Mutation profiling of anaplastic ependymoma grade III by Ion Proton next generation DNA sequencing

Introduction

Ependymal cells are macroglial cells which line the ventricles, the central canal of the spinal cord and form the blood-cerebrospinal fluid barrier, being involved in producing the cerebrospinal fluid^1,2. These tumors account for only 4–8% of gliomas and, after astrocytomas and oligodendrogliomas, ependymomas are the least common³. Nearly one-third of brain tumors in patients younger than three years old are ependymomas and constitute around 5%–9% of all neuroepithelial malignancies^1,4. These tumors are also found in the choroid plexus and may occur at any age, from one month to 81 years and without any gender preference⁵. In pediatric cases, the location of the tumor is intracranial, while adult ependymal tumors can have either an intracranial or a spinal localization^6,7. The prognosis is better in older children as compared to young infants but nonetheless, in children with intracranial ependymomas, event-free survival after five years is less than 50%⁸. In adults, about 50% to 60% intracranial ependymomas are supratentorial; however, pediatric supratentorial ependymomas account for 25% to 35% of all ependymomas^5,9. Adults present better prognosis with a 5-year survival of around 90%, while in the pediatric population it is around 60%. The five-year survival rate for supratentorial, infratentorial, and spinal cord ependymomas is 62%, 85%, and 97%, respectively, and for grade I, II, and III spinal cord ependymomas the five-year overall survival rate is 92%, 97% and 58%, respectively^10–12.

Ependymoma tumors are well circumscribed, soft, tan-red masses and may be associated with hemorrhage. Their microscopic appearance shows hypercellularity and distinct infiltrative margins with surrounding parenchyma, consisting of monomorphic cells with nuclear atypia and brisk mitotic activity. They may also have intramural or glomeruliod vascular proliferation, pseudopalisading necrosis, perivascular pseudo rosettes (5–10% cases), calcifications and hyalinized vessels¹. Other diagnostic hallmarks include areas of fibrillary and regressive changes such as myxoid degeneration, palisading necrotic areas and the formation of true rosettes, composed of columnar cells arranged around a central lumen^1,6. Immunologically, they are positive for epithelial membrane antigen (EMA), glial fibrillary acidic protein (GFAP) and S-100. According to the 2016 updated World Health Organization (WHO) classification of brain tumors, ependymomas are divided into 4 types on the basis of histologic appearance: (1) grade I subependymomas, (2) grade I myxopapillary ependymomas, (3) grade II ependymomas, (4) grade II or III RELA fusion-positive ependymomas and grade III anaplastic ependymomas^13,14.

Previous studies have shown the use of comparative genomic hybridization (CGH) arrays to distinguish intracranial ependymomas from spinal ependymomas¹⁵. In contrast to other types of brain tumors, histological grading is not a good prognostic marker for outcome for ependymomas^16,17. Several gene expression studies have been helpful in differentiating between intracranial and extra cranial ependymomas, but have not had clinical significance in directing therapy and their role in tumor origin and prognosis is not clear^18,19. Studies using cDNA micro-arrays have shown that gene expression patterns in ependymomas correlate with tumor location, grade and patient age²⁰. Cytogenetic studies have shown that chromosomal abnormalities are relatively common in ependymomas²¹. Loss of 22q has been the commonest abnormality found in ependymoma and, in some other tumors, gain of 1q or loss of 6q was observed^21,22.

To date, there is a lack of information regarding the mutational signatures which distinguish the various subgroups of ependymomas. Another ependymoma cohort study found very few mutations and gene amplifications but a high expression of multi-drug resistance, DNA repair and synthesis enzymes²³. Intracranial ependymomas differ from spinal ependymomas in the expression of these proteins, and protein expression is also dependent on the ependymoma grade²³. For both intracranial and spinal ependymomas, very few mutations were reported by using whole exome sequencing²⁴. In another study, profiling of NGS mutations was carried out for one case of grade II ependymoma using a GlioSeq panel, which contains a total of 30 genes²⁵. In order to determine the mutational patterns of grade III anaplastic ependymoma, we have sequenced DNA from this ependymoma tumor using the Ion Proton system for next generation DNA sequencing with the Ion Torrent’s AmpliSeq cancer HotSpot panel. This panel contains 50 genes, only 15 of which also appear in the GlioSeq panel used in previous research. These data provided an evaluation of mutational signatures of this anaplastic ependymoma which differs from the previous two studies, but confirms their conclusions about finding very few mutations in cancer driver genes, helping to direct diagnosis and therapy for ependymomal tumors.

