pages=8188–8193|doi=10.1073/pnas.1300252110|issn=1091-6490|pmc=3657784|pmid=23633565}}</ref>PMID:23633565; <ref>{{Cite journal|last=Ampie|first=Leonel|last2=Choy|first2=Winward|last3=DiDomenico|first3=Joseph D.|last4=Lamano|first4=Jonathan B.|last5=Williams|first5=Christopher Kazu|last6=Kesavabhotla|first6=Kartik|last7=Mao|first7=Qinwen|last8=Bloch|first8=Orin|date=2016-06|title=Clinical attributes and surgical outcomes of angiocentric gliomas|url=https://pubmed.ncbi.nlm.nih.gov/26778052|journal=Journal of Clinical Neuroscience: Official Journal of the Neurosurgical Society of Australasia|volume=28|pages=117–122|doi=10.1016/j.jocn.2015.11.015|issn=1532-2653|pmid=26778052}}</ref>PMID:26778052 <ref name=":3" />PMID:23583981
|-
|
|Ganglioglioma
|Only 30% are abnormal by karyotype <br>
'''Gain:''' polysomy 7
|'''Mutations:''' [[BRAF]] V600E in 20-60% of cases (can be concurrent with [[CDKN2A]] homozygous deletion)<br>
'''Fusions:''' [[KIAA1549]]-[[BRAF]]
|Generally indolent tumors for which  surgical resection can be curative
|<ref name=":0" />PMID:25461780; <ref name=":3" />PMID:23583981; <ref>{{Cite journal|last=Yin|first=Xiao Lu|last2=Hui|first2=Angela Bik-Yu|last3=Pang|first3=Jesse Chung-Sean|last4=Poon|first4=Wai Sang|last5=Ng|first5=Ho Keung|date=2002-04-01|title=Genome-wide survey for chromosomal imbalances in ganglioglioma using comparative genomic hybridization|url=https://pubmed.ncbi.nlm.nih.gov/11996800|journal=Cancer Genetics and Cytogenetics|volume=134|issue=1|pages=71–76|doi=10.1016/s0165-4608(01)00611-2|issn=0165-4608|pmid=11996800}}</ref>PMID:11996800 <ref>{{Cite journal|last=Dahiya|first=Sonika|last2=Haydon|first2=Devon H.|last3=Alvarado|first3=David|last4=Gurnett|first4=Christina A.|last5=Gutmann|first5=David H.|last6=Leonard|first6=Jeffrey R.|date=2013-06|title=BRAF(V600E) mutation is a negative prognosticator in pediatric ganglioglioma|url=https://pubmed.ncbi.nlm.nih.gov/23609006|journal=Acta Neuropathologica|volume=125|issue=6|pages=901–910|doi=10.1007/s00401-013-1120-y|issn=1432-0533|pmid=23609006}}</ref>PMID:23609006; <ref name=":7">{{Cite journal|last=Pekmezci|first=Melike|last2=Villanueva-Meyer|first2=Javier E.|last3=Goode|first3=Benjamin|last4=Van Ziffle|first4=Jessica|last5=Onodera|first5=Courtney|last6=Grenert|first6=James P.|last7=Bastian|first7=Boris C.|last8=Chamyan|first8=Gabriel|last9=Maher|first9=Ossama M.|date=2018-06-07|title=The genetic landscape of ganglioglioma|url=https://pubmed.ncbi.nlm.nih.gov/29880043|journal=Acta Neuropathologica Communications|volume=6|issue=1|pages=47|doi=10.1186/s40478-018-0551-z|issn=2051-5960|pmc=5992851|pmid=29880043}}</ref>PMID:29880043
|-
|Low grade glioma, WHO grade II
|Diffuse astrocytoma
|No diagnostic aberrations
|'''Rearrangement:''' [[MYBL1]] truncating rearrangements and tandem duplication, [[FGFR1]] rearrangements<br>
'''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
|-
|
|Pleomorphic xanthoastrocytoma (PXA)
|Polysomy 3, polysomy 7 observed<br>
'''Loss:''' monosomy 9 / 9p deletion
|'''Mutations:''' [[BRAF]] V600E in ~60%; [[TP53]] (5%)<br>
'''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
|-
|Anaplastic astrocytoma, WHO grade III
|IDH-mutant or IDH-wild type
|'''Gain:''' 1q, 7/7q, 8q, 10p<br>
'''Loss:''' 6q, 9p, 10q, -11/11p, 12q, 13q, 14q, 17p, 19q, -22/22q
|
|IDH-wild type astrocytomas can be more clinically aggressive than those that are IDH-mutant
|<ref name=":11">{{Cite journal|last=Rickert|first=Christian H.|last2=Sträter|first2=Ronald|last3=Kaatsch|first3=Peter|last4=Wassmann|first4=Hansdetlef|last5=Jürgens|first5=Heribert|last6=Dockhorn-Dworniczak|first6=Barbara|last7=Paulus|first7=Werner|date=2001-4|title=Pediatric High-Grade Astrocytomas Show Chromosomal Imbalances Distinct from Adult Cases|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891902/|journal=The American Journal of Pathology|volume=158|issue=4|pages=1525–1532|doi=10.1016/S0002-9440(10)64103-X|issn=0002-9440|pmc=1891902|pmid=11290570}}</ref>PMCID:1891902; <ref name=":10" />PMID:26004297; <ref name=":0" />PMID:25461780; <ref>{{Cite journal|last=Killela|first=Patrick J.|last2=Pirozzi|first2=Christopher J.|last3=Reitman|first3=Zachary J.|last4=Jones|first4=Sian|last5=Rasheed|first5=B. Ahmed|last6=Lipp|first6=Eric|last7=Friedman|first7=Henry|last8=Friedman|first8=Allan H.|last9=He|first9=Yiping|date=2014-03-30|title=The genetic landscape of anaplastic astrocytoma|url=https://pubmed.ncbi.nlm.nih.gov/24140581|journal=Oncotarget|volume=5|issue=6|pages=1452–1457|doi=10.18632/oncotarget.1505|issn=1949-2553|pmc=4039223|pmid=24140581}}</ref>PMID:24140581; <ref name=":12">{{Cite journal|last=Koschmann|first=Carl|last2=Zamler|first2=Daniel|last3=MacKay|first3=Alan|last4=Robinson|first4=Dan|last5=Wu|first5=Yi-Mi|last6=Doherty|first6=Robert|last7=Marini|first7=Bernard|last8=Tran|first8=Dustin|last9=Garton|first9=Hugh|date=2016-08-25|title=Characterizing and targeting PDGFRA alterations in pediatric high-grade glioma|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5323185/|journal=Oncotarget|volume=7|issue=40|pages=65696–65706|doi=10.18632/oncotarget.11602|issn=1949-2553|pmc=5323185|pmid=27582545}}</ref>PMCID:5323185; <ref>{{Cite journal|last=Grimm|first=Sean A.|last2=Chamberlain|first2=Marc C.|date=2016-07|title=Anaplastic astrocytoma|url=https://pubmed.ncbi.nlm.nih.gov/27230974|journal=CNS oncology|volume=5|issue=3|pages=145–157|doi=10.2217/cns-2016-0002|issn=2045-0915|pmc=6042632|pmid=27230974}}</ref>PMID:27230974 <ref>{{Cite journal|last=Hattori|first=Natsuki|last2=Hirose|first2=Yuichi|last3=Sasaki|first3=Hikaru|last4=Nakae|first4=Shunsuke|last5=Hayashi|first5=Saeko|last6=Ohba|first6=Shigeo|last7=Adachi|first7=Kazuhide|last8=Hayashi|first8=Takuro|last9=Nishiyama|first9=Yuya|date=2016-08|title=World Health Organization grade II-III astrocytomas consist of genetically distinct tumor lineages|url=https://pubmed.ncbi.nlm.nih.gov/27196377|journal=Cancer Science|volume=107|issue=8|pages=1159–1164|doi=10.1111/cas.12969|issn=1349-7006|pmc=4982592|pmid=27196377}}</ref>PMID:27196377; <ref name=":8" />PMID:26061751; <ref>{{Cite journal|last=Reuss|first=David E.|last2=Mamatjan|first2=Yasin|last3=Schrimpf|first3=Daniel|last4=Capper|first4=David|last5=Hovestadt|first5=Volker|last6=Kratz|first6=Annekathrin|last7=Sahm|first7=Felix|last8=Koelsche|first8=Christian|last9=Korshunov|first9=Andrey|date=2015-06|title=IDH mutant diffuse and anaplastic astrocytomas have similar age at presentation and little difference in survival: a grading problem for WHO|url=https://pubmed.ncbi.nlm.nih.gov/25962792|journal=Acta Neuropathologica|volume=129|issue=6|pages=867–873|doi=10.1007/s00401-015-1438-8|issn=1432-0533|pmc=4500039|pmid=25962792}}</ref>PMID:25962792; <ref name=":13">{{Cite journal|last=Shirahata|first=Mitsuaki|last2=Ono|first2=Takahiro|last3=Stichel|first3=Damian|last4=Schrimpf|first4=Daniel|last5=Reuss|first5=David E.|last6=Sahm|first6=Felix|last7=Koelsche|first7=Christian|last8=Wefers|first8=Annika|last9=Reinhardt|first9=Annekathrin|date=2018-07|title=Novel, improved grading system(s) for IDH-mutant astrocytic gliomas|url=https://pubmed.ncbi.nlm.nih.gov/29687258|journal=Acta Neuropathologica|volume=136|issue=1|pages=153–166|doi=10.1007/s00401-018-1849-4|issn=1432-0533|pmid=29687258}}</ref>PMID:29687258
|-
|Other
|Anaplastic PXA, WHO grade III / Ganglioglioma, WHO Grade III
|'''Loss:''' monosomy 9 / 9p deletion, but no diagnostic findings
|'''Mutation:'''  [[BRAF]] V600E less common here than in PXA, grade II<br>
'''Loss:''' [[CDKN2A]]/[[CDKN2B]]
|CDKN2A/CDKN2B loss may correlate with anaplastic histology
|WHO CNS Tumors (2016)<br>
