Difference between revisions of "Recurrent Genomic Alterations in Pediatric and Adult Central Nervous System Tumors Detected by Chromosomal Microarray"

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|<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
 
|<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
 
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<ref>{{Cite journal|last=Neill|first=Stewart G.|last2=Hauenstein|first2=Jennifer|last3=Li|first3=Marilyn M.|last4=Liu|first4=Yajuan J.|last5=Luo|first5=Minjie|last6=Saxe|first6=Debra F.|last7=Ligon|first7=Azra H.|date=2020-05|title=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|url=https://pubmed.ncbi.nlm.nih.gov/32203924|journal=Cancer Genetics|volume=243|pages=19–47|doi=10.1016/j.cancergen.2020.02.004|issn=2210-7762|pmid=32203924}}</ref><references />
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==Reference==
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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.
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<references />

Revision as of 14:59, 16 April 2021

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 [PMID: 32203924] with permission from Cancer Genetics.

TUMOR SUBTYPES BROAD ABERRATIONS (>10Mb) FOCAL ABERRATIONS (<10Mb) CLINICAL FEATURES REFERENCES
GLIOMAS 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)

Mutations: BRAF V600E (particularly extra-cerebellar tumors); FGFR1 (midline PA); NF1 (esp. germline), other MAPK pathway mutations
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 [1]PMID:19016743; [2]PMCID:2761618; [3]PMID:18716556 [4]PMID:25461780 [5]PMID:25664944; [6]PMID:26378811 [7]PMCID:3429698; [8]PMID:23817572; [9]PMID:23583981 [10]PMID:18974108; [11]PMID:23278243; [12]PMID:21274720
Angiocentric glioma Aberrations involving 6q24-q25 Fusions: MYB-QKI rearrangement/deletion (classic histology)

Rearrangement: MYB alone (atypical histology)
Amplification: MYB (atypical histology)

Generally indolent tumors; surgical resection can be curative [13]PMID:26829751; [14]PMID:23633565; [15]PMID:26778052 [9]PMID:23583981
Ganglioglioma Only 30% are abnormal by karyotype

Gain: polysomy 7

Mutations: BRAF V600E in 20-60% of cases (can be concurrent with CDKN2A homozygous deletion)

Fusions: KIAA1549-BRAF

Generally indolent tumors for which surgical resection can be curative [4]PMID:25461780; [9]PMID:23583981; [16]PMID:11996800 [17]PMID:23609006; [18]PMID:29880043
Low grade glioma, WHO grade II Diffuse astrocytoma No diagnostic aberrations Rearrangement: MYBL1 truncating rearrangements and tandem duplication, FGFR1 rearrangements

Mutation: FGFR1

Anaplastic features associated with decreased progression free survival [5]PMID:25664944; [14]PMID:23633565; [19]PMID:26061751 [20]PMID:26824661; [21]PMID:26004297; [4]PMID:25461780 [9]PMID:23583981
Pleomorphic xanthoastrocytoma (PXA) Polysomy 3, polysomy 7 observed

Loss: monosomy 9 / 9p deletion

Mutations: BRAF V600E in ~60%; TP53 (5%)

Loss: CDKN2A/CDKN2B

[4]PMID:25461780; [9]PMID:23583981; [22]PMID:16909113; [23]PMID:12484572
Anaplastic astrocytoma, WHO grade III IDH-mutant or IDH-wild type Gain: 1q, 7/7q, 8q, 10p

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 [24]PMCID:1891902; [21]PMID:26004297; [4]PMID:25461780; [25]PMID:24140581; [26]PMCID:5323185; [27]PMID:27230974 [28]PMID:27196377; [19]PMID:26061751; [29]PMID:25962792; [30]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

Loss: CDKN2A/CDKN2B

CDKN2A/CDKN2B loss may correlate with anaplastic histology WHO CNS Tumors (2016)

[31]PMID:25318587; [32]PMID:23096133; [12]PMID:21274720

Glioblastoma, WHO grade IV IDH-mutant Gain: 1q, 2q, 3q, 7, 16p, 17q, 21q

Loss: 6q, 8q, 9p, 9q, 10q, 13q, 17p, 22q
Chromothripsis: observed

Loss: PTEN, RB1, TP53, CDKN2A/CDKN2B/CDKN2C

Fusions: FGFR-TACC; NTRK fusions
Amplification: PDGFRA, MYCN, MET, CDK4, CDK6 (EGFR, MDM2 amp rare)
Mutations: IDH1/IDH2 (rare in pediatric GBM), KRAS, RAS pathway, RB1 pathway, TP53 pathway, FGFR1, H3.3/H3.1-K27M (exclusively in diffuse midline tumors), PDGFRA, NF1, SETD2, ATRX, DAXX

Overall poor prognosis [33]PMID:25752754; [34]PMID:25727226; [35]PMID:26328271; [36]PMID:22837387; [37]PMID:25754088; [4]PMID:25461780; [24]PMCID:1891902; [38]PMID:23417712; [26]PMCID:5323185; [30]PMID:29687258; [39]PMID:20479398; [40]PMID:24959384
Diffuse midline glioma, H3 K27M mutant Gain: 1q, 2, 7, 8

Loss: 10q
Chromothripsis: 2p

Three molecular subgroups:

MYCN subgroup: no mutations but chromothripsis leading to amp of MYCN and ID2
Silent subgroup: no recurrent copy # changes, few mutations
H3-K27M subgroup: MYC, PDGFRA gains/amp; RB1, TP53 deletions
Mutation: ACVR1, H3F3A, HIST1H3B, TP53 Loss: CDKN2A, PTEN, RB1, TP53
Amplification: MYC, MYCN, ID2, PDGFRA

Overall poor prognosis regardless of subgroup [41]PMCID:3280796; [42]PMID:24705254; [43]PMID:24705252 [44]PMID:27048880; [45]PMID:26175967; [46]PMID:24705251; [47]PMID:28966033
EPENDYMOMA

(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)

Mutation: NF2 (spinal tumors)
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)

[48]PMID:25965575; [49]PMID:21627842; [50]PMID:24939246; [51]PMID:22516549

Classic ependymoma (no WHO grade assigned) Gain: 1q, 5, 7, 9, 11, 18, 20

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 [48]PMID:25965575; [52]PMID:22338015; [53]PMID:28371821
Subependymoma, WHO grade I Typically balanced genomes

Loss: -6/6q in spinal tumors

No diagnostic mutations Favorable prognosis WHO CNS Tumors (2016)

[54]PMID:21959044; [55]PMID:21840481

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 [48]PMID:25965575; [56]PMCID:3991130; [57]PMID:20425037; [58]PMID:25957288; [51]PMID:22516549
Ependymoma, RELA fusion-positive, WHO grade II or III Gain: 1q

Aneuploidy: multiple chromosomes lost and gained
Chromothripsis: chromosome 11 (70% of supratentorial tumors)

Fusion: C11ORF95-RELA (supratentorial tumors)

Loss: CDKN2A/CDKN2B (may help distinguish from other supratentorial ependymomas)

Unfavorable prognosis; occur in infants or children [48]PMID:25965575; [59]PMID:24553141; [53]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

Fusion: RELA fusions, YAP1 fusions can correspond to anaplastic histology

Mostly intracranial tumors, rarely in spinal cord; YAP1 fusion tumors can occur in infants [48]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 [60]PMID:22832581, [61]PMID:24493713; [62]PMID:22134537 [63]PMID:24894640; [64]PMID:16258095; [65]PMID:22358457; [66]PMID:25043047 [67]PMID:22820256; [68]PMID:26976201; [69]PMID:20823417 [70]PMID:22265402; [71]PMCID:3889646; [72]PMID:16567768 [73]PMID:20940197
SHH-activated Gain: 3q

Loss: 9q, 10q, 17p
Ploidy changes: Tetraploidy associated with chromothripsis and TP53 mutations
Chromothripsis: associated with TP53 mutation

Mutation:

TP53 wild-type tumors: PTCH1 (germline mutations in Gorlin syndrome), SMO, SUFU (can be germline), TERT promoter
TP53-mutant tumors: can be germline
Loss: PTCH1, PTEN
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 [74]PMID:24651015; [75]PMID:21681522; [60]PMID:22832581 [61]PMID:24493713; [76]PMID:24077351; [62]PMID:22134537; [65]PMID:22358457 [66]PMID:25043047; [67]PMID:22820256; [68]PMID:26976201 [68]PMID:20823417; [70]PMID:22265402; [71]PMCID:3889646 [72]PMID:16567768; [73]PMID:20940197
Group3 Gain: 1q, 7, 18q

Loss: 5q, 8, 10q, 11p, 16q
Rearrangement: idic(17)(p11.2)
Ploidy changes: tetraploidy in 40-50% of Group3/Group4 tumors

Mutation/Amplification: MYC (mainly in infants), OTX2, CDK6, SMARC4A, CTDNEP1, LRP1B, KMT2D

Fusions: PVT1-MYC, PVT1-NDRG1; GFI1/GFI1B structural variants

Usually classic histology, ~ 50% are metastatic at time of diagnosis, Not generally observed in adults [60]PMID:22832581, [66]PMID:25043047; [61]PMID:24493713 [62]PMID:22134537; [65]PMID:22358457; [67]PMID:22820256; [68]PMID:26976201; [68]PMID:20823417 [70]PMID:22265402; [71]PMCID:3889646; [72]PMID:16567768 [73]PMID:20940197
Group4 Gain: 7, 18q

Loss: X, 8, 11p
Rearrangement: idic(17)(p11.2) in >80%
Chromothripsis: rare, but associated with TP53 loss when observed

Mutation: TP53, KDM6A, KMT2C

Amplification: MYCN, CDK4, CDK6, OTX2
Rearrangement: SNCAIP tandem duplication; GFI1/GFI1B structural variants

Rarely seen in infants; usually classic histology [60]PMID:22832581; [66]PMID:25043047; [61]PMID:24493713; [62]PMID:22134537; [65]PMID:22358457; [67]PMID:22820256; [68]PMID:26976201; [68]PMID:20823417 [70]PMID:22265402; [71]PMCID:3889646; [72]PMID:16567768 [73]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

AT/RT-like tumors: SMARCB1 can be retained (with SMARCA4 mutations)
Three molecular classes:
TYR: ~ 75% show broad 22q loss that includes SMARCB1
SHH: ~ 50% lack any SMARCB1 mutation; ~ 25% have focal SMARCB1 aberrations
MYC: ~ 75% show focal SMARCB1 loss

Most cases occur before 3 yrs of age

TYR subclass: mostly infratentorial
SHH subclass: supra/infratentorial
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)

[77]PMID:24839957; [78]PMID:24470553 [79]PMID:24337497; [80]PMID:22324795 [81]PMID:20407781, [82]PMID:19057917

Embryonal tumor, other CNS NB-FOXR2 group: 1q gain, 16q loss, polysomy 8

CNS EFT-CIC group: polysomy 8
CNS HGNET-MN1 group: 16q loss, polysomy 8
CNS HGNET-BCOR group: mostly balanced genomes

CNS NB-FOXR2 group: JMJD1C fusions, FOXR2 fusion or deletion

CNS EFT-CIC group: NUTM1 rearrangement/fusion, CIC rearrangement
CNS HGNET-MN1 group: MN1 rearrangement
CNS HGNET-BCOR group: BCOR intragenic tandem duplication

Most common in children, but may also occur in adolescents and adults WHO CNS Tumors (2016)

[83]PMID:26919435; [84]PMID:22691720; [85]PMID:22772606

CHOROID PLEXUS TUMORS (CPT) Choroid plexus papilloma(CPP, WHO grade I) and atypical choroid plexus papilloma (WHO grade II) Hyperdiploidy

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)

[86]PMID:23172371; [87]PMID:25575132; [88]PMID:25336695 [89]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

Gain: 1, 7, 12, 20 in > 80% of hyperdiploid CPCs
Loss: 3 (in all hypodiploid CPC), 6, 11, 12q, 16, 22

Mutation: TP53 in > 50%

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 [90]PMID:24478045; [91]PMID:21990040; [87]PMID:25575132; [92]PMID:18157090; [88]PMID:25336695

Table 2: Adult CNS Tumors. Table derived from CGC CNS Workgroup 2015-2018. Table derived from Neill et al., 2020 [PMID: 32203924] with permission from Cancer Genetics.

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

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

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

Mutation: FGFR1

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 [93]PMID: 24470550; [6]PMID:26378811; [5]PMID: 25664944; [94]PMID:26992069
Pleomorphic xanthoastrocytoma (PXA) Gain: 7, 2, 5, 21, 20, 12, 15

Loss: monosomy 9 / 9p deletion most common, 22, 14, 13, 10
CN-LOH: 9p, 22

Loss: homozygous loss CDKN2A/CDKN2B

Mutation: BRAF V600E

Adults and pediatric tumors show similar CNVs; CDKN2A/CDKN2B loss may correlate with anaplastic histology [95]PMID:23442159; [96]PMID:28181325
Ganglioglioma Gain: polysomy 5, polysomy 7, 10p

Loss: 1p loss, monosomy (with focal CDKN2A loss)

Mutation: BRAF V600E, TSC1, TSC2, FGFR1, FGFR2, KRAS Generally indolent tumors; surgical resection can be curative [95]PMID:23442159; [97]PMID:25764012; [18]PMID:29880043
Angiocentric glioma Loss: 6q24-q25 Fusion: MYB-QKI rearrangement/deletion (classic histology)

Rearrangement: MYB alone (atypical histology)
Amplification: MYB (atypical histology)

Generally indolent tumors; surgical resection can be curative [13]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 [98]PMID:26920151; [95]PMID:23442159; [99]PMID:21937911
Rosette forming glioneuronal tumor Gain:1q , 7, 9, 16

Loss: 1p
Amplification: 9q34.2, 19p13.3

Fusion: KIAA1549-BRAF fusion (via 3'BRAF duplication)

Mutation: PIK3CA, FGFR1
Amplification: SBNO2

Generally indolent tumors; surgical resection can be curative [100]PMID:27893178; [101]PMID:26371886
Infiltrating Gliomas Diffuse astrocytoma/anaplastic Astrocytoma, WHO grade II/III, IDH mutant Gain: 4q, 7q, 8q24, 12q

Loss: 9p, 19q (without 1p)

Gain: MYC

Loss: CDKN2A/CDKN2B, PML15q22

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. [20]PMID:26824661; [102]PMID:26061753; [103]PMID:25263767 [104]PMID:26061754; [105]PMID:28535583; [106]PMID:26091668 [107]PMID: 25701198; [108]PMID:26865861; [30]PMID:29687258
Diffuse astrocytoma/anaplastic astrocytoma, WHO grade II/III, IDH wild-type Gain: 7, 19

Loss: 4, 9p 10
Amplification: EGFR, MDM4, CDK4

Loss: homozygous CDKN2A/CDKN2B

Mutation: EGFR, NF1, PTEN
Amplification: EGFR, MDM4, CDK4

Poor prognosis with similar abnormalities to glioblastoma [104]PMID:26061754; [20]PMID:26824661; [105]PMID:28535583 [106]PMID:26091668; [109]PMID:26810070
Oligodendroglioma/anaplastic oligodendroglioma, WHO grade II/III, IDH mutant Rearrangement: der(1;19)(q10;p10) leads to 1p/19q co-deletion

Loss: 1p/19q, 9p, 14q, less frequent 4, 18q

Gain: MYC

Loss: MAX (14q), FBXW7, CDKN2A/CDKN2B
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 [110]PMID:27090007; [102]PMID:26061753; [103]PMID:25263767 [104]PMID:26061754; [111]PMID:24335697; [5]PMID:25664944; [112]PMID:26941959; [20]PMID:26824661 [19]PMID:26061751
Glioblastoma , grade IV, IDH mutant Gain: 1/1q, 6p