Methods

Results

Clinical presentation and radiology

A six-year-old female patient presented with a history of right facial palsy for few months with ataxia and right-sided weakness. The patient had a chronic headache, vomiting and had repeatedly been treated for sinusitis. Unenhanced computed tomography (CT) of the brain was performed (Figure 1, panels A, B and C). A large lesion (5.4 × 7.5cm) was noticed in the left cerebral frontoparietal region. There was an indication of a predominant cystic component and large, eccentric clump of coarse calcification. Additionally, mass effect resulting in midline shift, along with mild scalloping of the internal cortex of the parietal bone, was noted. No hydrocephalic changes or intrinsic hemorrhagic focus were seen (Figure 1).

Figure 1. Grade III ependymoma unenhanced computed tomography (CT) of the brain.

A large lesion (5.4 × 7.5cm) in the left cerebral frontoparietal location with predominantly cystic components (panel A, green arrow), and a large, eccentric clump of coarse calcification (panel B; yellow arrow). Mass effect and mid line shift (panel C, red arrow) can also be seen. No hydrocephalic changes or intrinsic active hemorrhagic focus were observed.

Histopathological examination revealed sheets of neoplastic cells with round to oval nuclei and abundant granular chromatin. A variable dense fibrillary background and endothelial proliferation was also noted. Hematoxylin and eosin (H&E) staining results are shown in Figure 2 and Figure 3. Panels A and B of Figure 2 show the tumor exhibiting delicate cytoplasmic processes, perivascular rosettes characteristic of ependymoma, focal calcification areas and pseudo palisading necrosis, characterized by a garland-like structure of hypercellular tumor nuclei lining up around irregular foci of tumor necrosis. Panel C shows glomeruloid vascular proliferation and panel D shows extensive palisading necrosis and true rosette formation. The exhibition of a true rosette with a central lumen and the formation of pseudo-palisading necrotic areas is also clear from Figure 3 (panel A). Panel B shows focal areas with numerous tumor giant cells and the presence of brisk mitotic activity, vascular formation and pseudo-palisading necrotic areas. Formation of true rosettes surrounding the microvascular proliferation within ependymal tumors usually signifies anaplastic transformation, which is characteristic of grade III ependymoma (panels C and D). Immunostaining is shown in Figure 4: (A) Ki-67 stain shows a high proliferation index, (B) vimentin positive, (C) GFAP positive, (D) EMA showing punctate cytoplasmic (perinuclear dot-like positivity) staining which is fairly diagnostic of ependymal tumor cells. Figure 5 shows beta-catenin positive (panels A and B) and E-cadherin positive (panels C and D) immunostaining, with both membranous and true rosette-like structures clearly visible in this staining. EGFR staining was negative (see Underlying data)³³.

Figure 2. Hematoxylin and eosin (H&E) staining showing anaplastic ependymoma features.

(A) Focal calcification areas (blue arrow), and perivascular pseudo-rosettes (white arrow). (B) Pseudo palisading necrosis, characterized by a garland-like structure of hypercellular tumor nuclei (black arrow) lining up around irregular foci of tumor necrosis (blue arrow). (C) The cellular tumor exhibiting glomeruloid vascular proliferation (black arrows). (D) Extensive palisading necrosis (green arrows) and true rosettes (yellow arrows).

Figure 3. Hematoxylin and eosin (H&E) staining showing anaplastic ependymoma features.

(A) Pseudo palisading necrotic areas, exhibiting true rosettes with central lumen (yellow arrow). (B) Focal areas with numerous tumor giant cells and the presence of a brisk mitotic activity (green arrows). (C) Tumor with vascular formation (yellow arrows) and pseudo palisading necrotic areas. (D) Formation of true rosettes (green arrows) surrounding the microvascular proliferation within ependymal tumors, usually signifies anaplastic transformation which is characteristic of ependymomas.

Figure 4. Photomicrographs of Ki-67, vimentin, GFAP, and EMA immunostaining of the ependymal tumor.

(A) Ki-67 immunostaining indicates a high proliferation index in the tumor (70%). (B) Vimentin stain is positive. (C) GFAP stain is positive. (D) EMA stain is positive and shows punctate cytoplasmic (perinuclear dot-like) staining, fairly diagnostic of the ependymal nature of the tumor cells.