<ref>{{Cite journal|last=Ida|first=Cristiane M.|last2=Rodriguez|first2=Fausto J.|last3=Burger|first3=Peter C.|last4=Caron|first4=Alissa A.|last5=Jenkins|first5=Sarah M.|last6=Spears|first6=Grant M.|last7=Aranguren|first7=Dawn L.|last8=Lachance|first8=Daniel H.|last9=Giannini|first9=Caterina|date=2015-09|title=Pleomorphic Xanthoastrocytoma: Natural History and Long-Term Follow-Up|url=https://pubmed.ncbi.nlm.nih.gov/25318587|journal=Brain Pathology (Zurich, Switzerland)|volume=25|issue=5|pages=575–586|doi=10.1111/bpa.12217|issn=1750-3639|pmc=4400218|pmid=25318587}}</ref>PMID:25318587; <ref>{{Cite journal|last=Schmidt|first=Yao|last2=Kleinschmidt-DeMasters|first2=B. K.|last3=Aisner|first3=Dara L.|last4=Lillehei|first4=Kevin O.|last5=Damek|first5=Denise|date=2013-01|title=Anaplastic PXA in adults: case series with clinicopathologic and molecular features|url=https://pubmed.ncbi.nlm.nih.gov/23096133|journal=Journal of Neuro-Oncology|volume=111|issue=1|pages=59–69|doi=10.1007/s11060-012-0991-4|issn=1573-7373|pmc=4617340|pmid=23096133}}</ref>PMID:23096133; <ref name=":4" />PMID:21274720
|-
|Glioblastoma, WHO grade IV
|IDH-mutant
|'''Gain:''' 1q, 2q, 3q, 7, 16p, 17q, 21q<br>
'''Loss:''' 6q, 8q, 9p, 9q, 10q, 13q, 17p, 22q<br>
''' Chromothripsis:''' observed
|'''Loss:''' [[PTEN]], [[RB1]], [[TP53]], [[CDKN2A]]/[[CDKN2B]]/[[CDKN2C]] 
'''Fusions:''' FGFR-[[TACC]]; NTRK fusions <br>
'''Amplification:''' [[PDGFRA]], [[MYCN]], [[MET]], [[CDK4]], [[CDK6]] ([[EGFR]], [[MDM2]] amp rare)<br>
'''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
|-
|Diffuse midline glioma, H3 K27M mutant
|
|'''Gain:''' 1q, 2, 7, 8<br>
'''Loss:''' 10q<br>
'''Chromothripsis:''' 2p
|'''Three molecular subgroups:''' <br>
'''MYCN subgroup:''' no mutations but chromothripsis leading to amp of [[MYCN]] and [[ID2]]<br>
'''Silent subgroup:''' no recurrent copy # changes, few mutations<br>
'''H3-K27M subgroup:''' [[MYC]], [[PDGFRA]] gains/amp; [[RB1]], [[TP53]] deletions<br>
'''Mutation:''' [[ACVR1]], [[H3F3A]], [[HIST1H3B]], [[TP53]] '''Loss:''' [[CDKN2A]], [[PTEN]], [[RB1]], [[TP53]]<br>
'''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
|-
|'''EPENDYMOMA'''<br>
(in order of increasing WHO grade)
|
|'''DNA-based methylation classifies''' tumors across anatomical sites (posterior fossa, supratentorial, spinal), grades and age groups
|'''Fusion:''' [[YAP1]] fusions (supratentorial tumors)<br>
'''Mutation:''' [[NF2]] (spinal tumors)<br>
'''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)<br>
<ref name=":16">{{Cite journal|last=Pajtler|first=Kristian W.|last2=Witt|first2=Hendrik|last3=Sill|first3=Martin|last4=Jones|first4=David T. W.|last5=Hovestadt|first5=Volker|last6=Kratochwil|first6=Fabian|last7=Wani|first7=Khalida|last8=Tatevossian|first8=Ruth|last9=Punchihewa|first9=Chandanamali|date=2015-05-11|title=Molecular Classification of Ependymal Tumors across All CNS Compartments, Histopathological Grades, and Age Groups|url=https://pubmed.ncbi.nlm.nih.gov/25965575|journal=Cancer Cell|volume=27|issue=5|pages=728–743|doi=10.1016/j.ccell.2015.04.002|issn=1878-3686|pmc=4712639|pmid=25965575}}</ref>PMID:25965575; <ref name=":17">{{Cite journal|last=Ellison|first=David W.|last2=Kocak|first2=Mehmet|last3=Figarella-Branger|first3=Dominique|last4=Felice|first4=Giangaspero|last5=Catherine|first5=Godfraind|last6=Pietsch|first6=Torsten|last7=Frappaz|first7=Didier|last8=Massimino|first8=Maura|last9=Grill|first9=Jacques|date=2011-05-31|title=Histopathological grading of pediatric ependymoma: reproducibility and clinical relevance in European trial cohorts|url=https://pubmed.ncbi.nlm.nih.gov/21627842|journal=Journal of Negative Results in Biomedicine|volume=10|pages=7|doi=10.1186/1477-5751-10-7|issn=1477-5751|pmc=3117833|pmid=21627842}}</ref>PMID:21627842; <ref name=":18">{{Cite journal|last=Olsen|first=Thale Kristin|last2=Gorunova|first2=Ludmila|last3=Meling|first3=Torstein R.|last4=Micci|first4=Francesca|last5=Scheie|first5=David|last6=Due-Tønnessen|first6=Bernt|last7=Heim|first7=Sverre|last8=Brandal|first8=Petter|date=2014-08|title=Genomic characterization of ependymomas reveals 6q loss as the most common aberration|url=https://pubmed.ncbi.nlm.nih.gov/24939246|journal=Oncology Reports|volume=32|issue=2|pages=483–490|doi=10.3892/or.2014.3271|issn=1791-2431|pmc=4091878|pmid=24939246}}</ref>PMID:24939246; <ref name=":19">{{Cite journal|last=Yang|first=Isaac|last2=Nagasawa|first2=Daniel T.|last3=Kim|first3=Won|last4=Spasic|first4=Marko|last5=Trang|first5=Andy|last6=Lu|first6=Daniel C.|last7=Martin|first7=Neil A.|date=2012-06|title=Chromosomal anomalies and prognostic markers for intracranial and spinal ependymomas|url=https://pubmed.ncbi.nlm.nih.gov/22516549|journal=Journal of Clinical Neuroscience: Official Journal of the Neurosurgical Society of Australasia|volume=19|issue=6|pages=779–785|doi=10.1016/j.jocn.2011.11.004|issn=1532-2653|pmc=3615711|pmid=22516549}}</ref>PMID:22516549 
|-
|
|Classic ependymoma (no WHO grade assigned)
|'''Gain:''' 1q, 5, 7, 9, 11, 18, 20<br>
'''Loss:''' 1p, 3, -6/6q, 9p, 13q, 17, 22
|Usually intracranial, spinal tumors (myxopapillary) are rare; 80% of pediatric tumors develop in posterior fossa (PF); Supratentorial tumors preferentially show monosomy 9; 1q gain is unfavorable prognostic indicator in PF tumors; spinal tumors associated with NF2 (germline); children have worse outcomes than adults
|<ref name=":16" />PMID:25965575; <ref name=":21">{{Cite journal|last=Kilday|first=John-Paul|last2=Mitra|first2=Biswaroop|last3=Domerg|first3=Caroline|last4=Ward|first4=Jennifer|last5=Andreiuolo|first5=Felipe|last6=Osteso-Ibanez|first6=Teresa|last7=Mauguen|first7=Audrey|last8=Varlet|first8=Pascale|last9=Le Deley|first9=Marie-Cecile|date=2012-04-01|title=Copy number gain of 1q25 predicts poor progression-free survival for pediatric intracranial ependymomas and enables patient risk stratification: a prospective European clinical trial cohort analysis on behalf of the Children's Cancer Leukaemia Group (CCLG), Societe Francaise d'Oncologie Pediatrique (SFOP), and International Society for Pediatric Oncology (SIOP)|url=https://pubmed.ncbi.nlm.nih.gov/22338015|journal=Clinical Cancer Research: An Official Journal of the American Association for Cancer Research|volume=18|issue=7|pages=2001–2011|doi=10.1158/1078-0432.CCR-11-2489|issn=1557-3265|pmid=22338015}}</ref>PMID:22338015; <ref name=":22">{{Cite journal|last=Gojo|first=Johannes|last2=Lötsch|first2=Daniela|last3=Spiegl-Kreinecker|first3=Sabine|last4=Pajtler|first4=Kristian W.|last5=Neumayer|first5=Katharina|last6=Korbel|first6=Pia|last7=Araki|first7=Asuka|last8=Brandstetter|first8=Anita|last9=Mohr|first9=Thomas|date=2017-09-01|title=Telomerase activation in posterior fossa group A ependymomas is associated with dismal prognosis and chromosome 1q gain|url=https://pubmed.ncbi.nlm.nih.gov/28371821|journal=Neuro-Oncology|volume=19|issue=9|pages=1183–1194|doi=10.1093/neuonc/nox027|issn=1523-5866|pmc=5570194|pmid=28371821}}</ref>PMID:28371821
|-
|
|Subependymoma, WHO grade I
|Typically '''balanced genomes'''<br>
'''Loss:''' -6/6q in spinal tumors
|No diagnostic mutations
|Favorable prognosis
|WHO CNS Tumors (2016) <br>
<ref name=":20">{{Cite journal|last=Yao|first=Yuan|last2=Mack|first2=Stephen C.|last3=Taylor|first3=Michael D.|date=2011-10|title=Molecular genetics of ependymoma|url=https://pubmed.ncbi.nlm.nih.gov/21959044|journal=Chinese Journal of Cancer|volume=30|issue=10|pages=669–681|doi=10.5732/cjc.011.10129|issn=1000-467X|pmc=4012267|pmid=21959044}}</ref>PMID:21959044; <ref name=":23">{{Cite journal|last=Witt|first=Hendrik|last2=Mack|first2=Stephen C.|last3=Ryzhova|first3=Marina|last4=Bender|first4=Sebastian|last5=Sill|first5=Martin|last6=Isserlin|first6=Ruth|last7=Benner|first7=Axel|last8=Hielscher|first8=Thomas|last9=Milde|first9=Till|date=2011-08-16|title=Delineation of two clinically and molecularly distinct subgroups of posterior fossa ependymoma|url=https://pubmed.ncbi.nlm.nih.gov/21840481|journal=Cancer Cell|volume=20|issue=2|pages=143–157|doi=10.1016/j.ccr.2011.07.007|issn=1878-3686|pmc=4154494|pmid=21840481}}</ref>PMID:21840481<br>
|-
|
|Myxopapillary ependymoma, WHO grade I
|'''Aneuploidy:''' multiple chromosomes lost and gained
|'''Mutation:''' [[NF2]] (including germline) in spinal tumors
|Less common but more aggressive in children