Loss: 3p, 10, 13, 14, 15, 22 (3, 4q, 19q, 16p, 21q, 5p seen in age <40)
Amplification: CDK6, cyclin E2 (CCNE2), CDK4, MET
Chromothripsis

Gain or Amplification: CDK4, CDK6, cyclin E2 (CCNE2)

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. [104]PMID:26061754; [37]PMID:25754088; [105]PMID:28535583 [113]PMID:25931051; [106]PMID:26091668; [4]PMID:25461780; [114]PMID:27157931; [34]PMID:25727226; [115]PMID:26323991 [19]PMID:26061751; [30]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)

Gain: 7, 19, 20 (1q, 12p, 11q, 9q, 4, 10p gain in age <40)
Amplification: EGFR, MDM4, CDK4, MET

Loss: homozygous CDKN2A/CDKN2B, PTEN, RB1

Mutation: TERT, EGFR, PTEN, NF1, RB1, PIK3CA or PIK3R1, TP53
Amplification: EGFR, MDM4, MDM2, CDK4, PDGFRA, MET

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. [104]PMID:26061754; [37]PMID:25754088; [105]PMID:28535583 [113]PMID:25931051; [106]PMID:26091668; [4]PMID:25461780; [114]PMID:27157931; [34]PMID:25727226; [19]PMID:26061751
MENINGIOMA
Grade 1 No copy number changes in 44%

Gain: multiple polysomies, 5
Loss: 22/22q- common as sole aberration
CN-LOH: 1p, 14q

Loss: NF2, CDKN2A, PTEN

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. [56]PMID:23528542; [116]PMID:27575681; [117]PMID:20015288 [118]PMID:21988727; [119]PMID19918127; [120]PMID:25347344 [121]PMID:23334667; [122]PMID:25963524; [123]PMID:26826201 [124]PMID:28195122; [125]PMID:26323607;

[126]PMID:11958368; [127]PMID:25965831; [128]PMID:24536048; [129]PMID:24722350 [130]PMID:12568317; [131]PMID:26771848; [132]PMID:27012381; [133]PMID:27480481; [134]PMID:27624470; [135]PMID:27458586; [136]PMID:17225936

Grade 2 atypical Gain: 1q, 9q, 12q, 15q, 17q, 20q

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

Loss: NF2, CDKN2A, PTEN

Mutation: NF2, CDKN2A/CDKN2C, SMARCE1, SMARCB1, TERT

Gain of 1q is assocociated with a shorter PFS; Loss of 1p, 9p and 10 appear with greater frequency as tumor grade increases. [56]PMID:23528542; [116]PMID:27575681; [117]PMID:20015288 [117]PMID:21988727; [119]PMID19918127; [120]PMID:25347344 [121]PMID:23334667; [122]PMID:25963524; [123]PMID:26826201 [124]PMID:28195122; [125]PMID:26323607; [126]PMID:11958368; [127]PMID:25965831; [128]PMID:24536048; [129]PMID:24722350 [130]PMID:12568317; [131]PMID:26771848; [132]PMID:27012381; [133]PMID:27480481; [134]PMID:27624470; [135]PMID:27458586; [136]PMID:17225936
Grade 3 anaplastic Gain: 1q, 9q, 12q, 15q, 17q23, 20q

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

Loss: NF2, CDKN2A, PTEN

Mutation: NF2, CDKN2A/CDKN2C, TERT
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. [56]PMID:23528542; [116]PMID:27575681; [117]PMID:20015288 [117]PMID:21988727; [119]PMID19918127; [120]PMID:25347344 [121]PMID:23334667; [122]PMID:25963524; [123]PMID:26826201 [124]PMID:28195122; [125]PMID:26323607; [126]PMID:11958368; [127]PMID:25965831; [128]PMID:24536048; [129]PMID:24722350 [130]PMID:12568317; [131]PMID:26771848; [132]PMID:27012381; [133]PMID:27480481; [134]PMID:27624470; [135]PMID:27458586; [136]PMID:17225936
EPENDYMOMA

(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)

Mutation: NF2 (spinal tumors)
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)

[48]PMID:25965575; [49]PMID:21627842; [50]PMID:24939246; [51]PMID:22516549

Classic ependymoma (no WHO grade assigned) Gain: 1q, 5, 7, 9, 11, 18, 20

Loss: 1p, 3, -6/6q, 9p, 13q, 17, 22

Loss: CDKN2A/CDKN2B (rare); NF2

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) [48]PMID:25965575; [52]PMID:22338015; [53]PMID:28371821
Subependymoma, WHO grade I

(intracranial or spinal)

Typically balanced genomes

Loss: -6/6q in spinal tumors

No diagnostic mutations Favorable prognosis WHO CNS Tumors (2016)

[54]PMID:21959044; [55]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 [48]PMID:25965575; [56]PMCID:3991130; [57]PMID:20425037 [58]PMID:25957288; [51]PMID:22516549
Ependymoma, RELA fusion-positive, WHO grade II or III

(intracranial)

Gain: 1q

Aneuploidy: multiple chromosomes lost and gained
Chromothripsis: chromosome 11 (70% of supratentorial tumors)

Fusion: C11ORF95-RELA (supratentorial tumors)

Loss: CDKN2A/CDKN2B (may help distinguish from other supratentorial ependymomas)

Unfavorable prognosis [48]PMID:25965575; [59]PMID:24553141; [53]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

Fusion: RELA fusions, YAP1 fusions can correspond to anaplastic histology

Mostly intracranial tumors, rarely in spinal cord [48]PMID: 25965575; [137]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.