Figure 5. Photomicrographs of beta-Catenin and E-Cadherin immunostaining of the ependymal tumor.

Immunostaining is strongly positive for beta-Catenin (panel A 20x, panel B 40x) and true rosettes (red arrows) and palisading cells (blue arrow) are clearly visible. E-Cadherin stain is also positive in this tumor. Red and blue arrows indicate tumor cells arranged in true rossettes and formation of palisading structures, respectively (panel C 20x, panel D 40x).

NGS data analysis variant identification and variant statistics

Alignment to the target regions (CHP2. 20131001.designed) of the reference genome (hg 19) was performed by the Ion Torrent Suite software v.5.0.2. For this tumor, NGS generated 6,252,341 mapped reads using the Ion PI v3 Chip, with more than 90% reads on target. Amplicon and target base read coverages for the sequencing are shown in Table 1. All 207 amplicons were sequenced with Ion AmpliSeq Cancer HotSpot Panel primer pool. As shown in Table 1, for this sample sequencing the uniformity of amplicon coverage was 95.17%, and the uniformity of base coverage on target was 94.81%. The average reads per amplicon was 34, 179, and the average target base coverage depth was 31,771. 100% of amplicons had at least 500 reads and the percentage of amplicons read end-to-end was 89.37% (Table 1). Initial analysis by the Ion Reporter 5.6 program found that a total of 1652 variants passed all filters. Initial analysis by Advaita’s iVariantGuide software showed 100% (1633) of variants passed all filters (see Extended data)³³. The filter flags signify variants which do not meet certain criteria during variant calling. The flags refer to the quality or confidence of the variant call. The parameters of flags were read in from the input vcf file. If a variant passes all filters, it is marked as having passed. Six hundred and fifteen variants were identified using a filter for clinical significance that identifies drug response, likely to be pathogenic and pathogenic variants. The distribution of these variants, based on chromosomal position, region within the gene, variant class, functional class, variant impact and clinical significance, are shown in doughnut charts A – F (Figure 6). As shown in doughnut chart A, chromosome 17 has the highest number of variants (26%) and chromosome 8 has lowest number of variants (0.8%). 98.7% of variants are exonic and, according to variant class distribution, 73.8% are SNPs, 70.2% are missense variants, 25.4% are high impact variants and 46.8% are pathogenic. We have considered true mutations to be those with a Phred score above 20 and significant mutations called by Ion Reporter software were those with a p-value below 0.05.

Table 1. Coverage analysis of the tumor DNA sequencing on Ion Proton.

Amplicon Read Coverage		Target Base Coverage
Number of amplicons	207	Bases in target regions	22,027
Percent assigned amplicon reads	97.53%	Percent base reads on target	89.69%
Average reads per amplicon	34, 179	Average base coverage depth	31,771
Uniformity of amplicon coverage	95.17%	Uniformity of base coverage	94.81%
Amplicons with at least 1 read	100%	Target base coverage at 1x	100%
Amplicons with at least 20 reads	100%	Target base coverage at 20x	100%
Amplicons with at least 100 reads	100%	Target base coverage at 100x	100%
Amplicons with at least 500 reads	100%	Target base coverage at 500x	100%
Amplicons with no strand bias	97.58%	Target bases with no strand bias	96.35%
Amplicons reading end-to-end	89.37%	Percent end-to-end reads	86.80%

Figure 6. iVariant analysis of variant characteristics.

Distribution of variants according to filters, showing characteristics including the relative number of variants located on each chromosome, variant class, substitution type and the functional consequences of each variant, in order to interpret and score the severity and impact of variants and therefore predict the severity of the disease. Doughnut charts in panels shows variants passed for each individual filter for (A) Chromosomal distribution, (B) Region in the gene, (C) Variant class, (D) Variant effect on the protein structure, (E) Variant impact on the protein function and (F) Clinical significance of the variants as annotated on the ClinVar database.