|<ref name=":16" />PMID:25965575; <ref name=":24">{{Cite journal|last=Zadnik|first=Patricia L.|last2=Gokaslan|first2=Ziya L.|last3=Burger|first3=Peter C.|last4=Bettegowda|first4=Chetan|date=2013-5|title=Spinal cord tumours: advances in genetics and their implications for treatment|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3991130/|journal=Nature reviews. Neurology|volume=9|issue=5|pages=257–266|doi=10.1038/nrneurol.2013.48|issn=1759-4758|pmc=3991130|pmid=23528542}}</ref>PMCID:3991130; <ref name=":25">{{Cite journal|last=Dubuc|first=Adrian M.|last2=Northcott|first2=Paul A.|last3=Mack|first3=Stephen|last4=Witt|first4=Hendrik|last5=Pfister|first5=Stefan|last6=Taylor|first6=Michael D.|date=2010-05|title=The genetics of pediatric brain tumors|url=https://pubmed.ncbi.nlm.nih.gov/20425037|journal=Current Neurology and Neuroscience Reports|volume=10|issue=3|pages=215–223|doi=10.1007/s11910-010-0103-9|issn=1534-6293|pmid=20425037}}</ref>PMID:20425037; <ref name=":26">{{Cite journal|last=Mack|first=Stephen C.|last2=Agnihotri|first2=Sameer|last3=Bertrand|first3=Kelsey C.|last4=Wang|first4=Xin|last5=Shih|first5=David J.|last6=Witt|first6=Hendrik|last7=Hill|first7=Nadia|last8=Zayne|first8=Kory|last9=Barszczyk|first9=Mark|date=2015-08-15|title=Spinal Myxopapillary Ependymomas Demonstrate a Warburg Phenotype|url=https://pubmed.ncbi.nlm.nih.gov/25957288|journal=Clinical Cancer Research: An Official Journal of the American Association for Cancer Research|volume=21|issue=16|pages=3750–3758|doi=10.1158/1078-0432.CCR-14-2650|issn=1557-3265|pmc=4537825|pmid=25957288}}</ref>PMID:25957288; <ref name=":19" />PMID:22516549
|-
|
|Ependymoma, RELA fusion-positive, WHO grade II or III
|'''Gain:''' 1q<br>
'''Aneuploidy:''' multiple chromosomes lost and gained<br>
'''Chromothripsis:''' chromosome 11 (70% of supratentorial tumors)
|'''Fusion:''' [[C11ORF95]]-[[RELA]] (supratentorial tumors)<br>
'''Loss:''' [[CDKN2A]]/[[CDKN2B]] (may help distinguish from other supratentorial ependymomas) 
|Unfavorable prognosis; occur in infants or children
|<ref name=":16" />PMID:25965575; <ref name=":27">{{Cite journal|last=Parker|first=Matthew|last2=Mohankumar|first2=Kumarasamypet M.|last3=Punchihewa|first3=Chandanamali|last4=Weinlich|first4=Ricardo|last5=Dalton|first5=James D.|last6=Li|first6=Yongjin|last7=Lee|first7=Ryan|last8=Tatevossian|first8=Ruth G.|last9=Phoenix|first9=Timothy N.|date=2014-02-27|title=C11orf95-RELA fusions drive oncogenic NF-κB signalling in ependymoma|url=https://pubmed.ncbi.nlm.nih.gov/24553141|journal=Nature|volume=506|issue=7489|pages=451–455|doi=10.1038/nature13109|issn=1476-4687|pmc=4050669|pmid=24553141}}</ref>PMID:24553141; <ref name=":22" />PMID:28371821
|-
|
|Anaplastic ependymoma (no WHO grade assigned)
|Epigenetic studies suggest range of abnormalities: balanced or unbalanced genomes
|'''Mutation:''' [[NF2]] (including germline) in spinal tumors<br>
'''Fusion:''' [[RELA]] fusions, [[YAP1]] fusions can correspond to anaplastic histology
|Mostly intracranial tumors, rarely in spinal cord; YAP1 fusion tumors can occur in infants
|<ref name=":16" />PMID: 25965575
|-
|'''EMBRYONAL TUMORS'''
|
|
|
|
|WHO CNS Tumors (2016)
|-
|Medulloblastoma
|WNT-activated
|'''Loss:''' monosomy 6/6q- as sole finding in 85%
|'''Mutation:''' [[CTNNB1]], [[DDX3X]], [[TP53]], [[SMARCA4]], [[KMT2D]], [[APC]] (germline mutations in Turcot syndrome)
|Common in children > 3 years of age; typically show classic histology, rarely metastasize; overall favorable prognosis
|<ref name=":28">{{Cite journal|last=Northcott|first=Paul A.|last2=Shih|first2=David J. H.|last3=Peacock|first3=John|last4=Garzia|first4=Livia|last5=Morrissy|first5=A. Sorana|last6=Zichner|first6=Thomas|last7=Stütz|first7=Adrian M.|last8=Korshunov|first8=Andrey|last9=Reimand|first9=Jüri|date=2012-08-02|title=Subgroup-specific structural variation across 1,000 medulloblastoma genomes|url=https://pubmed.ncbi.nlm.nih.gov/22832581|journal=Nature|volume=488|issue=7409|pages=49–56|doi=10.1038/nature11327|issn=1476-4687|pmc=3683624|pmid=22832581}}</ref>PMID:22832581, <ref name=":29">{{Cite journal|last=Shih|first=David J. 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H.|last8=Hovestadt|first8=Volker|last9=Zapatka|first9=Marc|date=2014-07-24|title=Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma|url=https://pubmed.ncbi.nlm.nih.gov/25043047|journal=Nature|volume=511|issue=7510|pages=428–434|doi=10.1038/nature13379|issn=1476-4687|pmc=4201514|pmid=25043047}}</ref>PMID:25043047 <ref name=":33">{{Cite journal|last=Pugh|first=Trevor J.|last2=Weeraratne|first2=Shyamal Dilhan|last3=Archer|first3=Tenley C.|last4=Pomeranz Krummel|first4=Daniel A.|last5=Auclair|first5=Daniel|last6=Bochicchio|first6=James|last7=Carneiro|first7=Mauricio O.|last8=Carter|first8=Scott L.|last9=Cibulskis|first9=Kristian|date=2012-08-02|title=Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations|url=https://pubmed.ncbi.nlm.nih.gov/22820256|journal=Nature|volume=488|issue=7409|pages=106–110|doi=10.1038/nature11329|issn=1476-4687|pmc=3413789|pmid=22820256}}</ref>PMID:22820256; <ref name=":34">{{Cite journal|last=Thompson|first=Eric M.|last2=Hielscher|first2=Thomas|last3=Bouffet|first3=Eric|last4=Remke|first4=Marc|last5=Luu|first5=Betty|last6=Gururangan|first6=Sridharan|last7=McLendon|first7=Roger E.|last8=Bigner|first8=Darell D.|last9=Lipp|first9=Eric S.|date=2016-04|title=Prognostic value of medulloblastoma extent of resection after accounting for molecular subgroup: a retrospective integrated clinical and molecular analysis|url=https://pubmed.ncbi.nlm.nih.gov/26976201|journal=The Lancet. Oncology|volume=17|issue=4|pages=484–495|doi=10.1016/S1470-2045(15)00581-1|issn=1474-5488|pmc=4907853|pmid=26976201}}</ref>PMID:26976201; <ref>{{Cite journal|last=Northcott|first=Paul A.|last2=Korshunov|first2=Andrey|last3=Witt|first3=Hendrik|last4=Hielscher|first4=Thomas|last5=Eberhart|first5=Charles G.|last6=Mack|first6=Stephen|last7=Bouffet|first7=Eric|last8=Clifford|first8=Steven C.|last9=Hawkins|first9=Cynthia E.|date=2011-04-10|title=Medulloblastoma comprises four distinct molecular variants|url=https://pubmed.ncbi.nlm.nih.gov/20823417|journal=Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology|volume=29|issue=11|pages=1408–1414|doi=10.1200/JCO.2009.27.4324|issn=1527-7755|pmc=4874239|pmid=20823417}}</ref>PMID:20823417 <ref name=":35">{{Cite journal|last=Rausch|first=Tobias|last2=Jones|first2=David T. W.|last3=Zapatka|first3=Marc|last4=Stütz|first4=Adrian M.|last5=Zichner|first5=Thomas|last6=Weischenfeldt|first6=Joachim|last7=Jäger|first7=Natalie|last8=Remke|first8=Marc|last9=Shih|first9=David|date=2012-01-20|title=Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations|url=https://pubmed.ncbi.nlm.nih.gov/22265402|journal=Cell|volume=148|issue=1-2|pages=59–71|doi=10.1016/j.cell.2011.12.013|issn=1097-4172|pmc=3332216|pmid=22265402}}</ref>PMID:22265402; <ref name=":36">{{Cite journal|last=Northcott|first=Paul A|last2=Jones|first2=David TW|last3=Kool|first3=Marcel|last4=Robinson|first4=Giles W|last5=Gilbertson|first5=Richard J|last6=Cho|first6=Yoon-Jae|last7=Pomeroy|first7=Scott L|last8=Korshunov|first8=Andrey|last9=Lichter|first9=Peter|date=2012-12|title=Medulloblastomics: The End of the Beginning|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3889646/|journal=Nature reviews. Cancer|volume=12|issue=12|pages=818–834|doi=10.1038/nrc3410|issn=1474-175X|pmc=3889646|pmid=23175120}}</ref>PMCID:3889646; <ref name=":37">{{Cite journal|last=Thompson|first=Margaret C.|last2=Fuller|first2=Christine|last3=Hogg|first3=Twala L.|last4=Dalton|first4=James|last5=Finkelstein|first5=David|last6=Lau|first6=Ching C.|last7=Chintagumpala|first7=Murali|last8=Adesina|first8=Adekunle|last9=Ashley|first9=David M.|date=2006-04-20|title=Genomics identifies medulloblastoma subgroups that are enriched for specific genetic alterations|url=https://pubmed.ncbi.nlm.nih.gov/16567768|journal=Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology|volume=24|issue=12|pages=1924–1931|doi=10.1200/JCO.2005.04.4974|issn=1527-7755|pmid=16567768}}</ref>PMID:16567768 <ref name=":38">{{Cite journal|last=Rutkowski|first=Stefan|last2=von Hoff|first2=Katja|last3=Emser|first3=Angela|last4=Zwiener|first4=Isabella|last5=Pietsch|first5=Torsten|last6=Figarella-Branger|first6=Dominique|last7=Giangaspero|first7=Felice|last8=Ellison|first8=David W.|last9=Garre|first9=Maria-Luisa|date=2010-11-20|title=Survival and prognostic factors of early childhood medulloblastoma: an international meta-analysis|url=https://pubmed.ncbi.nlm.nih.gov/20940197|journal=Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology|volume=28|issue=33|pages=4961–4968|doi=10.1200/JCO.2010.30.2299|issn=1527-7755|pmid=20940197}}</ref>PMID:20940197