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  2. ↑ Jones, David T. W.; et al. (2006-11). "Genomic Analysis of Pilocytic Astrocytomas at 0.97 Mb Resolution Shows an Increasing Tendency Toward Chromosomal Copy Number Change With Age". Journal of neuropathology and experimental neurology. 65 (11): 1049–1058. doi:10.1097/01.jnen.0000240465.33628.87. ISSN 0022-3069. PMC 2761618. PMID 17086101. Check date values in: |date= (help)
  3. ↑ Bar, Eli E.; et al. (2008-09). "Frequent gains at chromosome 7q34 involving BRAF in pilocytic astrocytoma". Journal of Neuropathology and Experimental Neurology. 67 (9): 878–887. doi:10.1097/NEN.0b013e3181845622. ISSN 0022-3069. PMID 18716556. Check date values in: |date= (help)
  4. ↑ 4.0 4.1 4.2 4.3 4.4 4.5 4.6 4.7 Appin, Christina L.; et al. (2015-01). "Molecular pathways in gliomagenesis and their relevance to neuropathologic diagnosis". Advances in Anatomic Pathology. 22 (1): 50–58. doi:10.1097/PAP.0000000000000048. ISSN 1533-4031. PMID 25461780. Check date values in: |date= (help)
  5. ↑ 5.0 5.1 5.2 5.3 Venneti, Sriram; et al. (2015-03). "The evolving molecular genetics of low-grade glioma". Advances in Anatomic Pathology. 22 (2): 94–101. doi:10.1097/PAP.0000000000000049. ISSN 1533-4031. PMC 4667550. PMID 25664944. Check date values in: |date= (help)
  6. ↑ 6.0 6.1 Fontebasso, Adam M.; et al. (2015-10-13). "Non-random aneuploidy specifies subgroups of pilocytic astrocytoma and correlates with older age". Oncotarget. 6 (31): 31844–31856. doi:10.18632/oncotarget.5571. ISSN 1949-2553. PMC 4741644. PMID 26378811.
  7. ↑ Rodriguez, Fausto J.; et al. (2012-9). "BRAF Duplications and MAPK Pathway Activation Are Frequent in Gliomas of the Optic Nerve Proper". Journal of neuropathology and experimental neurology. 71 (9): 789–794. doi:10.1097/NEN.0b013e3182656ef8. ISSN 0022-3069. PMC 3429698. PMID 22892521. Check date values in: |date= (help)
  8. ↑ Jones, David T. W.; et al. (2013-08). "Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma". Nature Genetics. 45 (8): 927–932. doi:10.1038/ng.2682. ISSN 1546-1718. PMC 3951336. PMID 23817572. Check date values in: |date= (help)
  9. ↑ 9.0 9.1 9.2 9.3 9.4 Zhang, Jinghui; et al. (2013-06). "Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas". Nature Genetics. 45 (6): 602–612. doi:10.1038/ng.2611. ISSN 1546-1718. PMC 3727232. PMID 23583981. Check date values in: |date= (help)
  10. ↑ Jones, David T. W.; et al. (2008-11-01). "Tandem duplication producing a novel oncogenic BRAF fusion gene defines the majority of pilocytic astrocytomas". Cancer Research. 68 (21): 8673–8677. doi:10.1158/0008-5472.CAN-08-2097. ISSN 1538-7445. PMC 2577184. PMID 18974108.
  11. ↑ Colin, C.; et al. (2013-10). "Outcome analysis of childhood pilocytic astrocytomas: a retrospective study of 148 cases at a single institution". Neuropathology and Applied Neurobiology. 39 (6): 693–705. doi:10.1111/nan.12013. ISSN 1365-2990. PMID 23278243. Check date values in: |date= (help)
  12. ↑ 12.0 12.1 Schindler, Genevieve; et al. (2011-03). "Analysis of BRAF V600E mutation in 1,320 nervous system tumors reveals high mutation frequencies in pleomorphic xanthoastrocytoma, ganglioglioma and extra-cerebellar pilocytic astrocytoma". Acta Neuropathologica. 121 (3): 397–405. doi:10.1007/s00401-011-0802-6. ISSN 1432-0533. PMID 21274720. Check date values in: |date= (help)
  13. ↑ 13.0 13.1 Bandopadhayay, Pratiti; et al. (2016-03). "MYB-QKI rearrangements in angiocentric glioma drive tumorigenicity through a tripartite mechanism". Nature Genetics. 48 (3): 273–282. doi:10.1038/ng.3500. ISSN 1546-1718. PMC 4767685. PMID 26829751. Check date values in: |date= (help)
  14. ↑ 14.0 14.1 Ramkissoon, Lori A.; et al. (2013-05-14). "Genomic analysis of diffuse pediatric low-grade gliomas identifies recurrent oncogenic truncating rearrangements in the transcription factor MYBL1". Proceedings of the National Academy of Sciences of the United States of America. 110 (20): 8188–8193. doi:10.1073/pnas.1300252110. ISSN 1091-6490. PMC 3657784. PMID 23633565.
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  16. ↑ Yin, Xiao Lu; et al. (2002-04-01). "Genome-wide survey for chromosomal imbalances in ganglioglioma using comparative genomic hybridization". Cancer Genetics and Cytogenetics. 134 (1): 71–76. doi:10.1016/s0165-4608(01)00611-2. ISSN 0165-4608. PMID 11996800.
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  18. ↑ 18.0 18.1 Pekmezci, Melike; et al. (2018-06-07). "The genetic landscape of ganglioglioma". Acta Neuropathologica Communications. 6 (1): 47. doi:10.1186/s40478-018-0551-z. ISSN 2051-5960. PMC 5992851. PMID 29880043.
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  22. ↑ Weber, R. G.; et al. (2007-02-15). "Frequent loss of chromosome 9, homozygous CDKN2A/p14(ARF)/CDKN2B deletion and low TSC1 mRNA expression in pleomorphic xanthoastrocytomas". Oncogene. 26 (7): 1088–1097. doi:10.1038/sj.onc.1209851. ISSN 0950-9232. PMID 16909113.
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  24. ↑ 24.0 24.1 Rickert, Christian H.; et al. (2001-4). "Pediatric High-Grade Astrocytomas Show Chromosomal Imbalances Distinct from Adult Cases". The American Journal of Pathology. 158 (4): 1525–1532. doi:10.1016/S0002-9440(10)64103-X. ISSN 0002-9440. PMC 1891902. PMID 11290570. Check date values in: |date= (help)
  25. ↑ Killela, Patrick J.; et al. (2014-03-30). "The genetic landscape of anaplastic astrocytoma". Oncotarget. 5 (6): 1452–1457. doi:10.18632/oncotarget.1505. ISSN 1949-2553. PMC 4039223. PMID 24140581.
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  29. ↑ Reuss, David E.; et al. (2015-06). "IDH mutant diffuse and anaplastic astrocytomas have similar age at presentation and little difference in survival: a grading problem for WHO". Acta Neuropathologica. 129 (6): 867–873. doi:10.1007/s00401-015-1438-8. ISSN 1432-0533. PMC 4500039. PMID 25962792. Check date values in: |date= (help)
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  31. ↑ Ida, Cristiane M.; et al. (2015-09). "Pleomorphic Xanthoastrocytoma: Natural History and Long-Term Follow-Up". Brain Pathology (Zurich, Switzerland). 25 (5): 575–586. doi:10.1111/bpa.12217. ISSN 1750-3639. PMC 4400218. PMID 25318587. Check date values in: |date= (help)
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  38. ↑ Fontebasso, Adam M.; et al. (2013-05). "Mutations in SETD2 and genes affecting histone H3K36 methylation target hemispheric high-grade gliomas". Acta Neuropathologica. 125 (5): 659–669. doi:10.1007/s00401-013-1095-8. ISSN 1432-0533. PMC 3631313. PMID 23417712. Check date values in: |date= (help)
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  42. ↑ Buczkowicz, Pawel; et al. (2014-05). "Genomic analysis of diffuse intrinsic pontine gliomas identifies three molecular subgroups and recurrent activating ACVR1 mutations". Nature Genetics. 46 (5): 451–456. doi:10.1038/ng.2936. ISSN 1546-1718. PMC 3997489. PMID 24705254. Check date values in: |date= (help)