A summary of the all missense mutations found in the grade III tumor is shown in Table 2. In this tumor, NGS data analysis identified 19 variants, of which four were missense mutations, eight were synonymous mutations and seven were intronic variants. Known missense mutation c.395G>A; p.(Arg132His) in exon 4 of the IDH1 gene, c.1173A>G; p.(Ile391Met) in exon 7 of the PIK3CA gene, c.1416A>T; p.(Gln472His) in exon 11 of the KDR gene and c.215C>G; p.(Pro72Arg) in exon 4 of the TP53 gene were found in this tumor. The frequency, allele coverage, allele ratio, p-value and Phred score for these mutations is shown in Table 3. The p-values and Phred scores were significant for all of these mutations. The frequencies of the three missense mutations, namely PIK3CA c.1173A>G, KDR c.1416A>T and TP53 c.215C>G, were high, suggesting that these are germ line variants, whereas the IDH1 variant frequency was low (4.81%). As shown in Table 2, eight synonymous mutations were found in this tumor, in exon 14 of FGFR3 p.(Thr651Thr), exon 12 of PDGFRA p.(Pro566Pro), exon 20 of EGFR p.(Gln787Gln), exon 13 of RET p.(Leu769Leu), exon 2 of HRAS p.(His27His), exon 14 of FLT3 p.(Val592Val), exon 16 of APC p.(Thr1493Thr) and exon 9 of SMAD4 p.(Phe362Phe). The synonymous mutation in FLT3 (c.1776T>C; p.(Val592Val) detected in this tumor was a novel variant, while the other variants were previously reported. Additionally, two known intronic variants were identified in KDR (c.798+54G>A and c.2615-36A>CA) (Table 2). A known splice site mutation (c.1310-3T>C) at an acceptor site in FLT3 (rs2491231) and a single nucleotide variant in the 3’-UTR of the CSF1R gene (rs2066934) were also identified. Additionally, in SMARCB1 a 5’-UTR variant, and an intronic variant in ERBB4 and PIK3CA respectively were found. In Figure 7, the heat map of the variant impact for each gene is presented. The color gradation from green to red indicates unknown, synonymous, missense, nonsense, and splice variants, based upon their SIFT, PolyPhen2 and Grantham scores. Only variants in four genes had a positive PolyPhen2 score (variants in TP53, PIK3CA, IDH1 and KDR genes had a PolyPhen2 score of 0.083, 0.011, 0127 and 0.003, respectively). However, FATHMM scores for the prediction of the functional consequences of a variant suggest that only the IDH1 variant is pathogenic, with a score of 0.94. As described in the COSMIC data base, FATHMM scores above 0.5 are deleterious, but only scores ≥ 0.7 are classified as pathogenic.

Table 2. Variants found in the grade III ependymoma tumor.

Chromosomal Position	Ref	Observed Allele	% Frequency	Gene	Coding	COSMIC/ dbSNP	AA Change	Exon
chr2:209113112	CG	TG	4.81	IDH1	c.395G>A	COSM28746	p. (Arg132His)	4
chr2:212812097	T	C	100	ERBB4	c.421+58A>G	rs839541	p.?
chr3:178917005	A	G	47.97	PIK3CA	c.352+40A>G	rs3729674	p.?
chr3:178927410	A	G	54.25	PIK3CA	c.1173A>G	COSM328028	p. (Ile391Met)	7
chr4:1807894	G	A	100	FGFR3	c.1953G>A	rs7688609	p. (Thr651Thr)	14
chr4:55141050	AGCCCAGA	AGCCCGGA	100.00	PDGFRA	c.1701A>G	rs1873778	p. (Pro566Pro)	12
chr4:55962545	T	TG	43.46	KDR	c.2615-36A>CA	rs34085292	p.?
chr4:55972974	T	A	51.35	KDR	c.1416A>T	rs1870377 COSM149673	p. (Gln472His)	11
chr4:55980239	C	T	98.35	KDR	c.798+54G>A	rs7692791	p.?
chr5:112175769	CGG	CAG	CAG=100	APC	c.4479G>A	COSM3760869	p. (Thr1493Thr)	16
chr5:149433596	TG	GA	100	CSF1R, HMGXB3	c.*1841TG>GA, c.2954_ 2955delCAinsTC	rs2066934	p.?
chr7:55249063	G	A	71.04	EGFR, EGFR-AS1	c.2361G>A	rs1050171	p. (Gln787Gln)	20
rs1800861	G	T	100	RET	c.2307G>T	COSM4418405	p. (Leu769Leu)	13
chr11:534242	A	G	49.07	HRAS	c.81T>C	rs12628	p. (His27His)	2
chr13:28608280	A	G	53.5	FLT3	c.1776T>C	Novel	p. (Val592Val)	14
chr13:28610183	A	G	100	FLT3	c.1310-3T>C	rs2491231	p.?
chr17:7579472	G	C	C=47.94	TP53	c.215C>G	rs1042522	p. (Pro72Arg)	4
chr18:48591923	T	C	63.63	SMAD4	c.1086T>C	rs1801250	p. (Phe362Phe)	9
chr22:24176287	G	A	52.5	DERL3, SMARCB1	c.1119-41G>A, c.*727C>T	rs5030613	p.?	4

Table 3. Sequencing quality of variants found in the grade III ependymoma.