|-
|
|SHH-activated
|'''Gain:''' 3q<br>
'''Loss:''' 9q, 10q, 17p<br>
'''Ploidy changes:''' Tetraploidy associated with chromothripsis and TP53 mutations<br>
'''Chromothripsis:''' associated with TP53 mutation   
|'''Mutation:'''<br>
'''TP53 wild-type tumors:''' [[PTCH1]] (germline mutations in Gorlin syndrome), [[SMO]], [[SUFU]] (can be germline), [[TERT]] promoter<br>
'''[[TP53]]-mutant tumors:''' can be germline<br>
'''Loss:''' [[PTCH1]], [[PTEN]]<br>
'''Amplification:''' [[GLI2]] ([[TP53]]-mutant tumors), [[IGF1R]], [[PPM1D]], [[MYCN]] ([[TP53]]-mutant tumors), [[YAP1]], MIR17/92, [[MDM4]]
|Common in infants, rare in children, most common type of medulloblastoma in adults; Desmoplastic (or nodular) histology common; TP53 wild-type usually correlate with extensive nodularity or desmoplastic histology; TP53-mutant tumors correlate with metastatic disease
|<ref>{{Cite journal|last=Kool|first=Marcel|last2=Jones|first2=David T. W.|last3=Jäger|first3=Natalie|last4=Northcott|first4=Paul A.|last5=Pugh|first5=Trevor J.|last6=Hovestadt|first6=Volker|last7=Piro|first7=Rosario M.|last8=Esparza|first8=L. Adriana|last9=Markant|first9=Shirley L.|date=2014-03-17|title=Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition|url=https://pubmed.ncbi.nlm.nih.gov/24651015|journal=Cancer Cell|volume=25|issue=3|pages=393–405|doi=10.1016/j.ccr.2014.02.004|issn=1878-3686|pmc=4493053|pmid=24651015}}</ref>PMID:24651015; <ref>{{Cite journal|last=Northcott|first=Paul A.|last2=Hielscher|first2=Thomas|last3=Dubuc|first3=Adrian|last4=Mack|first4=Stephen|last5=Shih|first5=David|last6=Remke|first6=Marc|last7=Al-Halabi|first7=Hani|last8=Albrecht|first8=Steffen|last9=Jabado|first9=Nada|date=2011-08|title=Pediatric and adult sonic hedgehog medulloblastomas are clinically and molecularly distinct|url=https://pubmed.ncbi.nlm.nih.gov/21681522|journal=Acta Neuropathologica|volume=122|issue=2|pages=231–240|doi=10.1007/s00401-011-0846-7|issn=1432-0533|pmc=4538327|pmid=21681522}}</ref>PMID:21681522; <ref name=":28" />PMID:22832581 <ref name=":29" />PMID:24493713; <ref>{{Cite journal|last=Gajjar|first=Amar|last2=Stewart|first2=Clinton F.|last3=Ellison|first3=David W.|last4=Kaste|first4=Sue|last5=Kun|first5=Larry E.|last6=Packer|first6=Roger J.|last7=Goldman|first7=Stewart|last8=Chintagumpala|first8=Murali|last9=Wallace|first9=Dana|date=2013-11-15|title=Phase I study of vismodegib in children with recurrent or refractory medulloblastoma: a pediatric brain tumor consortium study|url=https://pubmed.ncbi.nlm.nih.gov/24077351|journal=Clinical Cancer Research: An Official Journal of the American Association for Cancer Research|volume=19|issue=22|pages=6305–6312|doi=10.1158/1078-0432.CCR-13-1425|issn=1557-3265|pmc=3856244|pmid=24077351}}</ref>PMID:24077351; <ref name=":30" />PMID:22134537; <ref name=":31" />PMID:22358457 <ref name=":32" />PMID:25043047; <ref name=":33" />PMID:22820256; <ref name=":34" />PMID:26976201 <ref name=":34" />PMID:20823417; <ref name=":35" />PMID:22265402; <ref name=":36" />PMCID:3889646 <ref name=":37" />PMID:16567768; <ref name=":38" />PMID:20940197
|-
|
|Group3
|'''Gain:''' 1q, 7, 18q<br>
'''Loss:''' 5q, 8, 10q, 11p, 16q<br>
'''Rearrangement:''' idic(17)(p11.2)<br>
'''Ploidy changes:''' tetraploidy in 40-50% of Group3/Group4 tumors
|'''Mutation/Amplification:''' [[MYC]] (mainly in infants), [[OTX2]], [[CDK6]], [[SMARC4A]], [[CTDNEP1]], [[LRP1B]], [[KMT2D]]<br>
'''Fusions:''' [[PVT1]]-[[MYC]], [[PVT1]]-[[NDRG1]]; [[GFI1]]/[[GFI1B]] structural variants
|Usually classic histology, ~ 50% are metastatic at time of diagnosis, Not generally observed in adults
|<ref name=":28" />PMID:22832581, <ref name=":32" />PMID:25043047; <ref name=":29" />PMID:24493713 <ref name=":30" />PMID:22134537; <ref name=":31" />PMID:22358457; <ref name=":33" />PMID:22820256; <ref name=":34" />PMID:26976201; <ref name=":34" />PMID:20823417 <ref name=":35" />PMID:22265402; <ref name=":36" />PMCID:3889646; <ref name=":37" />PMID:16567768  <ref name=":38" />PMID:20940197
|-
|
|Group4
|'''Gain:''' 7, 18q<br>
'''Loss:''' X, 8, 11p<br>
'''Rearrangement:''' idic(17)(p11.2) in >80%<br>
'''Chromothripsis:''' rare, but associated with TP53 loss when observed 
|'''Mutation:''' [[TP53]], [[KDM6A]], [[KMT2C]] <br>
'''Amplification:''' [[MYCN]], [[CDK4]], [[CDK6]], [[OTX2]]<br>
'''Rearrangement:''' [[SNCAIP]] tandem duplication; [[GFI1]]/[[GFI1B]] structural variants
|Rarely seen in infants; usually classic histology
|<ref name=":28" />PMID:22832581; <ref name=":32" />PMID:25043047; <ref name=":29" />PMID:24493713; <ref name=":30" />PMID:22134537; <ref name=":31" />PMID:22358457; <ref name=":33" />PMID:22820256; <ref name=":34" />PMID:26976201; <ref name=":34" />PMID:20823417 <ref name=":35" />PMID:22265402; <ref name=":36" />PMCID:3889646; <ref name=":37" />PMID:16567768  <ref name=":38" />PMID:20940197
|-
|Atypical teratoid/rhabdoid tumor (AT/RT)
|
|'''Loss:''' 22/22q, though a subset of AT/RT-like tumors retain 22q
|Classic AT/RT: [[SMARCB1]] mutation/deletion/exonic duplication in 98% of tumors<br>
AT/RT-like tumors: [[SMARCB1]] can be retained (with [[SMARCA4]] mutations)<br>
'''Three molecular classes:'''<br>
'''TYR:''' ~ 75% show broad 22q loss that includes [[SMARCB1]]<br>
'''SHH:''' ~ 50% lack any [[SMARCB1]] mutation; ~ 25% have focal [[SMARCB1]] aberrations<br>
'''MYC:''' ~ 75% show focal [[SMARCB1]] loss
|Most cases occur before 3 yrs of age<br>
TYR subclass: mostly infratentorial<br>
SHH subclass: supra/infratentorial<br>
MYC subclass: mostly supratentorial
|
|-
|Embryonal tumor with multilayered rosettes, C19MC-altered
|
|'''ETMR (incl. ETANTR):''' occasionally polysomy 2
|'''ETANTR:''' miRNA cluster C19MC amplification
|Occurs mainly in children < 4 yrs old
|WHO CNS Tumors (2016)<br>
<ref>{{Cite journal|last=Spence|first=Tara|last2=Sin-Chan|first2=Patrick|last3=Picard|first3=Daniel|last4=Barszczyk|first4=Mark|last5=Hoss|first5=Katharina|last6=Lu|first6=Mei|last7=Kim|first7=Seung-Ki|last8=Ra|first8=Young-Shin|last9=Nakamura|first9=Hideo|date=2014-08|title=CNS-PNETs with C19MC amplification and/or LIN28 expression comprise a distinct histogenetic diagnostic and therapeutic entity|url=https://pubmed.ncbi.nlm.nih.gov/24839957|journal=Acta Neuropathologica|volume=128|issue=2|pages=291–303|doi=10.1007/s00401-014-1291-1|issn=1432-0533|pmc=4159569|pmid=24839957}}</ref>PMID:24839957; <ref>{{Cite journal|last=Gessi|first=Marco|last2=von Bueren|first2=André O.|last3=Treszl|first3=Andras|last4=zur Mühlen|first4=Anja|last5=Hartmann|first5=Wolfgang|last6=Warmuth-Metz|first6=Monika|last7=Rutkowski|first7=Stefan|last8=Pietsch|first8=Torsten|date=2014-07|title=MYCN amplification predicts poor outcome for patients with supratentorial primitive neuroectodermal tumors of the central nervous system|url=https://pubmed.ncbi.nlm.nih.gov/24470553|journal=Neuro-Oncology|volume=16|issue=7|pages=924–932|doi=10.1093/neuonc/not302|issn=1523-5866|pmc=4057132|pmid=24470553}}</ref>PMID:24470553 <ref>{{Cite journal|last=Korshunov|first=Andrey|last2=Sturm|first2=Dominik|last3=Ryzhova|first3=Marina|last4=Hovestadt|first4=Volker|last5=Gessi|first5=Marco|last6=Jones|first6=David T. W.