  43. ↑ Taylor, Kathryn R.; et al. (2014-05). "Recurrent activating ACVR1 mutations in diffuse intrinsic pontine glioma". Nature Genetics. 46 (5): 457–461. doi:10.1038/ng.2925. ISSN 1546-1718. PMC 4018681. PMID 24705252. Check date values in: |date= (help)
  44. ↑ Nikbakht, Hamid; et al. (2016-04-06). "Spatial and temporal homogeneity of driver mutations in diffuse intrinsic pontine glioma". Nature Communications. 7: 11185. doi:10.1038/ncomms11185. ISSN 2041-1723. PMC 4823825. PMID 27048880.
  45. ↑ Buczkowicz, Pawel; et al. (2015). "Pathology, Molecular Genetics, and Epigenetics of Diffuse Intrinsic Pontine Glioma". Frontiers in Oncology. 5: 147. doi:10.3389/fonc.2015.00147. ISSN 2234-943X. PMC 4485076. PMID 26175967.
  46. ↑ Wu, Gang; et al. (2014-05). "The genomic landscape of diffuse intrinsic pontine glioma and pediatric non-brainstem high-grade glioma". Nature Genetics. 46 (5): 444–450. doi:10.1038/ng.2938. ISSN 1546-1718. PMC 4056452. PMID 24705251. Check date values in: |date= (help)
  47. ↑ Mackay, Alan; et al. (2017-10-09). "Integrated Molecular Meta-Analysis of 1,000 Pediatric High-Grade and Diffuse Intrinsic Pontine Glioma". Cancer Cell. 32 (4): 520–537.e5. doi:10.1016/j.ccell.2017.08.017. ISSN 1878-3686. PMC 5637314. PMID 28966033.
  48. ↑ 48.0 48.1 48.2 48.3 48.4 48.5 48.6 48.7 48.8 48.9 Pajtler, Kristian W.; et al. (2015-05-11). "Molecular Classification of Ependymal Tumors across All CNS Compartments, Histopathological Grades, and Age Groups". Cancer Cell. 27 (5): 728–743. doi:10.1016/j.ccell.2015.04.002. ISSN 1878-3686. PMC 4712639. PMID 25965575.
  49. ↑ 49.0 49.1 Ellison, David W.; et al. (2011-05-31). "Histopathological grading of pediatric ependymoma: reproducibility and clinical relevance in European trial cohorts". Journal of Negative Results in Biomedicine. 10: 7. doi:10.1186/1477-5751-10-7. ISSN 1477-5751. PMC 3117833. PMID 21627842.
  50. ↑ 50.0 50.1 Olsen, Thale Kristin; et al. (2014-08). "Genomic characterization of ependymomas reveals 6q loss as the most common aberration". Oncology Reports. 32 (2): 483–490. doi:10.3892/or.2014.3271. ISSN 1791-2431. PMC 4091878. PMID 24939246. Check date values in: |date= (help)
  51. ↑ 51.0 51.1 51.2 51.3 Yang, Isaac; et al. (2012-06). "Chromosomal anomalies and prognostic markers for intracranial and spinal ependymomas". Journal of Clinical Neuroscience: Official Journal of the Neurosurgical Society of Australasia. 19 (6): 779–785. doi:10.1016/j.jocn.2011.11.004. ISSN 1532-2653. PMC 3615711. PMID 22516549. Check date values in: |date= (help)
  52. ↑ 52.0 52.1 Kilday, John-Paul; et al. (2012-04-01). "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)". Clinical Cancer Research: An Official Journal of the American Association for Cancer Research. 18 (7): 2001–2011. doi:10.1158/1078-0432.CCR-11-2489. ISSN 1557-3265. PMID 22338015.
  53. ↑ 53.0 53.1 53.2 53.3 Gojo, Johannes; et al. (2017-09-01). "Telomerase activation in posterior fossa group A ependymomas is associated with dismal prognosis and chromosome 1q gain". Neuro-Oncology. 19 (9): 1183–1194. doi:10.1093/neuonc/nox027. ISSN 1523-5866. PMC 5570194. PMID 28371821.
  54. ↑ 54.0 54.1 Yao, Yuan; et al. (2011-10). "Molecular genetics of ependymoma". Chinese Journal of Cancer. 30 (10): 669–681. doi:10.5732/cjc.011.10129. ISSN 1000-467X. PMC 4012267. PMID 21959044. Check date values in: |date= (help)
  55. ↑ 55.0 55.1 Witt, Hendrik; et al. (2011-08-16). "Delineation of two clinically and molecularly distinct subgroups of posterior fossa ependymoma". Cancer Cell. 20 (2): 143–157. doi:10.1016/j.ccr.2011.07.007. ISSN 1878-3686. PMC 4154494. PMID 21840481.
  56. ↑ 56.0 56.1 56.2 56.3 56.4 Zadnik, Patricia L.; et al. (2013-5). "Spinal cord tumours: advances in genetics and their implications for treatment". Nature reviews. Neurology. 9 (5): 257–266. doi:10.1038/nrneurol.2013.48. ISSN 1759-4758. PMC 3991130. PMID 23528542. Check date values in: |date= (help)
  57. ↑ 57.0 57.1 Dubuc, Adrian M.; et al. (2010-05). "The genetics of pediatric brain tumors". Current Neurology and Neuroscience Reports. 10 (3): 215–223. doi:10.1007/s11910-010-0103-9. ISSN 1534-6293. PMID 20425037. Check date values in: |date= (help)
  58. ↑ 58.0 58.1 Mack, Stephen C.; et al. (2015-08-15). "Spinal Myxopapillary Ependymomas Demonstrate a Warburg Phenotype". Clinical Cancer Research: An Official Journal of the American Association for Cancer Research. 21 (16): 3750–3758. doi:10.1158/1078-0432.CCR-14-2650. ISSN 1557-3265. PMC 4537825. PMID 25957288.
  59. ↑ 59.0 59.1 Parker, Matthew; et al. (2014-02-27). "C11orf95-RELA fusions drive oncogenic NF-κB signalling in ependymoma". Nature. 506 (7489): 451–455. doi:10.1038/nature13109. ISSN 1476-4687. PMC 4050669. PMID 24553141.
  60. ↑ 60.0 60.1 60.2 60.3 Northcott, Paul A.; et al. (2012-08-02). "Subgroup-specific structural variation across 1,000 medulloblastoma genomes". Nature. 488 (7409): 49–56. doi:10.1038/nature11327. ISSN 1476-4687. PMC 3683624. PMID 22832581.
  61. ↑ 61.0 61.1 61.2 61.3 Shih, David J. H.; et al. (2014-03-20). "Cytogenetic prognostication within medulloblastoma subgroups". Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology. 32 (9): 886–896. doi:10.1200/JCO.2013.50.9539. ISSN 1527-7755. PMC 3948094. PMID 24493713.
  62. ↑ 62.0 62.1 62.2 62.3 Taylor, Michael D.; et al. (2012-04). "Molecular subgroups of medulloblastoma: the current consensus". Acta Neuropathologica. 123 (4): 465–472. doi:10.1007/s00401-011-0922-z. ISSN 1432-0533. PMC 3306779. PMID 22134537. Check date values in: |date= (help)
  63. ↑ Goschzik, Tobias; et al. (2015-02). "Molecular stratification of medulloblastoma: comparison of histological and genetic methods to detect Wnt activated tumours". Neuropathology and Applied Neurobiology. 41 (2): 135–144. doi:10.1111/nan.12161. ISSN 1365-2990. PMID 24894640. Check date values in: |date= (help)
  64. ↑ Ellison, David W.; et al. (2005-11-01). "beta-Catenin status predicts a favorable outcome in childhood medulloblastoma: the United Kingdom Children's Cancer Study Group Brain Tumour Committee". Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology. 23 (31): 7951–7957. doi:10.1200/JCO.2005.01.5479. ISSN 0732-183X. PMID 16258095.
  65. ↑ 65.0 65.1 65.2 65.3 Kool, Marcel; et al. (2012-04). "Molecular subgroups of medulloblastoma: an international meta-analysis of transcriptome, genetic aberrations, and clinical data of WNT, SHH, Group 3, and Group 4 medulloblastomas". Acta Neuropathologica. 123 (4): 473–484. doi:10.1007/s00401-012-0958-8. ISSN 1432-0533. PMC 3306778. PMID 22358457. Check date values in: |date= (help)
  66. ↑ 66.0 66.1 66.2 66.3 Northcott, Paul A.; et al. (2014-07-24). "Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma". Nature. 511 (7510): 428–434. doi:10.1038/nature13379. ISSN 1476-4687. PMC 4201514. PMID 25043047.
  67. ↑ 67.0 67.1 67.2 67.3 Pugh, Trevor J.; et al. (2012-08-02). "Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations". Nature. 488 (7409): 106–110. doi:10.1038/nature11329. ISSN 1476-4687. PMC 3413789. PMID 22820256.