Genes	Coding	Allele Coverage	Allele Ratio	p-value	FATHMM predication	Phred Score	Coverage (x)
IDH1	c.395G>A	CG=1900, TG=96	CG=0.9519, TG=0.0481	0.00001	Pathogenic	221.064	1996
ERBB4	c.421+58A>G	C=1988	C=1.0	0.00001	NA	31774.6	1988
PIK3CA	c.352+40A>G	A=1038, G=957	A=0.5203, G=0.4797	0.00001	NA	9501.82	1995
PIK3CA	c.1173A>G	A=915, G=1085	A=0.4575, G=0.5425	0.00001	Benign	11555.8	2000
FGFR3	c.1953G>A	A=1993	A=1.0	0.00001	Benign	31840.6	1993
PDGFRA	c.1701A>G	AGCCCGGATGGACATG=1941	AGCCCGGATGGACATG=1.0	0.00001	Benign	35066.6	1941
KDR	c.2615-36A>CA	T=1124, TG=864	T=0.5654, TG=0.4346	0.00001	NA	5173.27	1988
KDR	c.1416A>T	T=971, A=1025	T=0.4865, A=0.5135	0.00001	Benign	10583.1	1996
KDR	c.798+54G>A	C=33, T=1965	C=0.0165, T=0.9835	0.00001	NA	30286.5	1998
APC	c.4479G>A	CAG=1985,	CAG=1.0	0.00001	Benign	35885.9	1985
CSF1R, HMGXB3	c.*1841TG>GA, c.2954_ 2955delCAinsTC	GA=1977	GA=1.0	0.00001	Benign	31540.7	1977
EGFR, EGFR-AS1	c.2361G>A	G=579, A=1420	G=0.2896, A=0.7104	0.00001	Benign	17657.6	1999
RET	c.2307G>T	T=1996	T=1.0	0.00001	Benign	31993.7	1996
HRAS	c.81T>C	A=1018, G=981	A=0.5093, G=0.4907	0.00001	Benign	11998.4	1999
FLT3	c.1776T>C	A=929, G=1069	A=0.465, G=0.535	0.00001	NA	11295.9	1998
FLT3	c.1310-3T>C	G=1998	G=1.0	0.00001	Benign	32026.3	1998
TP53	c.215C>G	G=1038, C=956	G=0.5206, C=0.4794	0.00001	Benign	11559.2	1994
SMAD4	c.1086T>C	T=727, C=1272	T=0.3637, C=0.6363	0.00001	Benign	14836.6	1999
DERL3, SMARCB1	c.1119-41G>A, c.*727C>T	G=950, A=1050	G=0.475, A=0.525	0.00001	NA	13246.6	2000

Figure 7. Heat Map showing variant impact of each gene detected in the ependymal tumor.

Variant impact takes into account the type of mutation (such as insertion, deletion or frame shift) and considers the location of the variant (intronic or exonic). The color gradation from green to red indicates unknown, synonymous, missense, nonsense and splice variants, calculated based upon their SIFT, PolyPhen2 and Grantham scores.