|last7=Remke|first7=Marc|last8=Northcott|first8=Paul|last9=Perry|first9=Arie|date=2014-08|title=Embryonal tumor with abundant neuropil and true rosettes (ETANTR), ependymoblastoma, and medulloepithelioma share molecular similarity and comprise a single clinicopathological entity|url=https://pubmed.ncbi.nlm.nih.gov/24337497|journal=Acta Neuropathologica|volume=128|issue=2|pages=279–289|doi=10.1007/s00401-013-1228-0|issn=1432-0533|pmc=4102829|pmid=24337497}}</ref>PMID:24337497; <ref>{{Cite journal|last=Nobusawa|first=Sumihito|last2=Yokoo|first2=Hideaki|last3=Hirato|first3=Junko|last4=Kakita|first4=Akiyoshi|last5=Takahashi|first5=Hitoshi|last6=Sugino|first6=Takashi|last7=Tasaki|first7=Kazuhiro|last8=Itoh|first8=Hideaki|last9=Hatori|first9=Tsutomu|date=2012-09|title=Analysis of chromosome 19q13.42 amplification in embryonal brain tumors with ependymoblastic multilayered rosettes|url=https://pubmed.ncbi.nlm.nih.gov/22324795|journal=Brain Pathology (Zurich, Switzerland)|volume=22|issue=5|pages=689–697|doi=10.1111/j.1750-3639.2012.00574.x|issn=1750-3639|pmid=22324795}}</ref>PMID:22324795 <ref>{{Cite journal|last=Korshunov|first=Andrey|last2=Remke|first2=Marc|last3=Gessi|first3=Marco|last4=Ryzhova|first4=Marina|last5=Hielscher|first5=Thomas|last6=Witt|first6=Hendrik|last7=Tobias|first7=Vivienne|last8=Buccoliero|first8=Anna Maria|last9=Sardi|first9=Iacopo|date=2010-08|title=Focal genomic amplification at 19q13.42 comprises a powerful diagnostic marker for embryonal tumors with ependymoblastic rosettes|url=https://pubmed.ncbi.nlm.nih.gov/20407781|journal=Acta Neuropathologica|volume=120|issue=2|pages=253–260|doi=10.1007/s00401-010-0688-8|issn=1432-0533|pmid=20407781}}</ref>PMID:20407781, <ref>{{Cite journal|last=Pfister|first=Stefan|last2=Remke|first2=Marc|last3=Castoldi|first3=Mirco|last4=Bai|first4=Alfa H. C.|last5=Muckenthaler|first5=Martina U.|last6=Kulozik|first6=Andreas|last7=von Deimling|first7=Andreas|last8=Pscherer|first8=Armin|last9=Lichter|first9=Peter|date=2009-04|title=Novel genomic amplification targeting the microRNA cluster at 19q13.42 in a pediatric embryonal tumor with abundant neuropil and true rosettes|url=https://pubmed.ncbi.nlm.nih.gov/19057917|journal=Acta Neuropathologica|volume=117|issue=4|pages=457–464|doi=10.1007/s00401-008-0467-y|issn=1432-0533|pmid=19057917}}</ref>PMID:19057917
|- 
|Embryonal tumor, other
|
|'''CNS NB-FOXR2 group:''' 1q gain, 16q loss, polysomy 8<br>
'''CNS EFT-CIC group:''' polysomy 8<br>
'''CNS HGNET-MN1 group:''' 16q loss, polysomy 8<br>
'''CNS HGNET-BCOR group:''' mostly balanced genomes
|'''CNS NB-FOXR2 group:''' [[JMJD1C]] fusions, [[FOXR2]] fusion or deletion<br>
'''CNS EFT-CIC group:''' [[NUTM1]] rearrangement/fusion, [[CIC]] rearrangement<br>
'''CNS HGNET-MN1 group:''' [[MN1]] rearrangement <br>
'''CNS HGNET-BCOR group:''' [[BCOR]] intragenic tandem duplication
|Most common in children, but may also occur in adolescents and adults
|WHO CNS Tumors (2016)<br>
<ref>{{Cite journal|last=Sturm|first=Dominik|last2=Orr|first2=Brent A.|last3=Toprak|first3=Umut H.|last4=Hovestadt|first4=Volker|last5=Jones|first5=David T. W.|last6=Capper|first6=David|last7=Sill|first7=Martin|last8=Buchhalter|first8=Ivo|last9=Northcott|first9=Paul A.|date=2016-02-25|title=New Brain Tumor Entities Emerge from Molecular Classification of CNS-PNETs|url=https://pubmed.ncbi.nlm.nih.gov/26919435|journal=Cell|volume=164|issue=5|pages=1060–1072|doi=10.1016/j.cell.2016.01.015|issn=1097-4172|pmc=5139621|pmid=26919435}}</ref>PMID:26919435; <ref>{{Cite journal|last=Picard|first=Daniel|last2=Miller|first2=Suzanne|last3=Hawkins|first3=Cynthia E.|last4=Bouffet|first4=Eric|last5=Rogers|first5=Hazel A.|last6=Chan|first6=Tiffany S. Y.|last7=Kim|first7=Seung-Ki|last8=Ra|first8=Young-Shin|last9=Fangusaro|first9=Jason|date=2012-08|title=Markers of survival and metastatic potential in childhood CNS primitive neuro-ectodermal brain tumours: an integrative genomic analysis|url=https://pubmed.ncbi.nlm.nih.gov/22691720|journal=The Lancet. Oncology|volume=13|issue=8|pages=838–848|doi=10.1016/S1470-2045(12)70257-7|issn=1474-5488|pmc=3615440|pmid=22691720}}</ref>PMID:22691720; <ref>{{Cite journal|last=von Bueren|first=André O.|last2=Gerss|first2=Joachim|last3=Hagel|first3=Christian|last4=Cai|first4=Haoyang|last5=Remke|first5=Marc|last6=Hasselblatt|first6=Martin|last7=Feuerstein|first7=Burt G.|last8=Pernet|first8=Sarah|last9=Delattre|first9=Olivier|date=2012-09|title=DNA copy number alterations in central primitive neuroectodermal tumors and tumors of the pineal region: an international individual patient data meta-analysis|url=https://pubmed.ncbi.nlm.nih.gov/22772606|journal=Journal of Neuro-Oncology|volume=109|issue=2|pages=415–423|doi=10.1007/s11060-012-0911-7|issn=1573-7373|pmid=22772606}}</ref>PMID:22772606 
|-
|'''CHOROID PLEXUS TUMORS (CPT)'''
|Choroid plexus papilloma(CPP, WHO grade I) and atypical choroid plexus papilloma (WHO grade II)
|'''Hyperdiploidy'''<br>
'''Loss:''' rare, no recurrent losses                                                                     
|No diagnostic mutations/events
|CPP and aCPP likely belong to same molecularly defined entity; CPP is a diagnostic feature of Aircardi syndrome
|WHO CNS Tumors (2016)<br>
<ref>{{Cite journal|last=Safaee|first=Michael|last2=Oh|first2=Michael C.|last3=Bloch|first3=Orin|last4=Sun|first4=Matthew Z.|last5=Kaur|first5=Gurvinder|last6=Auguste|first6=Kurtis I.|last7=Tihan|first7=Tarik|last8=Parsa|first8=Andrew T.|date=2013-03|title=Choroid plexus papillomas: advances in molecular biology and understanding of tumorigenesis|url=https://pubmed.ncbi.nlm.nih.gov/23172371|journal=Neuro-Oncology|volume=15|issue=3|pages=255–267|doi=10.1093/neuonc/nos289|issn=1523-5866|pmc=3578480|pmid=23172371}}</ref>PMID:23172371; <ref name=":39">{{Cite journal|last=Japp|first=Anna Sophia|last2=Gessi|first2=Marco|last3=Messing-Jünger|first3=Martina|last4=Denkhaus|first4=Dorota|last5=Zur Mühlen|first5=Anja|last6=Wolff|first6=Johannes Ernst|last7=Hartung|first7=Stefan|last8=Kordes|first8=Uwe|last9=Klein-Hitpass|first9=Ludger|date=2015-02|title=High-resolution genomic analysis does not qualify atypical plexus papilloma as a separate entity among choroid plexus tumors|url=https://pubmed.ncbi.nlm.nih.gov/25575132|journal=Journal of Neuropathology and Experimental Neurology|volume=74|issue=2|pages=110–120|doi=10.1097/NEN.0000000000000154|issn=1554-6578|pmid=25575132}}</ref>PMID:25575132; <ref name=":40">{{Cite journal|last=Merino|first=Diana M.|last2=Shlien|first2=Adam|last3=Villani|first3=Anita|last4=Pienkowska|first4=Malgorzata|last5=Mack|first5=Stephen|last6=Ramaswamy|first6=Vijay|last7=Shih|first7=David|last8=Tatevossian|first8=Ruth|last9=Novokmet|first9=Ana|date=2015-01-01|title=Molecular characterization of choroid plexus tumors reveals novel clinically relevant subgroups|url=https://pubmed.ncbi.nlm.nih.gov/25336695|journal=Clinical Cancer Research: An Official Journal of the American Association for Cancer Research|volume=21|issue=1|pages=184–192|doi=10.1158/1078-0432.CCR-14-1324|issn=1557-3265|pmid=25336695}}</ref>PMID:25336695 <ref>{{Cite journal|last=Rickert|first=Christian H.|last2=Wiestler|first2=Otmar D.|last3=Paulus|first3=Werner|date=2002-03|title=Chromosomal imbalances in choroid plexus tumors|url=https://pubmed.ncbi.nlm.nih.gov/11891207|journal=The American Journal of Pathology|volume=160|issue=3|pages=1105–1113|doi=10.1016/S0002-9440(10)64931-0|issn=0002-9440|pmc=1867193|pmid=11891207}}</ref>PMID:11891207
|-
|
|Choroid plexus carcinoma (CPC, WHO grade III)
|'''Aneuploidy''' (including both hypo- and hyperdiploidy types of CPC); copy neutral LOH is frequent, particularly involving chromosome 17<br>
'''Gain:''' 1, 7, 12, 20 in > 80% of hyperdiploid CPCs<br>
'''Loss:''' 3 (in all hypodiploid CPC), 6, 11, 12q, 16, 22
|'''Mutation:''' [[TP53]] in > 50%<br>
'''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 derived from Neill et al., 2020 [[https://pubmed.ncbi.nlm.nih.gov/32203924/ PMID: 32203924]] with permission from Cancer Genetics.