  68. ↑ 68.0 68.1 68.2 68.3 68.4 68.5 68.6 Thompson, Eric M.; et al. (2016-04). "Prognostic value of medulloblastoma extent of resection after accounting for molecular subgroup: a retrospective integrated clinical and molecular analysis". The Lancet. Oncology. 17 (4): 484–495. doi:10.1016/S1470-2045(15)00581-1. ISSN 1474-5488. PMC 4907853. PMID 26976201. Check date values in: |date= (help)
  69. ↑ Northcott, Paul A.; et al. (2011-04-10). "Medulloblastoma comprises four distinct molecular variants". Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology. 29 (11): 1408–1414. doi:10.1200/JCO.2009.27.4324. ISSN 1527-7755. PMC 4874239. PMID 20823417.
  70. ↑ 70.0 70.1 70.2 70.3 Rausch, Tobias; et al. (2012-01-20). "Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations". Cell. 148 (1–2): 59–71. doi:10.1016/j.cell.2011.12.013. ISSN 1097-4172. PMC 3332216. PMID 22265402.
  71. ↑ 71.0 71.1 71.2 71.3 Northcott, Paul A; et al. (2012-12). "Medulloblastomics: The End of the Beginning". Nature reviews. Cancer. 12 (12): 818–834. doi:10.1038/nrc3410. ISSN 1474-175X. PMC 3889646. PMID 23175120. Check date values in: |date= (help)
  72. ↑ 72.0 72.1 72.2 72.3 Thompson, Margaret C.; et al. (2006-04-20). "Genomics identifies medulloblastoma subgroups that are enriched for specific genetic alterations". Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology. 24 (12): 1924–1931. doi:10.1200/JCO.2005.04.4974. ISSN 1527-7755. PMID 16567768.
  73. ↑ 73.0 73.1 73.2 73.3 Rutkowski, Stefan; et al. (2010-11-20). "Survival and prognostic factors of early childhood medulloblastoma: an international meta-analysis". Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology. 28 (33): 4961–4968. doi:10.1200/JCO.2010.30.2299. ISSN 1527-7755. PMID 20940197.
  74. ↑ Kool, Marcel; et al. (2014-03-17). "Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition". Cancer Cell. 25 (3): 393–405. doi:10.1016/j.ccr.2014.02.004. ISSN 1878-3686. PMC 4493053. PMID 24651015.
  75. ↑ Northcott, Paul A.; et al. (2011-08). "Pediatric and adult sonic hedgehog medulloblastomas are clinically and molecularly distinct". Acta Neuropathologica. 122 (2): 231–240. doi:10.1007/s00401-011-0846-7. ISSN 1432-0533. PMC 4538327. PMID 21681522. Check date values in: |date= (help)
  76. ↑ Gajjar, Amar; et al. (2013-11-15). "Phase I study of vismodegib in children with recurrent or refractory medulloblastoma: a pediatric brain tumor consortium study". Clinical Cancer Research: An Official Journal of the American Association for Cancer Research. 19 (22): 6305–6312. doi:10.1158/1078-0432.CCR-13-1425. ISSN 1557-3265. PMC 3856244. PMID 24077351.
  77. ↑ Spence, Tara; et al. (2014-08). "CNS-PNETs with C19MC amplification and/or LIN28 expression comprise a distinct histogenetic diagnostic and therapeutic entity". Acta Neuropathologica. 128 (2): 291–303. doi:10.1007/s00401-014-1291-1. ISSN 1432-0533. PMC 4159569. PMID 24839957. Check date values in: |date= (help)
  78. ↑ Gessi, Marco; et al. (2014-07). "MYCN amplification predicts poor outcome for patients with supratentorial primitive neuroectodermal tumors of the central nervous system". Neuro-Oncology. 16 (7): 924–932. doi:10.1093/neuonc/not302. ISSN 1523-5866. PMC 4057132. PMID 24470553. Check date values in: |date= (help)
  79. ↑ Korshunov, Andrey; et al. (2014-08). "Embryonal tumor with abundant neuropil and true rosettes (ETANTR), ependymoblastoma, and medulloepithelioma share molecular similarity and comprise a single clinicopathological entity". Acta Neuropathologica. 128 (2): 279–289. doi:10.1007/s00401-013-1228-0. ISSN 1432-0533. PMC 4102829. PMID 24337497. Check date values in: |date= (help)
  80. ↑ Nobusawa, Sumihito; et al. (2012-09). "Analysis of chromosome 19q13.42 amplification in embryonal brain tumors with ependymoblastic multilayered rosettes". Brain Pathology (Zurich, Switzerland). 22 (5): 689–697. doi:10.1111/j.1750-3639.2012.00574.x. ISSN 1750-3639. PMID 22324795. Check date values in: |date= (help)
  81. ↑ Korshunov, Andrey; et al. (2010-08). "Focal genomic amplification at 19q13.42 comprises a powerful diagnostic marker for embryonal tumors with ependymoblastic rosettes". Acta Neuropathologica. 120 (2): 253–260. doi:10.1007/s00401-010-0688-8. ISSN 1432-0533. PMID 20407781. Check date values in: |date= (help)
  82. ↑ Pfister, Stefan; et al. (2009-04). "Novel genomic amplification targeting the microRNA cluster at 19q13.42 in a pediatric embryonal tumor with abundant neuropil and true rosettes". Acta Neuropathologica. 117 (4): 457–464. doi:10.1007/s00401-008-0467-y. ISSN 1432-0533. PMID 19057917. Check date values in: |date= (help)
  83. ↑ Sturm, Dominik; et al. (2016-02-25). "New Brain Tumor Entities Emerge from Molecular Classification of CNS-PNETs". Cell. 164 (5): 1060–1072. doi:10.1016/j.cell.2016.01.015. ISSN 1097-4172. PMC 5139621. PMID 26919435.
  84. ↑ Picard, Daniel; et al. (2012-08). "Markers of survival and metastatic potential in childhood CNS primitive neuro-ectodermal brain tumours: an integrative genomic analysis". The Lancet. Oncology. 13 (8): 838–848. doi:10.1016/S1470-2045(12)70257-7. ISSN 1474-5488. PMC 3615440. PMID 22691720. Check date values in: |date= (help)
  85. ↑ von Bueren, André O.; et al. (2012-09). "DNA copy number alterations in central primitive neuroectodermal tumors and tumors of the pineal region: an international individual patient data meta-analysis". Journal of Neuro-Oncology. 109 (2): 415–423. doi:10.1007/s11060-012-0911-7. ISSN 1573-7373. PMID 22772606. Check date values in: |date= (help)
  86. ↑ Safaee, Michael; et al. (2013-03). "Choroid plexus papillomas: advances in molecular biology and understanding of tumorigenesis". Neuro-Oncology. 15 (3): 255–267. doi:10.1093/neuonc/nos289. ISSN 1523-5866. PMC 3578480. PMID 23172371. Check date values in: |date= (help)
  87. ↑ 87.0 87.1 Japp, Anna Sophia; et al. (2015-02). "High-resolution genomic analysis does not qualify atypical plexus papilloma as a separate entity among choroid plexus tumors". Journal of Neuropathology and Experimental Neurology. 74 (2): 110–120. doi:10.1097/NEN.0000000000000154. ISSN 1554-6578. PMID 25575132. Check date values in: |date= (help)
  88. ↑ 88.0 88.1 Merino, Diana M.; et al. (2015-01-01). "Molecular characterization of choroid plexus tumors reveals novel clinically relevant subgroups". Clinical Cancer Research: An Official Journal of the American Association for Cancer Research. 21 (1): 184–192. doi:10.1158/1078-0432.CCR-14-1324. ISSN 1557-3265. PMID 25336695.
  89. ↑ Rickert, Christian H.; et al. (2002-03). "Chromosomal imbalances in choroid plexus tumors". The American Journal of Pathology. 160 (3): 1105–1113. doi:10.1016/S0002-9440(10)64931-0. ISSN 0002-9440. PMC 1867193. PMID 11891207. Check date values in: |date= (help)
  90. ↑ Ruland, Vincent; et al. (2014-05). "Choroid plexus carcinomas are characterized by complex chromosomal alterations related to patient age and prognosis". Genes, Chromosomes & Cancer. 53 (5): 373–380. doi:10.1002/gcc.22148. ISSN 1098-2264. PMID 24478045. Check date values in: |date= (help)