Discussion

Ependymomas are brain tumors that arise throughout the central nervous system, within the supratentorial areas, the posterior fossa and the spinal cord. Histologic low-grade (WHO grade I) tumors, such as subependymomas and myxopapillary ependymomas, are usually slow progressing variants of ependymomas. In contrast, grade III ependymomas display anaplastic features like hypercellularity, high mitosis, proliferation of endothelial cells and palisading necrosis³⁴. Histopathological evaluation of ependymoma tissue reveals pseudo-rosette formation, high mitotic activity, vascular proliferation and necrosis, EMA staining with perinuclear dot-like structures and with diffuse GFAP immunoreactivity³⁵. Immunological staining with GFAP and vimentin is very helpful for the differential diagnosis of ependymomas from other non-ependymal tumors, such as astrocytic and choroid plexus tumors, and also in differentiating between the various grades of ependymomas^13,14,36. It has been reported that the GFAP expression correlates with a loss of E-cadherin expression in anaplastic ependymomas, although in this case there was E-cadherin expression³⁶. Changes in E-cadherin expression promote tumor invasion and metastasis³⁷. Overexpression of EGFR is known to correlate with tumor grades in ependymomas (100%, 50%, and 0% in grade I, II and III, respectively)²³. The tumor in our case is grade III anaplastic ependymoma and it stained negatively for EGFR, confirming this observation. Based upon the expression profiles of numerous angiogenesis genes (HIF-1a signaling, VEGF signaling, cell migration) and signaling pathway genes (PDGF signaling, MAPK signaling, EGFR signaling), posterior fossa ependymomas are subdivided into two groups¹⁹. In this case, a diagnosis of anaplastic ependymoma (WHO grade III) was made upon the observation of the above characteristics for the tumor. The pathology of the resected tissue demonstrated a hypercellular tumor with areas of perivascular pseudo rosettes, consistent with a diagnosis of ependymoma.

Despite several investigations, the correlation between histological grading of ependymoma tumors and their prognosis is unclear^8,34,38. Apart from histopathological grading, previous studies have focused on gross deletions and chromosomal abnormalities through cytogenetic studies and array-CGH profiling of ependymomas^39,40. These studies helped to distinguish between intracranial and spinal cord ependymomas. Around 70% of supratentorial ependymas are known to carry a fusion gene which produces the C11orf95/RELA fusion transcript and the prognosis is poor for this tumor⁴¹. Ion Torrent PGM sequencing of a grade II ependymoma demonstrated MET and ATRX copy number gain²⁵. Overexpression of L1 cell adhesion molecule (L1CAM), 1q25 copy number gain and a homozygous deletion in CDKN2A was also reported in some aggressive supratentorial ependymomas⁴². However, in the present case we did not detect any MET or CDKN2A mutations using the Ion AmpliSeq Cancer HotSpot panel.

In the cancer genome atlas (TCGA) projects top mutated cancer genes were IDH1, TP53, EGFR, PIK3CA, and PDGFRA (cBioportal data base, https://www.cbioportal.org). The specific variants we found in the present ependymoma case such as in TP53, HRAS, SMAD4, PIK3CA are not in TCGA projects. However, genes that are mutated in this ependymoma tumor such as IDH1, TP53, and EGFR are in top 20 mutated cancer genes with high functional impact, other genes were not in top 20 genes in ICGC data portal (https://dcc.icgc.org). In the integrative onco-genomics data base (https://www.intogen.org/search?cancer) genes mutated such as, TP53 and PDGFRA are in high-grade glioma data from St. Jude children's research hospital (HGG_D_STJUDE), and IDH1, TP53, PIK3CA and EGFR, are most recurrently mutated cancer driver genes in GBM_TCGA dataset. Also, under ‘ependymoma’ only search, two cohorts are found, with total 94 samples. In the ependymoma – DKFZ cohort, (EPD_PRY_DKFZ_2017), total 55 samples are found. The IDH1 variant found in our case also detected as a mutational cancer driver in this cohort⁴³. Ependymoma data from St. Jude children's research hospital have 39 samples, and by WGS, PIK3CA is detected as a mutational cancer driver in the ependymoma cohort in 2 out of 39 (5.13%) samples (3:179203765: T>A; AA345, 3:179221147: A>C, AA726), were found to have mutation in this driver gene⁴¹.

Patients with neurofibromatosis type 2 are predisposed to the development of ependymomas, and the gene for neurofibromatosis type 2 (NF2) maps to chromosome 22 (q1216,17). Mutations in the NF2 gene are uncommon in sporadic ependymomas and appear to be restricted to spinal tumors⁴⁴. For spinal cord ependymomas, four out of eight tumors were found to have an NF2 mutation and all eight tumors had loss of heterozygosity (LOH) of chromosome 22, where the NF2 locus is found. However, five out of eight intracranial tumors exhibited LOH of chromosome 22 but no NF2 mutations²⁴. A high rate of truncating mutations such as nonsense and frameshift mutations in the NF2 gene were also reported previously in spinal ependymomas^45,46. Unfortunately, in the Ion AmpliSeq cancer HotSpot panel primer pool used in the present study NF2 gene was not included. The SMARCB1 germline mutations contribute to 10% of sporadic schwannomatosis. The SNP (rs5030613) found by us in this gene c.1119-41G>A is also reported in Schwannomatosis⁴⁷. However, this SNP was not reported previously in ependymomas.

