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

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

Table 1: Pediatric CNS Tumors. 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. 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

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