  91. ↑ Gozali, Alexa E.; et al. (2012-06). "Choroid plexus tumors; management, outcome, and association with the Li-Fraumeni syndrome: the Children's Hospital Los Angeles (CHLA) experience, 1991-2010". Pediatric Blood & Cancer. 58 (6): 905–909. doi:10.1002/pbc.23349. ISSN 1545-5017. PMID 21990040. Check date values in: |date= (help)
  92. ↑ Nupponen, Nina N.; et al. (2008-03). "Platelet-derived growth factor receptor expression and amplification in choroid plexus carcinomas". Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc. 21 (3): 265–270. doi:10.1038/modpathol.3800989. ISSN 0893-3952. PMID 18157090. Check date values in: |date= (help)
  93. ↑ Theeler, Brett J.; et al. (2014-06). "Adult pilocytic astrocytomas: clinical features and molecular analysis". Neuro-Oncology. 16 (6): 841–847. doi:10.1093/neuonc/not246. ISSN 1523-5866. PMC 4022218. PMID 24470550. Check date values in: |date= (help)
  94. ↑ Strowd, Roy E.; et al. (2016-06). "Histologically benign, clinically aggressive: Progressive non-optic pathway pilocytic astrocytomas in adults with NF1". American Journal of Medical Genetics. Part A. 170 (6): 1455–1461. doi:10.1002/ajmg.a.37622. ISSN 1552-4833. PMC 4938896. PMID 26992069. Check date values in: |date= (help)
  95. ↑ 95.0 95.1 95.2 Chappé, Céline; et al. (2013-09). "Dysembryoplastic neuroepithelial tumors share with pleomorphic xanthoastrocytomas and gangliogliomas BRAF(V600E) mutation and expression". Brain Pathology (Zurich, Switzerland). 23 (5): 574–583. doi:10.1111/bpa.12048. ISSN 1750-3639. PMID 23442159. Check date values in: |date= (help)
  96. ↑ Vaubel, Rachael A.; et al. (2018-03). "Recurrent copy number alterations in low-grade and anaplastic pleomorphic xanthoastrocytoma with and without BRAF V600E mutation". Brain Pathology (Zurich, Switzerland). 28 (2): 172–182. doi:10.1111/bpa.12495. ISSN 1750-3639. PMC 5807227. PMID 28181325. Check date values in: |date= (help)
  97. ↑ Prabowo, Avanita S.; et al. (2015-10). "Landscape of chromosomal copy number aberrations in gangliogliomas and dysembryoplastic neuroepithelial tumours". Neuropathology and Applied Neurobiology. 41 (6): 743–755. doi:10.1111/nan.12235. ISSN 1365-2990. PMID 25764012. Check date values in: |date= (help)
  98. ↑ Rivera, Barbara; et al. (2016-06). "Germline and somatic FGFR1 abnormalities in dysembryoplastic neuroepithelial tumors". Acta Neuropathologica. 131 (6): 847–863. doi:10.1007/s00401-016-1549-x. ISSN 1432-0533. PMC 5039033. PMID 26920151. Check date values in: |date= (help)
  99. ↑ Thom, Maria; et al. (2011-10). "One hundred and one dysembryoplastic neuroepithelial tumors: an adult epilepsy series with immunohistochemical, molecular genetic, and clinical correlations and a review of the literature". Journal of Neuropathology and Experimental Neurology. 70 (10): 859–878. doi:10.1097/NEN.0b013e3182302475. ISSN 1554-6578. PMID 21937911. Check date values in: |date= (help)
  100. ↑ Kitamura, Yohei; et al. (2018-01). "Comprehensive genetic characterization of rosette-forming glioneuronal tumors: independent component analysis by tissue microdissection". Brain Pathology (Zurich, Switzerland). 28 (1): 87–93. doi:10.1111/bpa.12468. ISSN 1750-3639. PMID 27893178. Check date values in: |date= (help)
  101. ↑ Bidinotto, Lucas Tadeu; et al. (2015). "Molecular Profiling of a Rare Rosette-Forming Glioneuronal Tumor Arising in the Spinal Cord". PloS One. 10 (9): e0137690. doi:10.1371/journal.pone.0137690. ISSN 1932-6203. PMC 4570813. PMID 26371886.
  102. ↑ 102.0 102.1 Eckel-Passow, Jeanette E.; et al. (2015-06-25). "Glioma Groups Based on 1p/19q, IDH, and TERT Promoter Mutations in Tumors". The New England Journal of Medicine. 372 (26): 2499–2508. doi:10.1056/NEJMoa1407279. ISSN 1533-4406. PMC 4489704. PMID 26061753.
  103. ↑ 103.0 103.1 Neill, Stewart G.; et al. (2014-09-XX). "Section III: molecular diagnostics in neuro-oncology". Current Problems in Cancer. 38 (5): 175–179. doi:10.1016/j.currproblcancer.2014.08.006. ISSN 1535-6345. PMID 25263767. Check date values in: |date= (help)
  104. ↑ 104.0 104.1 104.2 104.3 104.4 Ellison, David W. (2015-06-25). "Multiple Molecular Data Sets and the Classification of Adult Diffuse Gliomas". The New England Journal of Medicine. 372 (26): 2555–2557. doi:10.1056/NEJMe1506813. ISSN 1533-4406. PMID 26061754.
  105. ↑ 105.0 105.1 105.2 105.3 Park, Sung-Hye; et al. (2017-05). "Molecular Testing of Brain Tumor". Journal of Pathology and Translational Medicine. 51 (3): 205–223. doi:10.4132/jptm.2017.03.08. ISSN 2383-7837. PMC 5445205. PMID 28535583. Check date values in: |date= (help)
  106. ↑ 106.0 106.1 106.2 106.3 Cohen, Adam; et al. (2015-06-20). "DNA copy number analysis of Grade II-III and Grade IV gliomas reveals differences in molecular ontogeny including chromothripsis associated with IDH mutation status". Acta Neuropathologica Communications. 3: 34. doi:10.1186/s40478-015-0213-3. ISSN 2051-5960. PMC 4474351. PMID 26091668.
  107. ↑ Olar, Adriana; et al. (2015-04). "IDH mutation status and role of WHO grade and mitotic index in overall survival in grade II-III diffuse gliomas". Acta Neuropathologica. 129 (4): 585–596. doi:10.1007/s00401-015-1398-z. ISSN 1432-0533. PMC 4369189. PMID 25701198. Check date values in: |date= (help)
  108. ↑ Lhotska, Halka; et al. (2016). "Primary and recurrent diffuse astrocytomas: genomic profile comparison reveals acquisition of biologically relevant aberrations". Molecular Cytogenetics. 9: 13. doi:10.1186/s13039-016-0222-3. ISSN 1755-8166. PMC 4748601. PMID 26865861.
  109. ↑ Qaddoumi, Ibrahim; et al. (2016-06). "Genetic alterations in uncommon low-grade neuroepithelial tumors: BRAF, FGFR1, and MYB mutations occur at high frequency and align with morphology". Acta Neuropathologica. 131 (6): 833–845. doi:10.1007/s00401-016-1539-z. ISSN 1432-0533. PMC 4866893. PMID 26810070. Check date values in: |date= (help)
  110. ↑ Kamoun, Aurélie; et al. (2016-04-19). "Integrated multi-omics analysis of oligodendroglial tumours identifies three subgroups of 1p/19q co-deleted gliomas". Nature Communications. 7: 11263. doi:10.1038/ncomms11263. ISSN 2041-1723. PMC 4838899. PMID 27090007.
  111. ↑ Alentorn, Agustí; et al. (2014-03). "Clinical value of chromosome arms 19q and 11p losses in low-grade gliomas". Neuro-Oncology. 16 (3): 400–408. doi:10.1093/neuonc/not227. ISSN 1523-5866. PMC 3922518. PMID 24335697. Check date values in: |date= (help)
  112. ↑ Rice, Terri; et al. (2016-03). "Understanding inherited genetic risk of adult glioma - a review". Neuro-Oncology Practice. 3 (1): 10–16. doi:10.1093/nop/npv026. ISSN 2054-2577. PMC 4774334. PMID 26941959. Check date values in: |date= (help)
  113. ↑ 113.0 113.1 Geisenberger, Christoph; et al. (2015-09). "Molecular profiling of long-term survivors identifies a subgroup of glioblastoma characterized by chromosome 19/20 co-gain". Acta Neuropathologica. 130 (3): 419–434. doi:10.1007/s00401-015-1427-y. ISSN 1432-0533. PMID 25931051. Check date values in: |date= (help)