We have verified all mutations in various databases (COSMIC, ExAc and dbSNP) to confirm whether variants are novel. Only one detected in our case, a synonymous variant found in FLT3 (c.1776T>C; p.(Val592Val), is a novel variant. In 924 glioma cases tested FLT3 mutations found in 26 cases, a mutation in Val592 codon [c.1774G>A; p.(V592I)] was reported in 2 cases of astrocytoma grade IV. In this cohort 16 ependymoma case were included but their mutation status for FLT3 is negative⁴⁸. Identification of this novel variant in exon 14 of FLT3 does not have any structural functional impact as this is a synonymous variant coding for the same amino acid. However, this variant is not reported in COSMIC database or dbSNP also. In the Leiden open variation database (LOVD) 5 more synonymous mutations were reported in exon 14 (in the juxta membrane domain amino acids 572-609); in c.1746, c.1770, c.1773, c.1803 and in codon 1815 http://databases.lovd.nl/whole_genome/variants/FLT3. The IDH1 mutation c.395G>A; p.(Arg132His) we detected in this tumor is a substitution missense mutation which has been reported previously (COSM28746) in glioma tumors⁴⁹. In this codon, another missense G>T mutation (COSM28750), and a compound substitution c.394_395CG>GT (COSM28751) are also known. Somatic IDH1 mutations in this codon have been found with greater frequency in diffuse astrocytomas, oligodendrogliomas, oligoastrocytomas and secondary glioblastomas. And in anaplastic ependymoma grade III this variant is reported with 14.3% frequency⁵⁰. However, several grade II and grade III ependymal tumors tested did not show this mutation in the IDH1 gene⁵¹. For astrocytic tumors, the presence of this mutation is known to be associated with younger patients⁵². This observation supports our findings for this ependymoma tumor as the patient is six years-old. This mutation is pathogenic, having a FATHMM score of 0.94. Other variants detected in this tumor, such as those in FGFR3, PDGFRA, KDR (c.1416A>T), CSF1R, EGFR, RET, HRAS, PIK3CA, FLT3 (c.1310-3T>C), and SMAD4, are benign. The FLT3 splice variant c.1310-3T>C (rs2491231) was reported in 84% of triple negative breast cancer cases 53. This variant was not reported in ependymoma tumors previously, this is the first time we report it here. Variants detected in this tumor have also been reported in other cancers: PDGFRA mutations in cervical adeno-squamous carcinomas; ERBB4 mutations in lung adenocarcinomas; FGFR3 mutations in breast, endometrial and ovarian cancers; CSF1R mutations in prostate cancer; EGFR mutations in lung adenocarcinomas; RET mutations in thyroid carcinomas; HRAS mutations in melanomas; and SMAD4 mutations in breast cancer. However, with the exception of the KDR variant c.1416A>T, this is the first time the above variants are reported in a brain tumor^54–62.

We found an intronic variant in PIK3CA and one missense mutation in this gene. This missense mutation was also reported previously in hemangioblastoma and in colon adenocarcinoma^63,64. Missense mutations in PIK3CA are known to promote glioblastoma tumor progression⁶⁵. Mutations of the PTEN gene are rare in ependymomas and we have also not detected any PTEN mutations in this tumor⁶⁶. The KDR (VEGFR2) gene plays an important role in neovascularization and tumor initiation by glioma stem-like cells⁶⁷. In non-small cell lung cancer patients, the Gln472His SNP is associated with increased KDR activity, and was correlated with increased micro vessel density⁶⁸. This variant was not known in ependymoma tumors previously. This mutation is reported in Colo-rectal cancer, melanoma, non-small cell lung cancer, and it’s an important target for drugs like Avastin (Bevacizumab), Aflibrcept, and drugs reported in (http://atlasgeneticsoncology.org/Genes/GC_KDR.html).