{| class="wikitable"
|-
!TUMOR
!SUBTYPES
!BROAD ABERRATIONS (>10Mb)
!FOCAL ABERRATIONS (<10Mb)
!CLINICAL FEATURES
!REFERENCES
|-
|'''GLIOMAS'''
|
|
|
|
|
|-
|Low grade gliomas, WHO grade I-II
|Pilocytic astrocytoma
|'''Gain:''' 5, 7, 6, 11<br>
'''Loss:''' 1, 2, 3, 13, 14, 16, 17, 19
|'''Fusion:''' [[KIAA1549]]-[[BRAF]] fusion (via 3'[[BRAF]] duplication), other [[BRAF]] partners reported; NTRK fusions (rare)<br>
'''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
|-
|
|Pleomorphic xanthoastrocytoma (PXA)
|'''Gain:''' 7, 2, 5, 21, 20, 12, 15<br>
'''Loss:''' monosomy 9 / 9p deletion most common, 22, 14, 13, 10<br>
'''CN-LOH:''' 9p, 22
|'''Loss:''' homozygous loss [[CDKN2A]]/[[CDKN2B]]<br>
Mutation: [[BRAF]] V600E
|Adults and pediatric tumors show similar CNVs; CDKN2A/CDKN2B loss may correlate with anaplastic histology
|<ref name=":41">{{Cite journal|last=Chappé|first=Céline|last2=Padovani|first2=Laetitia|last3=Scavarda|first3=Didier|last4=Forest|first4=Fabien|last5=Nanni-Metellus|first5=Isabelle|last6=Loundou|first6=Anderson|last7=Mercurio|first7=Sandy|last8=Fina|first8=Frédéric|last9=Lena|first9=Gabriel|date=2013-09|title=Dysembryoplastic neuroepithelial tumors share with pleomorphic xanthoastrocytomas and gangliogliomas BRAF(V600E) mutation and expression|url=https://pubmed.ncbi.nlm.nih.gov/23442159|journal=Brain Pathology (Zurich, Switzerland)|volume=23|issue=5|pages=574–583|doi=10.1111/bpa.12048|issn=1750-3639|pmid=23442159}}</ref>PMID:23442159; <ref>{{Cite journal|last=Vaubel|first=Rachael A.|last2=Caron|first2=Alissa A.|last3=Yamada|first3=Seiji|last4=Decker|first4=Paul A.|last5=Eckel Passow|first5=Jeanette E.|last6=Rodriguez|first6=Fausto J.|last7=Nageswara Rao|first7=Amulya A.|last8=Lachance|first8=Daniel|last9=Parney|first9=Ian|date=2018-03|title=Recurrent copy number alterations in low-grade and anaplastic pleomorphic xanthoastrocytoma with and without BRAF V600E mutation|url=https://pubmed.ncbi.nlm.nih.gov/28181325|journal=Brain Pathology (Zurich, Switzerland)|volume=28|issue=2|pages=172–182|doi=10.1111/bpa.12495|issn=1750-3639|pmc=5807227|pmid=28181325}}</ref>PMID:28181325
|-
|
|Ganglioglioma
|'''Gain:''' polysomy 5, polysomy 7, 10p<br>
'''Loss:''' 1p loss, monosomy (with focal CDKN2A loss)
|'''Mutation:''' [[BRAF]] V600E, [[TSC1]], [[TSC2]], [[FGFR1]], [[FGFR2]], [[KRAS]]
|Generally indolent tumors; surgical resection can be curative
|<ref name=":41" />PMID:23442159; <ref>{{Cite journal|last=Prabowo|first=Avanita S.|last2=van Thuijl|first2=Hinke Foka|last3=Scheinin|first3=Ilari|last4=Sie|first4=Daoud|last5=van Essen|first5=Hendrik F.|last6=Iyer|first6=Anand M.|last7=Spliet|first7=Wim G. M.|last8=Ferrier|first8=Cyrille H.|last9=van Rijen|first9=Peter C.|date=2015-10|title=Landscape of chromosomal copy number aberrations in gangliogliomas and dysembryoplastic neuroepithelial tumours|url=https://pubmed.ncbi.nlm.nih.gov/25764012|journal=Neuropathology and Applied Neurobiology|volume=41|issue=6|pages=743–755|doi=10.1111/nan.12235|issn=1365-2990|pmid=25764012}}</ref>PMID:25764012; <ref name=":7" />PMID:29880043
|-
|
|Angiocentric glioma
|'''Loss:''' 6q24-q25
|'''Fusion:''' [[MYB]]-[[QKI]] rearrangement/deletion (classic histology)<br>
'''Rearrangement:''' [[MYB]] alone (atypical histology)<br>
'''Amplification:''' [[MYB]] (atypical histology)
|Generally indolent tumors; surgical resection can be curative
|<ref name=":5" />PMID:26829751
|-
|
|Dysembryoplastic neuroepithelial tumor (DNET)
|No specific changes
|'''Mutation:''' intragenic duplication or mutation [[FGFR1]]; [[BRAF]] V600E
|Rare in adults; Benign with excellent prognosis even with subtotal resection
|<ref>{{Cite journal|last=Rivera|first=Barbara|last2=Gayden|first2=Tenzin|last3=Carrot-Zhang|first3=Jian|last4=Nadaf|first4=Javad|last5=Boshari|first5=Talia|last6=Faury|first6=Damien|last7=Zeinieh|first7=Michele|last8=Blanc|first8=Romeo|last9=Burk|first9=David L.|date=2016-06|title=Germline and somatic FGFR1 abnormalities in dysembryoplastic neuroepithelial tumors|url=https://pubmed.ncbi.nlm.nih.gov/26920151|journal=Acta Neuropathologica|volume=131|issue=6|pages=847–863|doi=10.1007/s00401-016-1549-x|issn=1432-0533|pmc=5039033|pmid=26920151}}</ref>PMID:26920151; <ref name=":41" />PMID:23442159; <ref>{{Cite journal|last=Thom|first=Maria|last2=Toma|first2=Ahmed|last3=An|first3=Shu|last4=Martinian|first4=Lillian|last5=Hadjivassiliou|first5=George|last6=Ratilal|first6=Bernardo|last7=Dean|first7=Andrew|last8=McEvoy|first8=Andrew|last9=Sisodiya|first9=Sanjay M.|date=2011-10|title=One hundred and one dysembryoplastic neuroepithelial tumors: an adult epilepsy series with immunohistochemical, molecular genetic, and clinical correlations and a review of the literature|url=https://pubmed.ncbi.nlm.nih.gov/21937911|journal=Journal of Neuropathology and Experimental Neurology|volume=70|issue=10|pages=859–878|doi=10.1097/NEN.0b013e3182302475|issn=1554-6578|pmid=21937911}}</ref>PMID:21937911
|-
|
|Rosette forming glioneuronal tumor
|'''Gain:'''1q , 7, 9, 16<br>
'''Loss:''' 1p<br>
'''Amplification:''' 9q34.2, 19p13.3
|'''Fusion:''' [[KIAA1549]]-[[BRAF]] fusion (via 3'[[BRAF]] duplication)<br>
'''Mutation:''' [[PIK3CA]], [[FGFR1]]<br>
'''Amplification:''' [[SBNO2]]
|Generally indolent tumors; surgical resection can be curative
|<ref>{{Cite journal|last=Kitamura|first=Yohei|last2=Komori|first2=Takashi|last3=Shibuya|first3=Makoto|last4=Ohara|first4=Kentaro|last5=Saito|first5=Yuko|last6=Hayashi|first6=Saeko|last7=Sasaki|first7=Aya|last8=Nakagawa|first8=Eiji|last9=Tomio|first9=Ryosuke|date=2018-01|title=Comprehensive genetic characterization of rosette-forming glioneuronal tumors: independent component analysis by tissue microdissection|url=https://pubmed.ncbi.nlm.nih.gov/27893178|journal=Brain Pathology (Zurich, Switzerland)|volume=28|issue=1|pages=87–93|doi=10.1111/bpa.12468|issn=1750-3639|pmid=27893178}}</ref>PMID:27893178; <ref>{{Cite journal|last=Bidinotto|first=Lucas Tadeu|last2=Scapulatempo-Neto|first2=Cristovam|last3=Mackay|first3=Alan|last4=de Almeida|first4=Gisele Caravina|last5=Scheithauer|first5=Bernd Walter|last6=Berardinelli|first6=Gustavo Noriz|last7=Torrieri|first7=Raul|last8=Clara|first8=Carlos Afonso|last9=Feltrin|first9=Leonir Terezinha|date=2015|title=Molecular Profiling of a Rare Rosette-Forming Glioneuronal Tumor Arising in the Spinal Cord|url=https://pubmed.ncbi.nlm.nih.gov/26371886|journal=PloS One|volume=10|issue=9|pages=e0137690|doi=10.1371/journal.pone.0137690|issn=1932-6203|pmc=4570813|pmid=26371886}}</ref>PMID:26371886
|-
|Infiltrating Gliomas
|Diffuse astrocytoma/anaplastic Astrocytoma, WHO grade II/III, IDH mutant
|'''Gain:''' 4q, 7q, 8q24, 12q<br>
'''Loss:''' 9p, 19q (without 1p)   
|'''Gain:''' [[MYC]] <br>
'''Loss:''' [[CDKN2A]]/[[CDKN2B]],  [[PML]]15q22
|Better prognosis than IDH wildtype astrocytoma; Progression to grade IV will often involves loss of 10q,  gain of  CDK4, CDK6, and cyclin E2, and an increase in copy number alterations.