  114. ↑ 114.0 114.1 Louis, David N.; et al. (2016-06). "The 2016 World Health Organization Classification of Tumors of the Central Nervous System: a summary". Acta Neuropathologica. 131 (6): 803–820. doi:10.1007/s00401-016-1545-1. ISSN 1432-0533. PMID 27157931. Check date values in: |date= (help)
  115. ↑ Liu, Qun; et al. (2015-10). "Genetic, epigenetic, and molecular landscapes of multifocal and multicentric glioblastoma". Acta Neuropathologica. 130 (4): 587–597. doi:10.1007/s00401-015-1470-8. ISSN 1432-0533. PMC 4776337. PMID 26323991. Check date values in: |date= (help)
  116. ↑ 116.0 116.1 116.2 Och, Waldemar; et al. (2016-11-XX). "Recurrence-associated chromosomal anomalies in meningiomas: Single-institution study and a systematic review with meta-analysis". Neurologia I Neurochirurgia Polska. 50 (6): 439–448. doi:10.1016/j.pjnns.2016.08.003. ISSN 0028-3843. PMID 27575681. Check date values in: |date= (help)
  117. ↑ 117.0 117.1 117.2 117.3 117.4 Lee, Yohan; et al. (2010-07). "Genomic landscape of meningiomas". Brain Pathology (Zurich, Switzerland). 20 (4): 751–762. doi:10.1111/j.1750-3639.2009.00356.x. ISSN 1750-3639. PMC 3167483. PMID 20015288. Check date values in: |date= (help)
  118. ↑ Jansen, M.; et al. (2012-04). "Gain of chromosome arm 1q in atypical meningioma correlates with shorter progression-free survival". Neuropathology and Applied Neurobiology. 38 (2): 213–219. doi:10.1111/j.1365-2990.2011.01222.x. ISSN 1365-2990. PMC 3563294. PMID 21988727. Check date values in: |date= (help)
  119. ↑ 119.0 119.1 119.2 Gabeau-Lacet, Darlene; et al. (2009-10). "Genomic profiling of atypical meningiomas associates gain of 1q with poor clinical outcome". Journal of Neuropathology and Experimental Neurology. 68 (10): 1155–1165. doi:10.1097/NEN.0b013e3181ba3952. ISSN 1554-6578. PMC 2847373. PMID 19918127. Check date values in: |date= (help)
  120. ↑ 120.0 120.1 120.2 Abedalthagafi, Malak S.; et al. (2014-11-15). "Angiomatous meningiomas have a distinct genetic profile with multiple chromosomal polysomies including polysomy of chromosome 5". Oncotarget. 5 (21): 10596–10606. doi:10.18632/oncotarget.2517. ISSN 1949-2553. PMC 4279396. PMID 25347344.
  121. ↑ 121.0 121.1 121.2 Brastianos, Priscilla K.; et al. (2013-03). "Genomic sequencing of meningiomas identifies oncogenic SMO and AKT1 mutations". Nature Genetics. 45 (3): 285–289. doi:10.1038/ng.2526. ISSN 1546-1718. PMC 3739288. PMID 23334667. Check date values in: |date= (help)
  122. ↑ 122.0 122.1 122.2 Abedalthagafi, Malak S.; et al. (2015-06). "ARID1A and TERT promoter mutations in dedifferentiated meningioma". Cancer Genetics. 208 (6): 345–350. doi:10.1016/j.cancergen.2015.03.005. ISSN 2210-7762. PMC 4882906. PMID 25963524. Check date values in: |date= (help)
  123. ↑ 123.0 123.1 123.2 Abedalthagafi, Malak; et al. (2016-05). "Oncogenic PI3K mutations are as common as AKT1 and SMO mutations in meningioma". Neuro-Oncology. 18 (5): 649–655. doi:10.1093/neuonc/nov316. ISSN 1523-5866. PMC 4827048. PMID 26826201. Check date values in: |date= (help)
  124. ↑ 124.0 124.1 124.2 Harmancı, Akdes Serin; et al. (2017-02-14). "Integrated genomic analyses of de novo pathways underlying atypical meningiomas". Nature Communications. 8: 14433. doi:10.1038/ncomms14433. ISSN 2041-1723. PMC 5316884. PMID 28195122.
  125. ↑ 125.0 125.1 125.2 Aizer, Ayal A.; et al. (2016-02). "A prognostic cytogenetic scoring system to guide the adjuvant management of patients with atypical meningioma". Neuro-Oncology. 18 (2): 269–274. doi:10.1093/neuonc/nov177. ISSN 1523-5866. PMC 4724184. PMID 26323607. Check date values in: |date= (help)
  126. ↑ 126.0 126.1 126.2 Büschges, Rainer; et al. (2002-04). "Allelic gain and amplification on the long arm of chromosome 17 in anaplastic meningiomas". Brain Pathology (Zurich, Switzerland). 12 (2): 145–153. doi:10.1111/j.1750-3639.2002.tb00429.x. ISSN 1015-6305. PMID 11958368. Check date values in: |date= (help)
  127. ↑ 127.0 127.1 127.2 Domingues, Patrícia; et al. (2015-05-10). "Genetic/molecular alterations of meningiomas and the signaling pathways targeted". Oncotarget. 6 (13): 10671–10688. doi:10.18632/oncotarget.3870. ISSN 1949-2553. PMC 4484411. PMID 25965831.
  128. ↑ 128.0 128.1 128.2 Domingues, Patrícia Henriques; et al. (2014-05). "Proposal for a new risk stratification classification for meningioma based on patient age, WHO tumor grade, size, localization, and karyotype". Neuro-Oncology. 16 (5): 735–747. doi:10.1093/neuonc/not325. ISSN 1523-5866. PMC 3984558. PMID 24536048. Check date values in: |date= (help)
  129. ↑ 129.0 129.1 129.2 Linsler, Stefan; et al. (2014). "Molecular biological determinations of meningioma progression and recurrence". PloS One. 9 (4): e94987. doi:10.1371/journal.pone.0094987. ISSN 1932-6203. PMC 3983248. PMID 24722350.
  130. ↑ 130.0 130.1 130.2 Arslantas, Ali; et al. (2003-01). "Detection of chromosomal imbalances in spinal meningiomas by comparative genomic hybridization". Neurologia Medico-Chirurgica. 43 (1): 12–18, discussion 19. doi:10.2176/nmc.43.12. ISSN 0470-8105. PMID 12568317. Check date values in: |date= (help)
  131. ↑ 131.0 131.1 131.2 Bi, Wenya Linda; et al. (2016-09). "Genomic landscape of intracranial meningiomas". Journal of Neurosurgery. 125 (3): 525–535. doi:10.3171/2015.6.JNS15591. ISSN 1933-0693. PMID 26771848. Check date values in: |date= (help)
  132. ↑ 132.0 132.1 132.2 Bi, Wenya Linda; et al. (2016-04). "Genomic and Epigenomic Landscape in Meningioma". Neurosurgery Clinics of North America. 27 (2): 167–179. doi:10.1016/j.nec.2015.11.009. ISSN 1558-1349. PMID 27012381. Check date values in: |date= (help)
  133. ↑ 133.0 133.1 133.2 Och, Waldemar; et al. (2016-11-XX). "The correlation of clinical and chromosomal alterations of benign meningiomas and their recurrences". Neurologia I Neurochirurgia Polska. 50 (6): 395–402. doi:10.1016/j.pjnns.2016.07.001. ISSN 0028-3843. PMID 27480481. Check date values in: |date= (help)
  134. ↑ 134.0 134.1 134.2 Yuzawa, Sayaka; et al. (2016-10). "Genetic landscape of meningioma". Brain Tumor Pathology. 33 (4): 237–247. doi:10.1007/s10014-016-0271-7. ISSN 1861-387X. PMID 27624470. Check date values in: |date= (help)
  135. ↑ 135.0 135.1 135.2 Bi, Wenya Linda; et al. (2016). "Meningioma Genomics: Diagnostic, Prognostic, and Therapeutic Applications". Frontiers in Surgery. 3: 40. doi:10.3389/fsurg.2016.00040. ISSN 2296-875X. PMC 4933705. PMID 27458586.
  136. ↑ 136.0 136.1 136.2 Ketter, Ralf; et al. (2007-06). "Hyperdiploidy defines a distinct cytogenetic entity of meningiomas". Journal of Neuro-Oncology. 83 (2): 213–221. doi:10.1007/s11060-006-9318-7. ISSN 0167-594X. PMID 17225936. Check date values in: |date= (help)
  137. ↑ Wu, Jing; et al. (2016-07). "Biology and management of ependymomas". Neuro-Oncology. 18 (7): 902–913. doi:10.1093/neuonc/now016. ISSN 1523-5866. PMC 4896548. PMID 27022130. Check date values in: |date= (help)
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