Mutations in cancer driver genes such as TP53, CDKN2A, and EGFR, which are frequently affected in gliomas, have been shown to be rare in ependymomas^44,66,69. We have detected a TP53 mutation (c.215C>G, p.Pro72Arg, rs1042522) in this tumor with a frequency of 47.94%. This mutation p.(Pro72Arg) has also been reported previously in a medulloblastoma tumor in a young patient⁷⁰. Previous studies have shown that out of 15 ependymoma tumors tested, only one case, a patient with a malignant ependymoma of the posterior fossa, had a mutation in exon 6 of the TP53 gene, which was silent, and in another study only one out of 31 ependymoma tumors tested contained a mutation in the TP53 gene^71,72. However, in another study, out of 15 ependymoma tumors, none had a mutation in the TP53 gene, suggesting that this gene does not play an important role in the pathogenesis and development of ependymomas, unlike other brain tumor types^66,72,73. Miller et al., (2018) through whole-exome sequencing of an anaplastic ependymoma tumor, have shown mutations in several cancer-related genes, as well as genes related to metabolism, neuro-developmental disorder, epigenetic modifiers and intracellular signaling⁷⁴. These authors have shown resistance-promoting variant expression in a single ependymoma case at different stages of recurrence. However, these genes were not present in the cancer panel we used in this study. Using the human exome capture on Illumina, Bettegowda et al., (2013) have reported that in one out of eight grade III intracranial ependymomas, tumors have mutations in PTEN and TP53, and one tumor with HIST1H3C mutations²⁴. The HIST1H3C p.(Lys27Met) mutation has also been reported previously in posterior fossa ependymomas⁷⁵. Ependymomas may in fact represent a very heterogeneous class of tumors, each with distinct molecular profiles and, even within posterior fossa ependymomas, there are at least two distinct gene expression patterns, as demonstrated by Witt et al., (2011)^19,76. Overall, in previous studies, a very low frequency of mutations was observed in both intracranial and spinal ependymomas and our findings also supports this observation^19,24,25,41.

The Ion AmpliSeq Cancer HotSpot Panel consists of 207 primers in 1 tube, targeting 50 oncogenes and tumor suppressor genes that are frequently mutated in several types of cancers. The detected mutations were found to have high accuracy; 100% amplicons had at least 500 reads and 500x target base coverage was also 100%. This high level of accuracy and the high depth of coverage achieved with the Ion Proton system allowed us to reliably detect low frequency mutations with high confidence. Allele coverage in most of the variants is around 2000x, the p-value was 0.00001 and the Phred score was very high for all the variants, indicating high confidence in the variants found in this tumor. Apart from its use in whole-exome sequencing, cancer panel analysis has also become common practice for Ion Proton²⁶. The Ion Proton instrument has the advantage of pooling samples using barcodes and the Ion PI chip. For pooled samples, sequencing enables a high throughput up to 15 Gb of data, with more than 60–80 million reads passing read filtering. The purpose of read filtering is to discard the reads that contain low quality sequences, to remove polyclonal reads, remove reads with an off-scale signal, remove reads lacking a sequencing key, remove adapter dimers, and remove short reads etc. If the computed mean read length from all the reads and the minimum total mapped reads in the sample is less than the specified threshold, that sample does not pass the quality control.

Recent molecular diagnostics research had helped in subdividing glioblastomas, oligodendrogliomas and oligoastrocytomas into genetically diverse groups of tumors, and these mutational markers may help in predicting the prognosis and response to therapy⁷⁷. However, such a strategy for the molecular subdivision of ependymomas has been not successful so far using mutational profiling. Epigenetic markers and fusion protein analysis have also helped in identifying new groups of supratentorial ependymoma tumors and in spite of the histopathological signs of malignancy, a small set of ependymomas had a very good prognosis, suggesting that this subgroup of tumors should not be diagnosed as classic ependymomas⁷⁸. However, another study showed that methylation profiling did not identify a consistent molecular class within the supratentorial tumors, but successfully sub-classified posterior fossa ependymoma into two subgroups⁷⁹.

In conclusion, we have identified four known missense mutations, eight synonymous and seven intronic, in this grade III ependymoma. Out of these, only one mutation in FLT3 (c.1776T>C, synonymous) is novel, and only one mutation in IDH1 (c.395G>A, missense) is deleterious, with all other mutations benign. Many of the variants we reported here were not detected in the ependymal tumors analyzed by NGS previously. HRAS c.81T>C, PIK3CA c.1173A>G, RET c.2307G>T, KDR c.1416A>T, APC c.4479G>A, EGFR c.2361G>A and FLT3 c.1310-3T>C variants have not been previously reported in brain tissue, as verified in COSMIC data base, although they have been reported in other tissues like lung and breast. Further studies are warranted, using NGS methods in all three grades of intracranial ependymomas to identify the genetic signatures that may distinguish between these tumors at the molecular genetic level.

Data availability