|<ref name=":9" />PMID:26824661; <ref name=":42">{{Cite journal|last=Eckel-Passow|first=Jeanette E.|last2=Lachance|first2=Daniel H.|last3=Molinaro|first3=Annette M.|last4=Walsh|first4=Kyle M.|last5=Decker|first5=Paul A.|last6=Sicotte|first6=Hugues|last7=Pekmezci|first7=Melike|last8=Rice|first8=Terri|last9=Kosel|first9=Matt L.|date=2015-06-25|title=Glioma Groups Based on 1p/19q, IDH, and TERT Promoter Mutations in Tumors|url=https://pubmed.ncbi.nlm.nih.gov/26061753|journal=The New England Journal of Medicine|volume=372|issue=26|pages=2499–2508|doi=10.1056/NEJMoa1407279|issn=1533-4406|pmc=4489704|pmid=26061753}}</ref>PMID:26061753; <ref name=":43">{{Cite journal|last=Neill|first=Stewart G.|last2=Fisher|first2=Kevin E.|date=2014-09-XX|title=Section III: molecular diagnostics in neuro-oncology|url=https://pubmed.ncbi.nlm.nih.gov/25263767|journal=Current Problems in Cancer|volume=38|issue=5|pages=175–179|doi=10.1016/j.currproblcancer.2014.08.006|issn=1535-6345|pmid=25263767}}</ref>PMID:25263767 <ref name=":44">{{Cite journal|last=Ellison|first=David W.|date=2015-06-25|title=Multiple Molecular Data Sets and the Classification of Adult Diffuse Gliomas|url=https://pubmed.ncbi.nlm.nih.gov/26061754|journal=The New England Journal of Medicine|volume=372|issue=26|pages=2555–2557|doi=10.1056/NEJMe1506813|issn=1533-4406|pmid=26061754}}</ref>PMID:26061754; <ref name=":45">{{Cite journal|last=Park|first=Sung-Hye|last2=Won|first2=Jaekyung|last3=Kim|first3=Seong-Ik|last4=Lee|first4=Yujin|last5=Park|first5=Chul-Kee|last6=Kim|first6=Seung-Ki|last7=Choi|first7=Seung-Hong|date=2017-05|title=Molecular Testing of Brain Tumor|url=https://pubmed.ncbi.nlm.nih.gov/28535583|journal=Journal of Pathology and Translational Medicine|volume=51|issue=3|pages=205–223|doi=10.4132/jptm.2017.03.08|issn=2383-7837|pmc=5445205|pmid=28535583}}</ref>PMID:28535583; <ref name=":46">{{Cite journal|last=Cohen|first=Adam|last2=Sato|first2=Mariko|last3=Aldape|first3=Kenneth|last4=Mason|first4=Clinton C.|last5=Alfaro-Munoz|first5=Kristin|last6=Heathcock|first6=Lindsey|last7=South|first7=Sarah T.|last8=Abegglen|first8=Lisa M.|last9=Schiffman|first9=Joshua D.|date=2015-06-20|title=DNA copy number analysis of Grade II-III and Grade IV gliomas reveals differences in molecular ontogeny including chromothripsis associated with IDH mutation status|url=https://pubmed.ncbi.nlm.nih.gov/26091668|journal=Acta Neuropathologica Communications|volume=3|pages=34|doi=10.1186/s40478-015-0213-3|issn=2051-5960|pmc=4474351|pmid=26091668}}</ref>PMID:26091668 <ref>{{Cite journal|last=Olar|first=Adriana|last2=Wani|first2=Khalida M.|last3=Alfaro-Munoz|first3=Kristin D.|last4=Heathcock|first4=Lindsey E.|last5=van Thuijl|first5=Hinke F.|last6=Gilbert|first6=Mark R.|last7=Armstrong|first7=Terri S.|last8=Sulman|first8=Erik P.|last9=Cahill|first9=Daniel P.|date=2015-04|title=IDH mutation status and role of WHO grade and mitotic index in overall survival in grade II-III diffuse gliomas|url=https://pubmed.ncbi.nlm.nih.gov/25701198|journal=Acta Neuropathologica|volume=129|issue=4|pages=585–596|doi=10.1007/s00401-015-1398-z|issn=1432-0533|pmc=4369189|pmid=25701198}}</ref>PMID: 25701198; <ref>{{Cite journal|last=Lhotska|first=Halka|last2=Zemanova|first2=Zuzana|last3=Cechova|first3=Hana|last4=Ransdorfova|first4=Sarka|last5=Svobodova|first5=Karla|last6=Kramar|first6=Filip|last7=Krejcik|first7=Zdenek|last8=Michalova|first8=Kyra|date=2016|title=Primary and recurrent diffuse astrocytomas: genomic profile comparison reveals acquisition of biologically relevant aberrations|url=https://pubmed.ncbi.nlm.nih.gov/26865861|journal=Molecular Cytogenetics|volume=9|pages=13|doi=10.1186/s13039-016-0222-3|issn=1755-8166|pmc=4748601|pmid=26865861}}</ref>PMID:26865861; <ref name=":13" />PMID:29687258
|-
|
|Diffuse astrocytoma/anaplastic astrocytoma, WHO grade II/III, IDH wild-type
|'''Gain:''' 7, 19<br>
'''Loss:''' 4, 9p 10<br>
'''Amplification:''' [[EGFR]], [[MDM4]], [[CDK4]]
|'''Loss:''' homozygous [[CDKN2A]]/[[CDKN2B]]<br>
'''Mutation:''' [[EGFR]], [[NF1]], [[PTEN]]<br>
'''Amplification:'''  [[EGFR]], [[MDM4]], [[CDK4]]
|Poor prognosis with similar abnormalities to glioblastoma
|<ref name=":44" />PMID:26061754; <ref name=":9" />PMID:26824661; <ref name=":45" />PMID:28535583 <ref name=":46" />PMID:26091668; <ref>{{Cite journal|last=Qaddoumi|first=Ibrahim|last2=Orisme|first2=Wilda|last3=Wen|first3=Ji|last4=Santiago|first4=Teresa|last5=Gupta|first5=Kirti|last6=Dalton|first6=James D.|last7=Tang|first7=Bo|last8=Haupfear|first8=Kelly|last9=Punchihewa|first9=Chandanamali|date=2016-06|title=Genetic alterations in uncommon low-grade neuroepithelial tumors: BRAF, FGFR1, and MYB mutations occur at high frequency and align with morphology|url=https://pubmed.ncbi.nlm.nih.gov/26810070|journal=Acta Neuropathologica|volume=131|issue=6|pages=833–845|doi=10.1007/s00401-016-1539-z|issn=1432-0533|pmc=4866893|pmid=26810070}}</ref>PMID:26810070
|-
|
|Oligodendroglioma/anaplastic oligodendroglioma, WHO grade II/III, IDH mutant
|'''Rearrangement:''' der(1;19)(q10;p10) leads to 1p/19q co-deletion<br>
'''Loss:''' 1p/19q, 9p, 14q, less frequent 4, 18q
|'''Gain:''' [[MYC]]<br>
'''Loss:''' [[MAX]] (14q), [[FBXW7]], [[CDKN2A]]/[[CDKN2B]]<br>
'''Mutation:''' [[FUBP1]], [[CIC]], IDH, [[TERT]], [[NOTCH1]], [[PIK3CA]] or [[PIK3R1]]
|Activation of MYC pathway is often seen with loss of  9p (CDKN2A/B), and 14q (MAX gene)  and is reported to have a worse prognosis
|<ref>{{Cite journal|last=Kamoun|first=Aurélie|last2=Idbaih|first2=Ahmed|last3=Dehais|first3=Caroline|last4=Elarouci|first4=Nabila|last5=Carpentier|first5=Catherine|last6=Letouzé|first6=Eric|last7=Colin|first7=Carole|last8=Mokhtari|first8=Karima|last9=Jouvet|first9=Anne|date=2016-04-19|title=Integrated multi-omics analysis of oligodendroglial tumours identifies three subgroups of 1p/19q co-deleted gliomas|url=https://pubmed.ncbi.nlm.nih.gov/27090007|journal=Nature Communications|volume=7|pages=11263|doi=10.1038/ncomms11263|issn=2041-1723|pmc=4838899|pmid=27090007}}</ref>PMID:27090007; <ref name=":42" />PMID:26061753; <ref name=":43" />PMID:25263767 <ref name=":44" />PMID:26061754; <ref>{{Cite journal|last=Alentorn|first=Agustí|last2=van Thuijl|first2=Hinke F.|last3=Marie|first3=Yannick|last4=Alshehhi|first4=Hussa|last5=Carpentier|first5=Catherine|last6=Boisselier|first6=Blandine|last7=Laigle-Donadey|first7=Florence|last8=Mokhtari|first8=Karima|last9=Scheinin|first9=Ilari|date=2014-03|title=Clinical value of chromosome arms 19q and 11p losses in low-grade gliomas|url=https://pubmed.ncbi.nlm.nih.gov/24335697|journal=Neuro-Oncology|volume=16|issue=3|pages=400–408|doi=10.1093/neuonc/not227|issn=1523-5866|pmc=3922518|pmid=24335697}}</ref>PMID:24335697; <ref name=":1" />PMID:25664944; <ref>{{Cite journal|last=Rice|first=Terri|last2=Lachance|first2=Daniel H.|last3=Molinaro|first3=Annette M.|last4=Eckel-Passow|first4=Jeanette E.|last5=Walsh|first5=Kyle M.|last6=Barnholtz-Sloan|first6=Jill|last7=Ostrom|first7=Quinn T.|last8=Francis|first8=Stephen S.|last9=Wiemels|first9=Joseph|date=2016-03|title=Understanding inherited genetic risk of adult glioma - a review|url=https://pubmed.ncbi.nlm.nih.gov/26941959|journal=Neuro-Oncology Practice|volume=3|issue=1|pages=10–16|doi=10.1093/nop/npv026|issn=2054-2577|pmc=4774334|pmid=26941959}}</ref>PMID:26941959; <ref name=":9" />PMID:26824661 <ref name=":8" />PMID:26061751
|-
|
|Glioblastoma , grade IV, IDH mutant
|'''Gain:''' 1/1q, 6p<br>
'''Loss:''' 3p, 10, 13, 14, 15, 22 (3, 4q, 19q, 16p, 21q, 5p  seen in age <40)<br>
'''Amplification:''' [[CDK6]], cyclin E2 ([[CCNE2]]), [[CDK4]], [[MET]]<br>
'''Chromothripsis'''
|'''Gain or Amplification:''' [[CDK4]], [[CDK6]], cyclin E2 ([[CCNE2]])<br>
'''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
|-
|
|Glioblastoma , grade IV, IDH wildtype
|'''Loss:''' 4, 9p, 10, 13, 14, 15, 22 , (3, 4q, 19q, 16p, 21q, 5p loss in age <40)<br>
'''Gain:''' 7, 19, 20  (1q, 12p, 11q, 9q, 4, 10p gain in age <40) <br>
'''Amplification:''' [[EGFR]], [[MDM4]], [[CDK4]], [[MET]]
|'''Loss:''' homozygous [[CDKN2A]]/[[CDKN2B]], [[PTEN]], [[RB1]]<br>
'''Mutation:''' [[TERT]], [[EGFR]], [[PTEN]], [[NF1]], [[RB1]], [[PIK3CA]] or [[PIK3R1]], [[TP53]]<br>
'''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
|-
|'''MENINGIOMA'''
|-
|
|Grade 1
|No copy number changes in 44%<br>
'''Gain:''' multiple polysomies, 5<br>
'''Loss:''' 22/22q- common as sole aberration <br>
'''CN-LOH:''' 1p, 14q                                                                                                                                                                                                                                                   
|'''Loss:''' [[NF2]], [[CDKN2A]], [[PTEN]]<br>
'''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. 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<ref name=":65">{{Cite journal|last=Och|first=Waldemar|last2=Szmuda|first2=Tomasz|last3=Kulbacki|first3=Kamil|last4=Witek|first4=Krzysztof|last5=Sikorska|first5=Beata|last6=Zakrzewska|first6=Magdalena|last7=Springer|first7=Janusz|last8=Reszeć|first8=Joanna|last9=Parda|first9=Agnieszka|date=2016-11-XX|title=The correlation of clinical and chromosomal alterations of benign meningiomas and their recurrences|url=https://pubmed.ncbi.nlm.nih.gov/27480481|journal=Neurologia I Neurochirurgia Polska|volume=50|issue=6|pages=395–402|doi=10.1016/j.pjnns.2016.07.001|issn=0028-3843|pmid=27480481}}</ref>PMID:27480481; <ref name=":66">{{Cite journal|last=Yuzawa|first=Sayaka|last2=Nishihara|first2=Hiroshi|last3=Tanaka|first3=Shinya|date=2016-10|title=Genetic landscape of meningioma|url=https://pubmed.ncbi.nlm.nih.gov/27624470|journal=Brain Tumor Pathology|volume=33|issue=4|pages=237–247|doi=10.1007/s10014-016-0271-7|issn=1861-387X|pmid=27624470}}</ref>PMID:27624470; <ref name=":67">{{Cite journal|last=Bi|first=Wenya Linda|last2=Zhang|first2=Michael|last3=Wu|first3=Winona W.|last4=Mei|first4=Yu|last5=Dunn|first5=Ian F.|date=2016|title=Meningioma Genomics: Diagnostic, Prognostic, and Therapeutic Applications|url=https://pubmed.ncbi.nlm.nih.gov/27458586|journal=Frontiers in Surgery|volume=3|pages=40|doi=10.3389/fsurg.2016.00040|issn=2296-875X|pmc=4933705|pmid=27458586}}</ref>PMID:27458586; <ref name=":68">{{Cite journal|last=Ketter|first=Ralf|last2=Kim|first2=Yoo-Jin|last3=Storck|first3=Simone|last4=Rahnenführer|first4=Jörg|last5=Romeike|first5=Bernd F. M.|last6=Steudel|first6=Wolf-Ingo|last7=Zang|first7=Klaus D.|last8=Henn|first8=Wolfram|date=2007-06|title=Hyperdiploidy defines a distinct cytogenetic entity of meningiomas|url=https://pubmed.ncbi.nlm.nih.gov/17225936|journal=Journal of Neuro-Oncology|volume=83|issue=2|pages=213–221|doi=10.1007/s11060-006-9318-7|issn=0167-594X|pmid=17225936}}</ref>PMID:17225936
|-
|
|Grade 2 atypical
|'''Gain:''' 1q, 9q, 12q, 15q, 17q, 20q<br>
'''Loss:''' 1p, 3p, 6q, 7p, 14/14q, 9p, 10, 11p, 18/18q, 19q, 22/loss 22q  
|'''Loss:''' [[NF2]], [[CDKN2A]], [[PTEN]]<br>
'''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
|-
|
|Grade 3 anaplastic
|'''Gain:''' 1q, 9q, 12q, 15q, 17q23, 20q <br>
'''Loss:''' 1p, 3p, 6q, 7p, 14/14q, 9p, 10, 11p,18/18q,19q,22/loss 22q
|'''Loss:''' [[NF2]], [[CDKN2A]], [[PTEN]]<br>
'''Mutation:''' [[NF2]], [[CDKN2A]]/[[CDKN2C]], [[TERT]]<br>
'''Amplification:''' RPS6K in higher grades, 17q23
|Loss of 9p and amplification or gain of 17q23  are more frequent than other abnormalities.   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
|-
|'''EPENDYMOMA'''<br>
(in order of increasing WHO grade)
|
|'''DNA-based methylation classifies''' tumors across anatomical sites --- intracranial (posterior fossa or supratentorial) or spinal --- and across tumor grades and age groups
|'''Fusion:''' [[YAP1]] fusions (supratentorial tumors)<br>
'''Mutation:''' [[NF2]] (spinal tumors)<br>
'''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)<br>
<ref name=":16" />PMID:25965575; <ref name=":17" />PMID:21627842; <ref name=":18" />PMID:24939246; <ref name=":19" />PMID:22516549
|-
|
|Classic ependymoma (no WHO grade assigned)
|'''Gain:''' 1q, 5, 7, 9, 11, 18, 20<br>
'''Loss:''' 1p, 3, -6/6q, 9p, 13q, 17, 22
|'''Loss:''' [[CDKN2A]]/[[CDKN2B]] (rare); [[NF2]]<br>
'''Mutation:''' [[NF2]] (esp. in spinal tumors)    
|Usually intracranial, spinal tumors (myxopapillary) are rare; 80% of pediatric tumors develop in posterior fossa (PF); Supratentorial tumors preferentially show monosomy 9; 1q gain is unfavorable prognostic indicator in PF tumors; spinal tumors associated with NF2 mutation (germline)
|<ref name=":16" />PMID:25965575; <ref name=":21" />PMID:22338015; <ref name=":22" />PMID:28371821
|-
|
|Subependymoma, WHO grade I <br>
(intracranial or spinal)
|Typically '''balanced genomes'''<br>
'''Loss:''' -6/6q in spinal tumors   
|No diagnostic mutations
|Favorable prognosis
|WHO CNS Tumors (2016)<br>
<ref name=":20" />PMID:21959044; <ref name=":23" />PMID:21840481
|-
|
|Myxopapillary ependymoma, WHO grade I  (spinal)
|'''Aneuploidy:''' multiple chromosomes lost and gained
|'''Mutation:''' [[NF2]] (including germline) in spinal tumors
|More common in adults
|<ref name=":16" />PMID:25965575; <ref name=":24" />PMCID:3991130; <ref name=":25" />PMID:20425037 <ref name=":26" />PMID:25957288; <ref name=":19" />PMID:22516549
|-
|
|Ependymoma, RELA fusion-positive, WHO grade II or III<br>
(intracranial)
|'''Gain:''' 1q<br>
'''Aneuploidy:''' multiple chromosomes lost and gained<br>
'''Chromothripsis:''' chromosome 11 (70% of supratentorial tumors)
|'''Fusion:''' [[C11ORF95]]-[[RELA]] (supratentorial tumors)<br>
'''Loss:''' [[CDKN2A]]/[[CDKN2B]] (may help distinguish from other supratentorial ependymomas)
|Unfavorable prognosis
|<ref name=":16" />PMID:25965575; <ref name=":27" />PMID:24553141; <ref name=":22" />PMID:28371821
|-
|
|Anaplastic ependymoma (no WHO grade assigned; intracranial or spinal)
|'''Epigenetic studies''' suggest range of abnormalities: balanced or unbalanced genomes
|'''Mutation:''' [[NF2]] (including germline) in spinal tumors<br>
'''Fusion:''' [[RELA]] fusions, [[YAP1]] fusions can correspond to anaplastic histology
|Mostly intracranial tumors, rarely in spinal cord
|<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.
<references />